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PDBsum entry 1gqi

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protein ligands metals Protein-protein interface(s) links
Glucuronidase PDB id
1gqi
Jmol
Contents
Protein chains
708 a.a. *
Ligands
EDO ×12
Metals
_MG ×2
_CO ×8
Waters ×1766
* Residue conservation analysis
PDB id:
1gqi
Name: Glucuronidase
Title: Structure of pseudomonas cellulosa alpha-d-glucuronidase
Structure: Alpha-glucuronidase. Chain: a, b. Engineered: yes
Source: Pseudomonas cellulosa. Organism_taxid: 155077. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PDB file)
Resolution:
1.48Å     R-factor:   0.133     R-free:   0.168
Authors: D.Nurizzo,T.Nagy,H.J.Gilbert,G.J.Davies
Key ref:
D.Nurizzo et al. (2002). The structural basis for catalysis and specificity of the Pseudomonas cellulosa alpha-glucuronidase, GlcA67A. Structure, 10, 547-556. PubMed id: 11937059 DOI: 10.1016/S0969-2126(02)00742-6
Date:
26-Nov-01     Release date:   26-Sep-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
B3PC73  (B3PC73_CELJU) -  Extracellular xylan exo-alpha-(1->2)-glucuronosidase
Seq:
Struc:
 
Seq:
Struc:
732 a.a.
708 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.2.1.131  - Xylan alpha-1,2-glucuronosidase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Hydrolysis of alpha-D-1,2-(4-O-methyl)glucuronosyl links in the main chain of hardwood xylans.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   3 terms 
  Biological process     metabolic process   5 terms 
  Biochemical function     hydrolase activity     4 terms  

 

 
DOI no: 10.1016/S0969-2126(02)00742-6 Structure 10:547-556 (2002)
PubMed id: 11937059  
 
 
The structural basis for catalysis and specificity of the Pseudomonas cellulosa alpha-glucuronidase, GlcA67A.
D.Nurizzo, T.Nagy, H.J.Gilbert, G.J.Davies.
 
  ABSTRACT  
 
Alpha-glucuronidases, components of an ensemble of enzymes central to the recycling of photosynthetic biomass, remove the alpha-1,2 linked 4-O-methyl glucuronic acid from xylans. The structure of the alpha-glucuronidase, GlcA67A, from Pseudomonas cellulosa reveals three domains, the central of which is a (beta/alpha)(8) barrel housing the catalytic apparatus. Complexes of the enzyme with the individual reaction products, either xylobiose or glucuronic acid, and the ternary complex of both glucuronic acid and xylotriose reveal a "blind" pocket which selects for short decorated xylooligosaccharides substituted with the uronic acid at their nonreducing end, consistent with kinetic data. The catalytic center reveals a constellation of carboxylates; Glu292 is poised to provide protonic assistance to leaving group departure with Glu393 and Asp365 both appropriately positioned to provide base-catalyzed assistance for inverting nucleophilic attack by water.
 
  Selected figure(s)  
 
Figure 5.
Figure 5. Schematic Representation of Some of the Recognition Elements in Glucuronate and Xyloside Binding Discussed in the TextTrp543, which forms a hydrophobic base for xyloside binding, is disordered in the native structure and becomes ordered upon ligand binding.
 
