Structural and functional properties of low molecular weight endo-1,4-β -xylanases

ELSEVIER Journal of Biotechnology 57 (1997) 137-149

Biotechnology

Minireview

Structural and functional properties of low molecular weight endo- 1,4-p -xylanases

Anneli Tiirriinen ‘, Juha Rouvinen *

Department of Chemistry, University qf Joensuu, P.0. Box I1 I, FIN-80 iO1 Joensuu, Fin/a&

Accepted 30 March 1997

Abstract

There are currently four crystal structures of low molecular weight endo-1,C/3-xylanases (E.C.3.2.1.Q i.e. family G/l 1 xylanases, available at the Brookhaven Data Bank: 2 xylanases from Trichoderma reesei (Tiirriinen et al., 1994; TGrr6nen and Rouvinen, 1995) and one from Bacillus circulans and another from Trichoderma harzianum (Campbell et al., 1993). They consist of two P-sheets and one a-helix and have been described to resemble a partly-closed right hand. The catalytic residues are two conserved glutamate residues, which are located opposite to each other in an open active site cleft. The catalytic mechanism is thought to resemble that of the widely-studied enzyme lysozyme. The role of one glutamate is to act as an acid/base catalyst whereas the other is a nucleophile and stabilizes the reaction intermediate. Complex structures of partly-bound xylotetraose in mutated XYN from Bacillus circulans (Wakarchuck et al., 1994a) and three recently-obtained structures of XYNII from Trichoderma reesei with epoxyalkyl-xylose derivatives (Havukainen et al., 1996) have provided important information on substrate binding. Family G/l1 xylanases show clear amino acid homology and thus have a common fold. However, variations in their functional properties, such as catalytic activity, substrate cleaving patterns, pH optima and thermostabilities, exist. 0 1997 Elsevier Science B.V.

Keywords: Xylanase; Structural comparison; Catalytic mechanism; Conformational change

1. Introduction

* Corresponding author. ’ Present address: Cultor Food Science, FIN-02460 Kantvik,

Finland.

Endo-1,4-j?-xylanases (E.C.3.2.1.8) are endo-

glycosidases which catalyze the hydrolysis of xy-

lan, the most abundant hemicellulose in nature.

The xylanases are of considerable interest as cata-

0168-1656/97/$17.00 0 1997 Elsevier Science B.V. All rights reserved.

PII SO1 68-1656(97)00095-3

138 A. Tiirr6nen, J. Roucinm Journd of Biotrc~hnology 57 (1997) 137- 149

lysts in various biotechnological applications, e.g. in biobleaching and the food and feed industry (Coughlan and Hazlewood, 1993).

Henrissat and Bairoch (1993) have classified glycosidases into several families originally on the basis of homologies in structural elements, hydrophobic clusters, which are derived from the two- dimensional representation of the amino acid sequence. Xylanases are found in two families, i.e. in the families F/l 0 and G/ 11. The family F/l0 xylanases consist of a cellulose-binding domain and a catalytic domain connected by a flexible linker region.

The family G/l 1 is composed of highly specific low molecular weight endoxylanases (here after referred to as XYNs) from eukaryotic and bacterial species, in which the sequence identity varies from 40 to 90% (Tbrronen et al., 1993). Although the family G/l 1 is a very homologous group of enzymes, it can be divided into alkaline pI and acidic pl xylanases based on the physicochemical properties of the enzymes. Some micro-organisms, such as Aspergillus and Trichoderma spp, produce both acidic and alkaline pI xylanases. Torronen et al. (1993) have shown that the phylogenetic tree constructed according to the method of Saitou and Nei (1987) reveals three kinds of XYN clusters. Surprisingly, the clusters are related to the XYNs with different pi’s, i.e. XYNs of p1 445, 8-9 and p1 9. The p1 8-9 XYN cluster is most diverged. Although isoelectric point is not very good for judging the grouping of proteins, it can in this particular case reflect functional differences between these enzymes.

Up to today there are four crystal structures of XYNs available at the Brookhaven Data Bank (PDB), i.e. XYNI from Trichodermu reesei, XYN from Bacillus circuluns, XYNII from Trichoderma reesei and XYN from Trichoderma hrcrziunum, which represent quite well members of the p1 445, 8-9 and 9 XYNs, respectively. In addition, the NMR assignment of XYN from Bacillus circufuns has also been reported (Plesniak et al., 1996). All XYN structures resemble each other and have a common fold. Structurally, they belong to the class of all /?-structures of the ConA-like lectins/ glucanases, which has thus far been found to contain eight subgroups including other glycosi-

dases like P-glucanase and cellobiohydrolase I (Murzin et al., 1995).

In this paper different family G/l 1 xylanases are compared structurally and the catalytic mechanism as well as the functional differences between these enzymes are discussed.

2. Overall structure

XYNs fold into a single ellipsoidal domain comprising two p sheets (A and B) and a single three turn r-helix (Fig. 1). The overall structures of XYNs are similar and have been described as a partially closed right hand. The sheets are mostly composed of antiparallel strands and twisted at almost 90”. The hydrophobic faces of the two p sheets pack together to form a sandwich, which is described as fingers. The twisted parts of the p-sheets form a cleft in one side of the molecule, which together with the helix are described as a palm. The active site is located at the concave side of the cleft. A long loop between the B8 and B7 strands is described as a thumb. An unusual feature is the chord which runs across the mouth of the cleft, partly closing it at one side. It does not make any hydrogen bonds with other parts of the molecule (Torriinen et al., 1994).

