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PDBsum entry 1vd5

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protein ligands links
Hydrolase PDB id
1vd5
Jmol
Contents
Protein chain
377 a.a. *
Ligands
GLY ×4
DTT ×2
MPD
Waters ×478
* Residue conservation analysis
PDB id:
1vd5
Name: Hydrolase
Title: Crystal structure of unsaturated glucuronyl hydrolase, respo the degradation of glycosaminoglycan, from bacillus sp. Gl1 resolution
Structure: Unsaturated glucuronyl hydrolase. Chain: a. Engineered: yes
Source: Bacillus sp.. Organism_taxid: 84635. Strain: gl1. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
Resolution:
1.80Å     R-factor:   0.168     R-free:   0.189
Authors: T.Itoh,S.Akao,W.Hashimoto,B.Mikami,K.Murata
Key ref:
T.Itoh et al. (2004). Crystal structure of unsaturated glucuronyl hydrolase, responsible for the degradation of glycosaminoglycan, from Bacillus sp. GL1 at 1.8 A resolution. J Biol Chem, 279, 31804-31812. PubMed id: 15148314 DOI: 10.1074/jbc.M403288200
Date:
18-Mar-04     Release date:   13-Jul-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q9RC92  (UGL_BACGL) -  Unsaturated glucuronyl hydrolase
Seq:
Struc:
377 a.a.
377 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.2.1.179  - Gellan tetrasaccharide unsaturated glucuronyl hydrolase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Beta-D-4-deoxy-Delta4-GlcAp-(1->4)-beta-D-Glcp-(1->4)-alpha-L-Rhap- (1->3)-beta-D-Glcp + H2O = 5-dehydro-4-deoxy-D-glucuronate + beta-D- Glcp-(1->4)-alpha-L-Rhap-(1->3)-beta-D-Glcp
Beta-D-4-deoxy-Delta(4)-GlcAp-(1->4)-beta-D-Glcp-(1->4)-alpha-L-Rhap- (1->3)-beta-D-Glcp
+ H(2)O
= 5-dehydro-4-deoxy-D-glucuronate
+ beta-D- Glcp-(1->4)-alpha-L-Rhap-(1->3)-beta-D-Glcp
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     metabolic process   3 terms 
  Biochemical function     catalytic activity     3 terms  

 

 
    Key reference    
 
 
DOI no: 10.1074/jbc.M403288200 J Biol Chem 279:31804-31812 (2004)
PubMed id: 15148314  
 
 
Crystal structure of unsaturated glucuronyl hydrolase, responsible for the degradation of glycosaminoglycan, from Bacillus sp. GL1 at 1.8 A resolution.
T.Itoh, S.Akao, W.Hashimoto, B.Mikami, K.Murata.
 
  ABSTRACT  
 
Unsaturated glucuronyl hydrolase (UGL) is a novel glycosaminoglycan hydrolase that releases unsaturated d-glucuronic acid from oligosaccharides produced by polysaccharide lyases. The x-ray crystallographic structure of UGL from Bacillus sp. GL1 was first determined by multiple isomorphous replacement (mir) and refined at 1.8 A resolution with a final R-factor of 16.8% for 25 to 1.8 A resolution data. The refined UGL structure consists of 377 amino acid residues and 478 water molecules, four glycine molecules, two dithiothreitol (DTT) molecules, and one 2-methyl-2,4-pentanediol (MPD) molecule. UGL includes an alpha(6)/alpha(6)-barrel, whose structure is found in the six-hairpin enzyme superfamily of an alpha/alpha-toroidal fold. One side of the UGL alpha(6)/alpha(6)-barrel structure consists of long loops containing three short beta-sheets and contributes to the formation of a deep pocket. One glycine molecule and two DTT molecules surrounded by highly conserved amino acid residues in UGLs were found in the pocket, suggesting that catalytic and substrate-binding sites are located in this pocket. The overall UGL structure, with the exception of some loops, very much resembled that of the Bacillus subtilis hypothetical protein Yter, whose function is unknown and which exhibits little amino acid sequence identity with UGL. In the active pocket, residues possibly involved in substrate recognition and catalysis by UGL are conserved in UGLs and Yter. The most likely candidate catalytic residues for glycosyl hydrolysis are Asp(88) and Asp(149). This was supported by site-directed mutagenesis studies in Asp(88) and Asp(149).
 
  Selected figure(s)  
 
Figure 4.
FIG. 4. Structural comparison of overall structures of UGL (pink) and hypothetical protein Yter (blue). Superimposed results are shown schematically in C^ traces. Coordinates of Yter (1NC5 [PDB] ) were taken from the RCSB Protein Data Bank (28). The figure was drawn using the GRASP (32) program.
Figure 7.
FIG. 7. Structural comparison of the active site arrangement of UGL and hypothetical protein Yter. Main chains are pink for UGL and blue for Yter. Side chains are red for UGL and cyan for Yter. The figure was prepared using MOLSCRIPT (30) and RASTER3D (31).
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2004, 279, 31804-31812) copyright 2004.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19416976 Y.Maruyama, Y.Nakamichi, T.Itoh, B.Mikami, W.Hashimoto, and K.Murata (2009).
Substrate specificity of streptococcal unsaturated glucuronyl hydrolases for sulfated glycosaminoglycan.
  J Biol Chem, 284, 18059-18069.  
17823855 D.Wong (2008).
Enzymatic deconstruction of backbone structures of the ramified regions in pectins.
  Protein J, 27, 30-42.  
18256495 K.Murata, S.Kawai, B.Mikami, and W.Hashimoto (2008).
Superchannel of bacteria: biological significance and new horizons.
  Biosci Biotechnol Biochem, 72, 265-277.  
17938954 P.N.Bocock, A.M.Morse, C.Dervinis, and J.M.Davis (2008).
Evolution and diversity of invertase genes in Populus trichocarpa.
  Planta, 227, 565-576.  
15906318 R.Zhang, T.Minh, L.Lezondra, S.Korolev, S.F.Moy, F.Collart, and A.Joachimiak (2005).
1.6 A crystal structure of YteR protein from Bacillus subtilis, a predicted lyase.
  Proteins, 60, 561-565.
PDB code: 1nc5
15849405 W.Hashimoto, K.Momma, Y.Maruyama, M.Yamasaki, B.Mikami, and K.Murata (2005).
Structure and function of bacterial super-biosystem responsible for import and depolymerization of macromolecules.
  Biosci Biotechnol Biochem, 69, 673-692.  
15983871 X.Ji, W.Van den Ende, A.Van Laere, S.Cheng, and J.Bennett (2005).
Structure, evolution, and expression of the two invertase gene families of rice.
  J Mol Evol, 60, 615-634.  
  16233728 W.Hashimoto, M.Yamasaki, T.Itoh, K.Momma, B.Mikami, and K.Murata (2004).
Super-channel in bacteria: structural and functional aspects of a novel biosystem for the import and depolymerization of macromolecules.
  J Biosci Bioeng, 98, 399-413.  
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 code is shown on the right.