PDBsum entry 2w1q

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Hydrolase PDB id
Protein chains
140 a.a. *
_NA ×2
_CA ×2
Waters ×475
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Unique ligand binding specificity for a family 32 carbohydrate-binding module from the mu toxin produced by clostridium perfringens
Structure: Hyaluronoglucosaminidase. Chain: a, b. Fragment: carbohydrate binding module, residues 807-975. Synonym: mu toxin, family 84 glycoside hydrolase. Engineered: yes
Source: Clostridium perfringens. Organism_taxid: 1502. Atcc: 13124. Expressed in: escherichia coli. Expression_system_taxid: 562.
1.60Å     R-factor:   0.152     R-free:   0.199
Authors: E.Ficko-Blean,A.B.Boraston
Key ref:
E.Ficko-Blean and A.B.Boraston (2009). N-acetylglucosamine recognition by a family 32 carbohydrate-binding module from Clostridium perfringens NagH. J Mol Biol, 390, 208-220. PubMed id: 19422833 DOI: 10.1016/j.jmb.2009.04.066
20-Oct-08     Release date:   05-May-09    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P26831  (NAGH_CLOPE) -  Hyaluronoglucosaminidase
1628 a.a.
140 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.  - Hyaluronoglucosaminidase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Random hydrolysis of 1->4-linkages between N-acetyl-beta-D-glucosamine and D-glucuronate residues in hyaluronate.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     cell adhesion   1 term 


DOI no: 10.1016/j.jmb.2009.04.066 J Mol Biol 390:208-220 (2009)
PubMed id: 19422833  
N-acetylglucosamine recognition by a family 32 carbohydrate-binding module from Clostridium perfringens NagH.
E.Ficko-Blean, A.B.Boraston.
Many carbohydrate-active enzymes have complex architectures comprising multiple modules that may be involved in catalysis, carbohydrate binding, or protein-protein interactions. Carbohydrate-binding modules (CBMs) are a common ancillary module whose function is to promote the adherence of the complete enzyme to carbohydrate substrates. CBM family 32 has been proposed to be one of the most diverse CBM families classified to date, yet all of the structurally characterized CBM32s thus far recognize galactose-based ligands. Here, we report a unique binding specificity and mode of ligand binding for a family 32 CBM. NagHCBM32-2 is one of four CBM32 modules in NagH, a family 84 glycoside hydrolase secreted by Clostridium perfringens. NagHCBM32-2 has the beta-sandwich scaffold common to members of the family; however, its specificity for N-acetylglucosamine is unusual among CBMs. X-ray crystallographic analysis of the module at resolutions from 1.45 to 2.0 A and in complex with disaccharides reveals that its mode of sugar recognition is quite different from that observed for galactose-specific CBM32s. This study continues to unravel the diversity of CBMs found in family 32 and how these CBMs might impart the carbohydrate-binding specificity to the extracellular glycoside hydrolases in C. perfringens.
  Selected figure(s)  
Figure 2.
Fig. 2. Electron density of (a) glcNAcβ1-3galNAc and (b) glcNAcβ1-2mannose bound to NagHCBM32-2. Sugars are shown in cyan stick representation. Blue mesh represents the maximum-likelihood^26/σ[a]-weighted^27 2F[obs] − F[calc] electron density maps contoured at 1 σ (0.41 electrons/Å^3 for glcNAcβ1-3galNAc and 0.31 electrons/Å^3 for glcNAcβ1-2mannose). Green mesh represents the maximum-likelihood/σ[a]-weighted F[obs] − F[calc] electron density maps obtained from refinements with the sugar atoms omitted and contoured at 3 σ (0.25 electrons/Å^3 for glcNAcβ1-3galNAc and 0.18 electrons/Å^3 for glcNAcβ1-2mannose). For simplicity, only the sugars bound to monomer A (of four monomers) in the asymmetric unit are shown. Images are shown in divergent stereo.
Figure 3.
Fig. 3. Structural properties of ligand binding by NagHCBM32-2. (a) Surface properties of the NagHCBM32-2 binding site. The solvent-accessible surface of NagHCBM32-2 is shown in gray with the surface contributed by a Trp935 colored in purple. The sugar is shown in yellow stick representation. O3 and O4 of the non-reducing end are labeled for reference. (b) Representation of the interactions made in the active site. Residues in the active site involved in binding glcNAcb1-3galNAc are shown in yellow stick representation and labeled with the backbone of the protein shown in ribbon representation. The sugar is shown in green stick representation. Possible hydrogen bonds are shown as black dotted lines. Relevant waters are shown as red spheres. These interactions are identical for the four molecules in the active site. (c) Overlap of glcNAcβ1-3galNAc (green) with glcNAcβ1-2mannose (blue; only from monomer A). Only the side chains from the glcNAcβ1-3galNAc complex are shown as the conformations of the side chains in both complexes were nearly identical. All panels are shown in divergent stereo.
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2009, 390, 208-220) copyright 2009.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19908036 D.Guillén, S.Sánchez, and R.Rodríguez-Sanoja (2010).
Carbohydrate-binding domains: multiplicity of biological roles.
  Appl Microbiol Biotechnol, 85, 1241-1249.  
19930717 Y.M.Cheng, F.C.Hsieh, and M.Meng (2009).
Functional analysis of conserved aromatic amino acids in the discoidin domain of Paenibacillus beta-1,3-glucanase.
  Microb Cell Fact, 8, 62.  
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