There has been some controversy in assigning the secondary structure elements in the XYN fold. Campbell et al. (1993) have reported that the XYN fold consists of three /I sheet instead of two. The twisted part of p sheet B has been described as a separate sheet. However, the continuity in hydrogen bonding strongly support the idea of two sheets. Recently, Plesniak et al. (1996) have also reported NMR studies and the secondary structure determination of Bacillus circuluns xylanase. This matches perfectly with the crystal studies and indicates that the XYN fold is similar in solution and in the crystalline state.

The reported structures of XYNs can be used to model all other family G/l 1 members. The XYN domain is unique and found only in this class of enzymes. Table 1 shows rms deviations of Ca atoms for each crystal structure of XYN. The sequences of Trichodermu reesei and Trichoderma harziunum xylanases are about 98% homologous.

A. Tiirrtinen, J. Rouvinen /Journal qf Biotechnology 57 (1997) 137-149 139

(b)

Fig. 1. (a) The schematic drawing of XYNII from T. reexl (figure generated using MOLSCRIPT, Kraulis, 1991); (b) as in (a) but rotated about 90”.

Table 1

The rms differences for Cr atoms between XYN molecules”

TH BC XYNI

XYNII,,, 4 5 0.66 1.38 1.11

XYNII,, 6 5 0.61 1.36 I .37

TH 1.10 1.10

BC 1.40

XYNII, XYNI from T. reesei (Torriinen et al., 1994; Tiirronen

and Rouvinen. 1995), TH, XYN from T. harzianum, BC,

XYN from B. circulans (Campbell et al., 1993).

“Calculated by the lsq option of the program 0 (Jones et al.,

1991).

Thus it is not surprising that these structures resemble one another most. The bacterial xylanase is closer to the structure of the acidic XYN, i.e. XYNI from Trichoderma reesei than the two alkaline XYN structures.

Recently, several structures of the catalytic domain of family F xylanases have also been reported (Derewenda et al., 1994; Dominguez et al., 1995; Harris et al., 1994; White et al., 1994). They fold in a totally different way than XYNs, con- sisting of an &fold /?/a-barrel, the so-called TIM barrel fold (Banner et al., 1975) which is common to many functionally unrelated enzymes. How- ever, the active site is also an open cleft and the catalytic residues are a pair of glutamates (Jenkins et al., 1995).

The sequences of about 20 family G/l 1 xylanases have been reported. The alignment of 13 selected amino acid sequences is shown in Fig. 2, which represents the divergence in this family. Most of the differences between XYNs are found in the N-terminus. Some structures, such as XYNI from Trichoderma reesei (Tiirronen and Rouvinen, 1995) and XYN of Bacillus circulans (Campbell et al., 1993) lack the first p-strand Bl. We could be speculate that the long unique part of the N-terminus of XYN from Clostridium acetobutylicum (Zappe et al., 1990) probably does not form an extra strand, but represents a longer version of Bl. The longer Bl strand could (Zhang and Flint, 1992) participate in forming additional binding sites for the substrate. In the Ruminococ- cusjfauefaciens structure the XYN domain is only one part of the protein, the other consists of xylanases belonging to family F glycosidases. In-

