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PDBsum entry 2bwc

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protein ligands Protein-protein interface(s) links
Hydrolase PDB id
2bwc
Jmol
Contents
Protein chains
226 a.a. *
Ligands
GOL ×8
GLC-BGC-BGC
SO4
GLC-BGC-BGC-BGC
Waters ×372
* Residue conservation analysis
PDB id:
2bwc
Name: Hydrolase
Title: Structure of endoglucanase 12a (cel12a) from rhodothermus marinus in complex with cellopentaose (5 minute soak)
Structure: Endoglucanase. Chain: a, b. Engineered: yes
Source: Rhodothermus marinus. Organism_taxid: 29549. Strain: iti-378. Expressed in: escherichia coli. Expression_system_taxid: 511693. Expression_system_variant: de3. Other_details: marine thermophilic eubacterium ioslated from alkaline submarine hot springs
Resolution:
2.15Å     R-factor:   0.183     R-free:   0.232
Authors: S.J.Crennell,E.Nordberg-Karlsson
Key ref:
S.J.Crennell et al. (2006). Dimerisation and an increase in active site aromatic groups as adaptations to high temperatures: X-ray Solution scattering and substrate-bound crystal structures of Rhodothermus marinus endoglucanase Cel12A. J Mol Biol, 356, 57-71. PubMed id: 16343530 DOI: 10.1016/j.jmb.2005.11.004
Date:
13-Jul-05     Release date:   21-Dec-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
O33897  (O33897_RHOMR) -  Cellulase
Seq:
Struc:
260 a.a.
226 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 18 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.3.2.1.4  - Cellulase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Endohydrolysis of 1,4-beta-D-glucosidic linkages in cellulose, lichenin and cereal beta-D-glucans.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     polysaccharide catabolic process   1 term 
  Biochemical function     hydrolase activity, hydrolyzing O-glycosyl compounds     2 terms  

 

 
DOI no: 10.1016/j.jmb.2005.11.004 J Mol Biol 356:57-71 (2006)
PubMed id: 16343530  
 
 
Dimerisation and an increase in active site aromatic groups as adaptations to high temperatures: X-ray Solution scattering and substrate-bound crystal structures of Rhodothermus marinus endoglucanase Cel12A.
S.J.Crennell, D.Cook, A.Minns, D.Svergun, R.L.Andersen, E.Nordberg Karlsson.
 
  ABSTRACT  
 
Cellulose, a polysaccharide consisting of beta-1,4-linked glucose, is the major component of plant cell walls and consequently one of the most abundant biopolymers on earth. Carbohydrate polymers such as cellulose are molecules with vast diversity in structure and function, and a multiplicity of hydrolases operating in concert are required for depolymerisation. The bacterium Rhodothermus marinus, isolated from shallow water marine hot springs, produces a number of carbohydrate-degrading enzymes including a family 12 cellulase Cel12A. The structure of R.marinus Cel12A in the ligand-free form (at 1.54 angstroms) and structures of RmCel12A after crystals were soaked in cellopentaose for two different lengths of time, have been determined. The shorter soaked complex revealed the conformation of unhydrolysed cellotetraose, while cellopentaose had been degraded more completely during the longer soak. Comparison of these structures with those of mesophilic family 12 cellulases in complex with inhibitors and substrate revealed that RmCel12A has a more extensive aromatic network in the active site cleft which ejects products after hydrolysis. The substrate structure confirms that during hydrolysis by family 12 cellulases glucose does not pass through a (2,5)B conformation. Small-angle X-ray scattering analysis of RmCel12A showed that the enzyme forms a loosely associated antiparallel dimer in solution, which may target the enzyme to the antiparallel polymer strands in cellulose.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. The structure of the RmCel12A dimer, the two monomers being coloured in brown and green with the "cord" which terminates the active site cleft and causes substrate bending, drawn in purple in both monomers. Residues involved in the interfacial ion-pairs are drawn in ball-and-stick representation. The Figure was prepared using MOLSCRIPT47 and Raster 3D.48
Figure 3.
Figure 3. Comparison of the 2F[o] -F[c] electron density observed in the RmCel12A active sites of (a) Sub2B, (b) Sub2A, (c) Sub1, together with that of the acid-base E207 as an indicator of the overall quality of the maps. The catalytic E124 and E207 have orange bonds, the main species modelled into the density is drawn with black bonds and the subsidiary one with yellow. The b-strand containing E124 and the cord (drawn in purple) are also included. The Figure was prepared using Bobscript.49
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2006, 356, 57-71) copyright 2006.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20715051 J.H.Tomlinson, V.L.Green, P.J.Baker, and M.P.Williamson (2010).
Structural origins of pH-dependent chemical shifts in the B1 domain of protein G.
  Proteins, 78, 3000-3016.
PDB code: 3mp9
17359551 P.Turner, G.Mamo, and E.N.Karlsson (2007).
Potential and utilization of thermophiles and thermostable enzymes in biorefining.
  Microb Cell Fact, 6, 9.  
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