PDBsum entry: 1us2

Hydrolase

PDB-id: 1us2

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PROCHECK

Protein chain

507 a.a. *

Ligands

XYP-XYP-XYP-XYP ×2

Waters ×833

* Residue conservation analysis

Tools

Clefts Calculation

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PDB id:

1us2

Name:

Hydrolase

Title:

Xylanase10c (mutant e385a) from cellvibrio japonicus in complex with xylopentaose

Structure:

Endo-beta-1,4-xylanase. Chain: a. Fragment: carbohydrate binding module and catalytic module, residues (86-606). Synonym: xylanase10c. Engineered: yes. Mutation: yes

Source:

Cellvibrio japonicus. Organism_taxid: 155077. Expressed in: escherichia coli. Expression_system_taxid: 562.

UniProt:

Q59675 (Q59675_9GAMM)

Seq:

Struc:

Seq:

Struc:

Seq:

606 a.a.

Struc:

507 a.a.*

Key:	PfamA domain
Secondary structure	CATH domain

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme class:

E.C.3.2.1.8   [IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

Reaction:

Endohydrolysis of 1,4-beta-D-xylosidic linkages in xylans.

Resolution:

1.85Å

R-factor:

0.181

R-free:

0.226

Authors:

G.Pell,L.Szabo,S.J.Charnock,H.Xie,T.M.Gloster,G.J.Davies, H.J.Gilbert

Key ref:

G.Pell et al. (2004). Structural and biochemical analysis of Cellvibrio japonicus xylanase 10C: how variation in substrate-binding cleft influences the catalytic profile of family GH-10 xylanases.. J Biol Chem, 279, 11777-11788. [PubMed id: 14670951] [DOI: 10.1074/jbc.M311947200]

Date:

17-Nov-03

Release date:

18-Dec-03

Related entries:

1gny xylan-binding module cbm15
1us3 native xylanase10c from cellvibrio japonicus

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Clefts

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Key reference

DOI no: 10.1074/jbc.M311947200

J Biol Chem 279:11777-11788 (2004)

PubMed id: 14670951

Structural and biochemical analysis of Cellvibrio japonicus xylanase 10C: how variation in substrate-binding cleft influences the catalytic profile of family GH-10 xylanases.

G.Pell, L.Szabo, S.J.Charnock, H.Xie, T.M.Gloster, G.J.Davies, H.J.Gilbert.

ABSTRACT

Microbial degradation of the plant cell wall is the primary mechanism by which carbon is utilized in the biosphere. The hydrolysis of xylan, by endo-beta-1,4-xylanases (xylanases), is one of the key reactions in this process. Although amino acid sequence variations are evident in the substrate binding cleft of "family GH10" xylanases (see afmb.cnrs-mrs.fr/CAZY/), their biochemical significance is unclear. The Cellvibrio japonicus GH10 xylanase CjXyn10C is a bi-modular enzyme comprising a GH10 catalytic module and a family 15 carbohydrate-binding module. The three-dimensional structure at 1.85 A, presented here, shows that the sequence joining the two modules is disordered, confirming that linker sequences in modular glycoside hydrolases are highly flexible. CjXyn10C hydrolyzes xylan at a rate similar to other previously described GH10 enzymes but displays very low activity against xylooligosaccharides. The poor activity on short substrates reflects weak binding at the -2 subsite of the enzyme. Comparison of CjXyn10C with other family GH10 enzymes reveals "polymorphisms" in the substrate binding cleft including a glutamate/glycine substitution at the -2 subsite and a tyrosine insertion in the -2/-3 glycone region of the substrate binding cleft, both of which contribute to the unusual properties of the enzyme. The CjXyn10C-substrate complex shows that Tyr-340 stacks against the xylose residue located at the -3 subsite, and the properties of Y340A support the view that this tyrosine plays a pivotal role in substrate binding at this location. The generic importance of using CjXyn10C as a template in predicting the biochemical properties of GH10 xylanases is discussed.

Selected figure(s)

Figure 5.
FIG. 5. Schematic representation of the protein-ligand interactions in the -4 to -1 subsites of CjXyn10C. Only direct hydrogen-bonding residues (with H-bond distances of <3.2 Å) and important aromatic/hydrophobic side chains mentioned in the text are shown.

Figure 7.
FIG. 7. Schematic of xylan hydrolysis by the xylan degrading enzymes of C. japonicus. The structures shown for CjXyn11A and CjXyn11B are representative bacterial GH11 enzymes from Bacillus agaradhaerens and Nonomuraea flexuosa, respectively, the structure shown for CjAbf51A is from Geobacillus stearothermophilus, and the structure shown for CjXyn10D is of the homologous (93% similar) enzyme CmXyn10B from C. mixtus. The enzymes CjAbf51A, CjGlcA67A, and CjXyn10C are all attached to the outer membrane of the bacterium, whereas CjXyn10A, CjXyn11A, and CjXyn11B are secreted into the culture medium (40, 42, 43). The sugar side chains released by the -glucuronidase and arabinofuranosidase, respectively, are likely to be transported into the cytoplasm of C. japonicus. (The depiction of the plant cell wall is reproduced from Carpita and Gieaut (44). Reproduced with permission from Blackwell Publishing, ©1993.)

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2004, 279, 11777-11788) copyright 2004.

Figures were selected by an automated process.