140 A. Ti_irriinm, J. Rouvinen /Journal of Biotechnology 57 (1997) 137-119

TRII TRI AAC TH BC ClA BP SC SLC SLB NPb NPa RF

1 10 =Bl=>

QTIQPGTGYNNGY

ASIN . . SAG1

QTIGPGTGYSNGY ASTD

ATNLNTTESTFSKEVLSTQICTYSAFNTQ~PKTITSNEIGVNGGY RTITNNEMGNHSGY SGTPSSTGTDGGY

ATTITTNOTGTDGM DTWTTNQ6GTNNGY

. TVGNGQNQHKGVNDGF . TVGNGQTQHKGVAEGY

. ..QTRGNVGGY

20 30 40 50 60 ==B2==, =AZ=> =A3=> ==B3==> z=;A5==

TRII FYSYWND.GHGGVTYTNGPGGQFSVNOTSNS...GNFVGGK(IWQPGTKNK........VINFS.G TRI YDQNUQT..GGQVSYSPS.NTGFSVNlflJTQ...DDFWGVQ~TGSS.........APINFG.G AAC WQNYNG.NLADFTYDES.AGTFSMYI(EDGVS.SDFWGLQ~TGSSN.........AISYS.A TH WSYWND.GHAGVTYTNGGGGSFTNS...GNFVAGKQWQPGT~K........VINFS.G EC YWQNWTD.GGGIVNAVNGSGGNYSVNPlSNT...GNFWGKQWTTGSPFR........TINYNAG ClA DYELWKD..YGNTSMTLKNGGAFSCQWSNI...GNALFRKOKKFNDTQT.YKQLGNISVNYD.C BP DYELWKD..YGNTSMTLNNGGAFSA~I...GNALFRKOKKFDSTRT.HHOLGNISINYN.A SC WSWWTD.GAGDATYQNNGGGSYTL~SGNN..GNLVGGKOWNPGAASR...:....SISYS.G SLC YYSFWTD.GGGSVSMTLNGGGSYSTQlCTNC...GNFVAGKOWSTGDG..........NVRYN.G SLB WSFWTD.SQGTVSMNMGSGGQYSTSIT...GNFVAGKQWANGGR.........RTVQYS.G NPb SYEIWLDNTGGNGSMTLGSGATF~~~~GNFLARRaLDFGSOKK.ATDYDY1GLDYA.A NPa SYEIWLDNTGGSGSMTLGSGATFKADINASVNRGNFLARRKK.ATDYSY1GLDYT.A RF DYEMWNQNGQGQASMNP..GASFTCSIISNI...ENFLARMOKNYDSQKKNYKAFGNIVLTYD .V

70 80 90 100 110 ===> ====B5===, =B6b==> B6a> chord =B9=> ==BS

TRII SYNPN....GNSYLSVY~SRN......PLILYYIVENFGTYNPST.GATKLGEVTSWSWD I TRI SFSVN...SGTGLLSWQWSTN......PLVIYYIMEDNHNY.PA..QGTVKGTVTSDOATYT I AAC EYSAS...GSSSYLsAVXGWVNY .... ..PQAEYYIVEDYGDYNPCSS.ATSLGTVYSWSTYQ V TH SYNPN ... .GNSYLSIYQIlSRN......PLILYYIVENFGTYNPST.GATKLGEVTSDQSVYD I BC VWAF'N....GNGYLTLYQWTRS .... ..PLI6YYVVDSWGTYRPT...GTYKGTVKSDQGTYD I ClA NYQPY....GNSYLCW~Ss......PLVIYYIVDSWGSWRPP..GGTSKGTITVWGIYD I BP SFNPG....GNSYLCWOIFTQS......PLALYYIVDSWGTYRPT...GAYKGSFYADaGTYD I SC TYQPN....GNSYLSWOI(TRS......SLIIWIVESYGSYDPSS.AASHKGSVTCNQATYD I SLC YFNPV....GNGYGCLYaffPSN......PLVLYYIVDNWGSYRPT...GTYKGTVSSWGTYD I SLB SFNPS....GNAYLALYQ)FTSN......PLVIYYIVDNWGTYRPT...GEYKGTVTSWGTYD I NPb TYKQTASASGNSRLCWQWFQNRGLNGVPLVLY*IIEDWVDWVPD....AQGKMVTIWAQYK I NPa TYRQTGSASGNSRLCWQI(FQNRGVQGVQGVPL~~IIED~D~SD....AQGRMVTIWAQYK I RF EYTPR....GNSYMCWO~RN......PL~~IVEGWGDWRPPGNDEVKGTVS~~T~ I

120 130 140 150 160 170 ====> thumb ==B7==> =A6> -_-helix-_- =

TRII YRTQRVNQPSIIa.TAT~QYWSVRRNHRS........SGSVNTANBFNAWAQQGLTL.GTMD Y TRI WENTRVNEPSIPa.TAT~QYIBVRNSPRT........SGTVTVQNHFNAWASLGLHL.GQMN Y AAC CTDTRTNEPSITQ.TSTITQYF8VRESTRT........SGTVTVANHFNFI(AQHGFGN.SDFN Y TH YRTQRVNQPSIIO.TATPYQYWBVRRNHRS........SGSVNTANaFNAWASHGLTL.GTMD Y EC YTTTRYNAPSIWDRTTPTQYWBVRQSKRPT.....GSNATITFTNHVNAWKSHGMNLGSN WAY ClA YETTRINQPSIQo.NTTTKQYW8YRRTKRT........SGTISVSKllFAAWESKGMPL.GKMH E BP YETTRVNQPSIIB.IATIKQYWIPVRQTKRT ..... ..SGTVSVSAEFRKWESLGMPM.GKMY E SC LSTWRYNAPSIDQ.TQTrEQFW(IVRNPKKAP...GGSISGTVDVQCHFDAlQKGLGMNLGSEHN Y SLC YQTTRYNAPSVEa.TKT~QQYWBVRQSKVT......SGSGTITTGNBFDAWARAGMQFRY Y SLB YKTTRVNKPSVEa.TRT?DQYWsVllQSKRT........GGTITTGNHFDAWARAGMPLGNFSY Y NPb FQMoHT.GPTINaGSET~QYFsVRQQKRT........SGHImSDBFKEWAKQGWGI.GNLY E NPa FQMDHT.GPTINOGSET~KQYFBVRQQKRT........SGHITVSDBFKEWAKQGWGI.GNLY E RF RKTMRYNQPSLW.TATIPQYWBVRQTSGSANNQTNYMKGTIDVTKBFDAWSAAGLDMSGTLYE

180 190 ==E4==, ===A4==>

TRII QIVAVXGYFSSQSASITVS TRI QWAVEGWGGSQSASQSVSN AAC QVMAVXAWSGAQSASVTISS TH OIVAVLGYFSSOSASITVS BC P~TEGYQSSQSSNVTVW ClA TAFNIIGYQSSQKADVNSMSINIGK BP TAFlVBGYQSSQSANVMTNQLFIGN SC QIVATIGYQSSOTATITVT SLC MIUATZGYQSSCSSNITVSG SLB MIMATIGYQSSOTSSINVGGTGGGDSG.. NPb VALNAEGWOSSQVADVTLLDVYTTPKG.. NPa VALNASGWiiSSQIALXlTKLDVYTTQKGSNPAPT.... RF VSLNIIGYRSNGSANVKSVSVTQGGSSDN...