  The above figure is reprinted by permission from Cell Press: Structure (2002, 10, 547-556) copyright 2002.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20081828 Y.Zhu, M.D.Suits, A.J.Thompson, S.Chavan, Z.Dinev, C.Dumon, N.Smith, K.W.Moremen, Y.Xiang, A.Siriwardena, S.J.Williams, H.J.Gilbert, and G.J.Davies (2010).
Mechanistic insights into a Ca2+-dependent family of alpha-mannosidases in a human gut symbiont.
  Nat Chem Biol, 6, 125-132.
PDB codes: 2wvx 2wvy 2wvz 2ww0 2ww1 2ww2 2ww3 2wzs
  20431716 D.Dodd, and I.O.Cann (2009).
Enzymatic deconstruction of xylan for biofuel production.
  Glob Change Biol Bioenergy, 1, 2.  
18922794 K.Emami, E.Topakas, T.Nagy, J.Henshaw, K.A.Jackson, K.E.Nelson, E.F.Mongodin, J.W.Murray, R.J.Lewis, and H.J.Gilbert (2009).
Regulation of the Xylan-degrading Apparatus of Cellvibrio japonicus by a Novel Two-component System.
  J Biol Chem, 284, 1086-1096.
PDB code: 2va0
17028274 F.J.St John, J.D.Rice, and J.F.Preston (2006).
Characterization of XynC from Bacillus subtilis subsp. subtilis strain 168 and analysis of its role in depolymerization of glucuronoxylan.
  J Bacteriol, 188, 8617-8626.  
16461704 F.J.Stjohn, J.D.Rice, and J.F.Preston (2006).
Paenibacillus sp. strain JDR-2 and XynA1: a novel system for methylglucuronoxylan utilization.
  Appl Environ Microbiol, 72, 1496-1506.  
14573597 G.Golan, D.Shallom, A.Teplitsky, G.Zaide, S.Shulami, T.Baasov, V.Stojanoff, A.Thompson, Y.Shoham, and G.Shoham (2004).
Crystal structures of Geobacillus stearothermophilus alpha-glucuronidase complexed with its substrate and products: mechanistic implications.
  J Biol Chem, 279, 3014-3024.
PDB codes: 1k9d 1k9e 1k9f 1l8n 1mqp 1mqq 1mqr
14668328 G.Pell, E.J.Taylor, T.M.Gloster, J.P.Turkenburg, C.M.Fontes, L.M.Ferreira, T.Nagy, S.J.Clark, G.J.Davies, and H.J.Gilbert (2004).
The mechanisms by which family 10 glycoside hydrolases bind decorated substrates.
  J Biol Chem, 279, 9597-9605.
PDB codes: 1uqy 1uqz 1ur1 1ur2
14670951 G.Pell, L.Szabo, S.J.Charnock, H.Xie, T.M.Gloster, G.J.Davies, and H.J.Gilbert (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.
PDB codes: 1us2 1us3
14747991 T.Pons, D.G.Naumoff, C.Martínez-Fleites, and L.Hernández (2004).
Three acidic residues are at the active site of a beta-propeller architecture in glycoside hydrolase families 32, 43, 62, and 68.
  Proteins, 54, 424-432.  
12831897 D.Shallom, and Y.Shoham (2003).
Microbial hemicellulases.
  Curr Opin Microbiol, 6, 219-228.  
12654910 T.Nagy, D.Nurizzo, G.J.Davies, P.Biely, J.H.Lakey, D.N.Bolam, and H.J.Gilbert (2003).
The alpha-glucuronidase, GlcA67A, of Cellvibrio japonicus utilizes the carboxylate and methyl groups of aldobiouronic acid as important substrate recognition determinants.
  J Biol Chem, 278, 20286-20292.
PDB code: 1h41
12454501 A.Varrot, T.P.Frandsen, H.Driguez, and G.J.Davies (2002).
Structure of the Humicola insolens cellobiohydrolase Cel6A D416A mutant in complex with a non-hydrolysable substrate analogue, methyl cellobiosyl-4-thio-beta-cellobioside, at 1.9 A.
  Acta Crystallogr D Biol Crystallogr, 58, 2201-2204.
PDB code: 1gz1
12413546 A.Vasella, G.J.Davies, and M.Böhm (2002).
Glycosidase mechanisms.
  Curr Opin Chem Biol, 6, 619-629.  
12198486 D.Nurizzo, J.P.Turkenburg, S.J.Charnock, S.M.Roberts, E.J.Dodson, V.A.McKie, E.J.Taylor, H.J.Gilbert, and G.J.Davies (2002).
Cellvibrio japonicus alpha-L-arabinanase 43A has a novel five-blade beta-propeller fold.
  Nat Struct Biol, 9, 665-668.
PDB codes: 1gyd 1gye 1gyh
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.