Fig. 2

A. Tiirrtinen, J. Rouvinen /Journal of’ Biotechnology 57 (1997) 137-149 141

terestingly, the xylanase from Neocallimastix patriciarum (Gilbert et al., 1992) contains two XYN domains which are linked together with a linker sequence. It would be valuable to determine how these two similar domains are situated relative to each other. Although the folds of different XYNs are very similar, there are eight regions between the secondary structure elements where insertions/ deletions exist. The length of these insertions varies from one to about ten residues, the longest being located between strands B3 and A5. An inspection of the crystal structures reveals that the insertion between B.5 and B6b may affect the width of the thumb and the insertion between B7

and A6 may enlarge the active site cleft. The loop between strands B6a and B9 closes

the active site at one end and part of it has been described as a chord, which seems to be a quite well-defined region in reported crystal structures. It is composed of five to eight residues, of which

conserved proline is likely to play a structurally important role by defining the conformation of the chord. The chords of two XYN domains in Neocallimastix patriciarum xylanase (Gilbert et

al., 1992) seem to contain only four residues and the conserved proline is replaced by serine in the

latter. A comparison of crystal structures reveals that the conserved aromatic residue (tyrosine/ tryptophan) in the XYNI structure of Tricho- derma reesei has an unique location compared to

the other XYNs. In the XYNI structure this residue (Y85) points to the interior of the protein and is packed against residues L62 and M79, whereas in other structures it points towards the cleft and makes a potential subsite for the substrate (Tiirriinen and Rouvinen, 1995).

There are also some odd residues and their locations should be mentioned. The crystal structure of the XYN ‘from Bacillus circulans (Camp-

bell et al., 1993) reveals that the extra alanine,

which is lacking in the other crystal structures, causes the A5 B-strand to bulge. The XYN from Bacillus circulans also has two hydrophobic residues with unusual positions, namely, the phenylalanine just before the helix and the C-terminal trypthophan are on the surface of the molecule and face towards the solvent.

There are about 20 residues which are completely conserved in the family G/l 1 xylanases. In addition to the catalytically important residues

there are also some structurally interesting conser- vations. The glycine located at the end of B3 allows the strand to twist in a special manner. Another conserved glycine, which is located between B9 and B8, is important in hairpin formation. The conserved glycine in the middle of A4 is of interest since it packs in a particular manner against another conserved tryptophan residue located in strand A3.

The thumb region has a similar fold in all crystal structures. It contains a conserved proline

residue, which is in trans conformation and bends the tip of the thumb which becomes partly twisted. The thumb of the XYN of Bacillus circu- Zans (Campbell et al., 1993) contains one extra aspartate residue and is slightly longer than in other XYN structures. It has been shown that the thumb region is able to move and thus regulate the width of the active site cleft (Havukainen et al., 1996).

The solved XYN crystal structures do not contain any cysteine residues. We assume that the overall structure itself is quite stable and does not need any disulphide bridges. However, there are some XYNs with cysteine residues as well. In p strand B5 the serine residue (S76 in the XYNII of Trichoderma reesei) is often replaced by cysteine. This residue is located in the middle of B5 and

Fig. 2. Sequence alignment of representative family G xylanases. The secondary structure elements (the arrows indicate b-strands and the dotted line indicates helix) and amino acid numbering refer to the XYNII from T. reesei (Tiirronen et al., 1994). The

completely conserved residues are marked. TRII, TRI = XYNII and XYNI from Trichoderma reesei (Torronen et al., 1992), AAC =

XYN from Aspergillus awamori (Ito et al., 1992). TH = XYN from Trichoderma harzianum (Yaguchi et al., 1992). BC = XYN from

Bacillus circulans (Yang et al., 1988) CIA = XYN from Clostridium acetobutylicum (Zappe et al., 1990), BP = XYN from Bacillus pumilus (Fukusaki et al., 1984) SC = XYN from Schizophyllum commune (Oku et al., 1993), SLC, SLB = XYNC and XYNB from

Sfreptomyces lividans (Shareck et al., 1991) Npb (C-terminal domain), NPa (N-terminal domain) = Neocallimastix patriciarum (Gilbert et al., 1992), RF = Ruminococcus jlavefaciens (Zhang and Flint, 1992).

142 A. TS~iinen, J. Roucinen / Jo~wnal of Biotechnology 57 (1997) 137- 149

Table 2

The volumes and molecular surfaces as well as solvent accessible surfaces for different XYNs

Molecule No. of residues Volume (A’) Mol surf (A’) Solvent acces. surf (A’)

XYN%, 4 5) 190 23 167 6822 1793

XYN’J,,,, 6 5) 190 23 703 6708 7173

TH 190 23 480 6817 7646

BC 185 23 315 6593 7679

XYNI 178 21 663 6402 7365

XYNII, XYNI from T. verse? (T&rBnen et al., 1994; Torrijnen and Rouvinen, 1995), TH, XYN from T. lurzianunz. BC, XYN from

B. circulans (Campbell et al., 1993).

a Calculated by the options of the program GRASP (Nicholls et al., 1991).

points towards the active site cleft without making any disulphide bonds. However, the disulphide bridges in the XYNs of Aspergillus awamori (Ito et al., 1992) and Schizophyllum commune (Oku et al., 1993) can be predicted. In the XYN from Aspergillus awamori a putative disulphide bond is

formed between two cysteines located in the chord region and in the middle of p strand B8. This disulphide bridge would suggest that the conformation of the chord is quite stable and does not change, e.g. during catalysis. In the Schizophyllum

commune structure the disulphide bond is likely to be formed between the cysteines which are located at the beginning of the /? strand B8 and just before the helix. This bond is located near the N-terminus of the helix and probably stabilizes it.

In contrast, the C-terminus of the helix seems to be quite flexible in all XYN structures.

Table 2 shows the volumes as well as the surface and solvent accessible surface areas for the

four XYN structures. The XYNI clearly seems to be smallest and this is a significant difference in respect to the other XYNs. However, being quite compact in construction, XYN molecules are thought, i.e. to be able to efficiently penetrate into the small pores which exist in wood components. In comparison, the surface area and volume of the catalytic domain of family F xylanases is about twice as large as that of XYNs.

It has become quite popular to show surface charge potentials calculated and rendered often by the GRASP program (Nicholls et al., 1991). Fig. 3 represents such constructions of XYN structures. Inspection of the surfaces can help to determine the binding surfaces common to protein families

and to localize other important functional inter-

faces. In this respect, the convex flat face of

P-sheet A is an interesting surface and probably

takes part in substrate binding. It consists of

conserved serine and threonine residues, which

are often found in cellulose-binding domains

Fig. 3. Electrostatic potential surfaces of XYNI (a) XYNII:

(b) from T. rresei; (c) XYN from B. circulans and (d) XYN from T. harrianum. The molecules are orientated as in Fig. la.

Blue regions represent positive, red negative and white neutral potentials. The calculations and displaying were done by program GRASP (Nicholls et al.. 1991).

A. Tiirrdnen, J. Rominen /Journal of Biorechnology 57 (1997) 137-149 143

(Gilbert and Hazlewood, 1993). The active site is clearly acidic in all XYN structures, but the negative potential spread is wider on the XYNI surface than in the other XYN structures, partly explaining its low isoelectric point (Fig. 3). How- ever, very positive areas are found on the surface of XYNII and the XYNs from Trichodermu harziunum and Bacillus circulans (Campbell et al., 1993). This may be important in molecular recog- nition and substrate specificities, i.e. a preference to xylan which has a certain degree of substitu- tion, especially negatively charged glucuronic acid substituents.

3. Catalytic residues

The active site is located in an extended open cleft, which correlates well with the endo-activity of these enzymes. Two conserved glutamate residues are catalytically active residues and are located on either side of the cleft. According to mutagenesis and mechanism-based inhibitors these residues have been identified as a nucleophile and an acid/base catalyst (E86 and El77 in the XYNII structure, respectively; Miao et al., 1994; Tdrrbnen et al., 1994; Wakarchuck et al., 1994a).

The environment of the nucleophile (E86 in XYNII) is more conserved than that of the acid/ base catalyst. The cluster of the five residues around the nucleophile forms a hydrogen bond network which is capable of fine-tuning the properties of this glutamate residue. In the XYNII structure this cluster consists of residues 4136, Y77, Y88, W79 and Y 17 1. There are direct hydrogen bonds from E86 to Q136, Y77, Y88 (Fig. 4) and second-layer hydrogen bonds from Y77 to W79 and Y171 (Tiirrbnen et al., 1994). The hy- drophilic environment may help to keep the nucleophile in its ionized form by lowering its pKa, a value which has been measured to be 4.6 for the corresponding residue in the XYN of BacillIus circuluns (McIntosh et al., 1996). E86 is strongly hydrogen-bonded to the conserved tyrosine Y77 in the XYNII structure (Torriinen et al., 1994). The mutation of this corresponding tyrosine in XYN from B circuluns (Y69F) resulted in a totally inactive enzyme (Wakarchuck et al., 1994a).

The acid/base glutamate El77 was observed to have two clearly different conformations in the XYNII structure (Tori&en et al., 1994). The El77 undergoes0 a 100” torsion angle change re- sulting in a 2.8 A displacement of the carboxylate group; this has been described as down-up movement. This change reduced the distance between the two catalytic residues from about 9 to 6 A and could be induced either by pH change or ligand binding. Torriinen and Rouvinen (1995) have determined high resolution XYNII structures at pH 4.0, 6.0 and 6.5. At pH 4.0 structure El77 was in the down position and at pH 6.5 structure in the up position. Interestingly, at pH 6.0 both of these conformations for El77 were observed. At the lower pH, but in the presence of a ligand, El77 was observed to be in the up position. The conformational change of El77 from the down to the up position induced a significant 4 A change in the position of Oy in Y73. The structural rear- rangement, from the down to the up position, also permits the formation of an additional hydrogen bond between El77 and Y88. The tyrosine residue Y88, which is 100% conserved in all XYN structures and also undergoes a small conformational change, actually acts as a charge-stabilizing residue forming a link between the two catalytic residues. Although no change in the conformation of the other catalytic residue, E86, was observed, its hydrogen bond pattern is slightly different at different pHs. The clear hydrogen bond between E86 and Y88 exists at the lower pH but disap- pears as a result of a small movement of Y88 at the higher pH. The mutation Y80F, corresponding to Y88 in XYNII, in the XYN of Bacillus circuluns resulted in a dramatic decrease in activity (Wakarchuck et al., 1994a).

The two conformations of El77 suggest that it is able to change its pK, value. It is protonated and uncharged at a pH below 5.0 and loses its proton and changes its conformation at a higher pH or during catalysis. Recently, the pK, change of the acid/base catalyst in the XYN from Bacillus

circuluns was reported (McIntosh et al., 1996). The pK, value for the acid/base catalyst was measured to be 6.7. However, in the presence of a ligand which was bound covalently to the nucleophile, the pK, of the acid/base residue was calcu-

A. TiirrBnen, J. Rouvinen 1 Journal of Biotechnology 57 (1997) 137- 149

Fig. 4. Hydrogen bonding around the catalytic residues (E86 and El77) of XYNII from T. rersei. The proposed catalytic mechanism

proceeds as follows: (1) The substrate binding triggers conformational change in El77 (from the down to up position) and increases

its pK,; (2) El77 acts as an acid and breaks the glycosidic bond between the xylose units of the substrate. Y88 changes also its

conformation; (3) Y88 is hydrogen bonded to El77 and a water molecule attacks to the carboniumion intermediate; (4) Y88 forms a hydrogen bond with E86 and El77 changes its conformation from the up to the down position.

lated to be 4.2. This change was thought to be The hydrogen bonding pattern and the change

caused by a similar kind of conformational around the catalytic residues of XYNII are sum-

change as that of observed in the XYNII struc- marized in Fig. 4, which also represents the puta-

ture of Trichoderma reesei. The reported down tive catalytic mechanism for this enzyme. XYNs

position for the acid/base glutamate has so far are retaining enzymes, i.e. they retain the

been observed only in the XYNII structure, anomeric configuration of the substrate in the

whereas in the XYNI structure, which has been product (Gebler et al., 1992). Recently solved

determined at pH 4.5, the acid/base glutamate is three-dimensional structures of XYNII complexed

in the up position as well as in the XYN struc- with the mechanism-based inhibitors 4,5-

tures of Bacillus circulans and Trichoderma harzi- epoxypentyl-a-D-xyloside (X-0-CS), 3,4-epoxy- anum (both at pH 7.5; Campbell et al., 1993). butyl-/l-D-xyloside (X-0-C4) and 2,3-epoxypro-

A. Ttirriinen, J. Rouvinen /Journal of‘ Biotechnology 57 (1997) 137-149 145

pyi-/?-D-xyloside (X-0-C3) have given valuable information on ligand binding as well as on the catalytic mechanism (Havukainen et al., 1996). Interesting observations concerned the differences found in the covalent bond formation between the enzyme and epoxy1 oxygen of the ligand. It was previously suggested that the epoxy alkyl gly- cosides are likely to react with the residue, which acts as a nucleophile in the actual catalysis (Keitel et al., 1993). However, Havukainen et al. (1996) have shown that both catalytic glutamate residues in XYNII are able to form a bond with the epoxy1 oxygen. In XYNII complexed with X-O-C5 the aliphatic chain was strongly twisted and reached the nucleophile E86. The X-0-C4, however, fa- vored the position towards the acid/base catalyst E177, the unprotonated hydroxyl group of which actually acted as the nucleophile. The shortest X-O-C3 seemed to fit best into the active site by bonding with E86.

The alkaline XYNs tend to be active in the pH range from 4.0 to 8.0, whereas the active pH range of acidic XYNs is narrower, varying from pH 3 to 6. The variations are probably due to the different amino acid residues in the neighborhood of the acid/base catalyst, where the stereochemical environment is less restrained than that of the nucleophile. Tbrriinen and Rouvinen (1995) have suggested that residue D33 in XYNI, corresponding to N44 in XYNII, has an important role in determining the effect of pH on the activity of the enzyme. D33 in its neutral form (protonated) makes a stronger hydrogen bond to the acid/base catalyst El64 in acidic XYNI than does the N44 to El77 in the XYNII structure. It could be stated that this strong bond in acidic XYNs causes the acid/base residue to donate its proton more easily, i.e. at a low pH. We may even speculate that the conformational change does not occur in XYN enzymes, which have clearly acidic pH optima. This could partly explain why the active pH range of acidic XYNs is narrower than that of XYNII type enzymes. The wider pH profile of alkaline XYNs could indicate the pK, change of the acid/ base residue.

Interestingly, the sequence comparison (Fig. 2) reveals that in the XYN from Aspergillus awamori as well, the pH profile of which resembles that of

XYNI, the aspartate corresponds to the D33 of XYNI. The XYN from Schizophyllum commune may form a link between acidic and alkaline XYNs. Its p1 is clearly acidic, but the asparagine corresponds to the D33 of XYNI and, as ex- pected, its pH optimum is in the alkaline range (Oku et al., 1993).

4. Substrate binding residues

Although there are a number of three dimensional structures of xylanases available, we still lack a complex structure sufficiently enough to provide explicit binding site information. So far, only two of the binding sites of XYNs are well characterized (Wakarchuck et al., 1994a; Havukainen et al., 1996) and thus the biochemical information and inspection of the crystal structures remain the main tools for binding site characterization. The active sites of glycosyl hydrolases often contain aromatic residues, such as tyrosine and tryptophan, which can pack against the sugar ring as well as the side chains which make hydrogen bonds to hydroxyl groups of substrate (Vyas, 1991).

The subsites are marked as - 2, - 1, + 1, + 2, and + 3, where positive numbers represent the reducing end direction and negative the non reducing end direction of the substrate (Bray and Clarke, 1992; Torronen and Rouvinen, 1995). The cleavage is assumed to take place between subsites - 1 and + 1. Subsites - 2 and - 1 are well-characterized by the inspection of the complex structures, i.e. partly-bound xylotetraose in mutated XYN from Bacillus circuluns (Wakarchuck et al., 1994a) and three structures of XYNII from Tri- choderma reesei with epoxyalkyl-xyloside derivatives (Havukainen et al., 1996). However, the characterization of the reducing end subsites is based only on modelling. The inspection of the structures suggests that the XYNII of Tricho- derma reesei, XYN of Trichoderma harzianum and XYN of Bacillus circulans have five subsites, whereas the number of reducing end subsites in XYNI from Trichoderma reesei is probably less.

The structure of the complex of the inactive mutant E172C of Bacillus circuluns with xylote-

146 A. Tiirrti’nen. J. Rout;inen /I Journul qf Biotechnology 57 (1997) 137- 149

traose revealed the stacking interaction of W9 ( - 2) with one of the xylose rings. The hydrogen bonds between the hydroxyl groups of sugar and residues Y69, Y166 and Rl12 in subsite - 2 could be seen. Interestingly, the mutant Y 166F of Bucillus circuluns retained a wild-type activity, whereas Y69F had no detectable activity (Wakarchuck et al., 1994a). Subsite - 2 and its contacts to xylose residues also became evident from the XYNII structures complexed with epoxyalkyl-xyloses. In all three structures the xylose molecule was in a chair form and occupied the subsite determined by WI8 ( - 2) and formed hydrogen bonds between its hydroxyl groups and the side chains of residues Y77 and Y 171, corresponding to Y69 and Y166 in the XYN from Bacillus circulms. The aglycon occupied subsite - 1 (Havukainen et al., 1996). In XYNII the residues Y 179 and Y96, located between B4 and A4 and in the the chord, respectively, are assumed to determine subsites + 2 and + 3. These aromatic residues are conserved in family G xylanases, yet the position of the side chain in the structures may vary. The side chain of Y85 in the chord region of XYNI, corresponding to Y96 in XYNII, projects outwards from the active site cleft and is unable to form any subsite for a ligand (Tiirronen and Rouvinen, 1995).

The distribution of the subsites may explain some of the catalytic properties of XYNs. In the XYNI structure the substrate binding seems to be directed towards the non-reducing end whereas in XYNII the reducing end is preferred. Biely et al. (1993) have found that xylotetraose is cleaved at the second and third glycosidic linkages from the reducing end. This could be explained by assum- ing that the xylotetraose is bound to XYNII in such a manner that the first or the last subsite is empty. The remaining four subsites would participate in ligand binding. Xylopentaose, on the other hand, is cleaved at the second, third or fourth glycosidic linkages, which would mean that either all the subsites are occupied or that site - 2 or + 3 is empty and the rest are occupied.

Tenkanen et al. (1992) have shown that XYNI is capable of hydrolyzing acetylated glucuronoxylan into smaller units than XYNII whereas XYNII hydrolyses deacetylated glucuronoxylan

better. As a smaller molecule, XYNI is likely to reach branched xylan efficiently and have broader catalytic properties than XYNII. Because there are more subsites, the substrate can bind efficiently in XYNII and catalysis occurs faster.

Both enzymes are reported to have trans-glycosidase activity but that of XYNII is more evident (Tenkanen et al., 1992). This could also be explained by comparing the distribution of subsites in the enzymes. In fvans-glycosylation the reaction intermediate molecule would occupy subsite - 1. The rest of the intermediate would bind to subsite - 2 or even further. The second xylo- oligomer taking part in the tvans-glycosylation reaction would occupy subsites on the other side of the cleft, i.e. starting from subsite + 1. In XYNI there are probably fewer subsites in that direction and the xylo-oligomer binding is probably very weak whereas in XYNII there are three subsites, + 1, + 2 and + 3, which make the binding of the second oligomer more probable and trctns-glycosylation more likely to occur.

5. Movements in the XYN structure

The crystal structure of protein is not a rigid construction of the molecule but interesting changes can be observed by pH variations, ligand binding and by comparing homologous structures. Crystal packing may also cause some variations.

Major differences between the available crystal structures of XYNs are related to the position of the thumb. Table 3 shows the variation in the distance between the C?; of the conserved proline residue of the thumb and the aromatic residue (Cl2 of tryptophan or 0~ of tyrosine), which forms subsite - 2, in different XYN structures. The thumb is closed more in the native XYN structures of Trichodernm harzianum, Bacillus circuluns (Campbell et al., 1993) and XYNI than in XYNII (Tiirronen and Rouvinen, 1995). Surpris- ingly, the pH variations did not change the position of the thumb in XYNII, but the ligand binding, i.e. epoxyalkyl-xyloses, to the active site in XYNII caused significant movement of the thumb (Havukainen et al., 1996). The change was

Table 3

A. Tiirriinen, J. Rouvinen /Journal of Biotechnology 57 (1997) 137-149 147

The distance (A) between proline and tryptophan/tyrosine residues describing the position of the thumb in different XYN structures

Structure PH Ligand Atoms between which the distance is defined Distance (A)

XYNI 4.5

XYNII 4.5

TH 7.5

BC 7.5

BC 1.5

XYNll 6.1

XYNIl 5.3

XYNII 5.8

x4

x-o-c5

x-o-c4

x-o-c3

CyPll33OqY9 4.3 CyPl266C;WIS 6.7 CyPl266CcWl8 4.8 CyPll66CiW9 4.7 CyPll6cjw9 4.6 CyPl266C;WIS 5.5 CyPl266C[Wl8 5.5 CyPl26-C[Wl8 4.8

XYNII, XYNI from T. reesei (Torronen et al., 1994; Torronen and Rouvinen, 1995; Havukainen et al., 1996), TH, XYN from T.

harzianum, BC, XYN from B. circulans (Campbell et al, 1993), BCcompX4, Inactive mutant (E172C) of XYN from B. circulans

with xylotetraose (Wakarchuck et al., 1994a.b).

largest when the shortest ligand, X-0-C3, was

bound (Fig. 5). In contrast the complex structure

of XYN from Bacillus circulans with xylotetraose

showed no significant changes in the native struc-

ture.

Gerstein et al. (1994) describe two kinds of

movement in proteins: shear and hinge motions.

The hinge motion is often observed in multi-

Fig. 5. The superimposed structures of the native and com-

plexed (with X-0-C3) structures of XYNII from T. reesei. The arrows indicate the movements observed in the crystal structures (Havukainen et al., 1996).

domain proteins and major conformational changes are observed in the localized area in the polypeptide chain. However, XYN molecules consist of a single domain and during the thumb movement small changes occur in the whole structure. This suggests that shear motion takes place in these molecules. The X-O-C3 binding to the XYNII revealed two larger changes in the side chain torsion angle. The highly conserved side chains Y137 and L164, located in the area of the base of the thumb, undergo conformational changes. Y 137 rotates about 90” as a consequence of the movement of the thumb (Havukainen et al., 1996). Moreover, the positions of the corresponding residues in the XYN structures of Bacillus circulans and Trichoderma harzianum (Campbell et al., 1993) are similar to those observed in the XYNII X-O-C3 complex structure. This may be related to the position of the thumb, which is reasonably closed in all of these structures.

6. Knowing the structure-what can it give biotechnology?

XYNs are an important group of enzymes and have a wide range of biotechnological applications. They are also thought to have a role in the plant defense mechanism (Coughlan and Hazle- wood, 1993). Once the structure is known we can ask the question how to impart any desired prop- erty to the molecule. Properties such as substrate

148 A. Ttirrtinen, J. Rouvinen ,‘Journal of Biotechnology 57 (1997) 137-149

specificity, thermostability and the pH profile of enzymes also play important roles in industrial processes. It is thus of considerable interest to engineer these molecules. It has often been stated that knowledge-based mutagenesis saves time, money and human resources. However, understanding the physiological role, if any, of an indi- vidual amino acid is not easy.

A proper understanding of substrate binding pattern is necessary in order to tune the substrate specificity of XYNs. The sequence comparison already reveals some potential insertion/deletion regions for constructing artifical subsites for the substrate. The core region of XYNs is very stable and the residues have low B factors, however, there are some surface residues with higher B factors, and thus offer the potential for planning more thermostable proteins. Constructing disulphide bridges, e.g. near the flexible C-terminus of the cc-helix, may also increase the thermostability of XYNs (Wakarchuck et al., 1994b). The pH profile of different XYNs is most likely dependent on the neighborhood residues of the acid/base catalyst (Tiirriinen et al., 1994). The changes in these residues might enable us to alter the active pH range of these enzymes.

Unfortunately, it is still very difficult to manip- ulate the properties of enzymes in a predictable manner and even small changes can cause a dramatic decrease in activity. The structural studies on XYNs reveal, e.g. that catalytic mechanism involves conformational changes, the interpreta- tions of which are still controversal.

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