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PDBsum entry 3eyx

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protein ligands metals Protein-protein interface(s) links
Lyase PDB id
3eyx
Jmol
Contents
Protein chains
197 a.a. *
Ligands
ACT ×2
EDO ×4
Metals
_ZN ×2
Waters ×152
* Residue conservation analysis
PDB id:
3eyx
Name: Lyase
Title: Crystal structure of carbonic anhydrase nce103 from saccharomyces cerevisiae
Structure: Carbonic anhydrase. Chain: a, b. Fragment: residues 14-221. Synonym: beta-carbonic anhydrase, carbonate dehydratase, non-classical export protein 3. Engineered: yes
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Strain: s288c. Gene: nce103. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.04Å     R-factor:   0.199     R-free:   0.241
Authors: Y.B.Teng,Y.L.Jiang,Y.Chen,C.Z.Zhou
Key ref: Y.B.Teng et al. (2009). Structural insights into the substrate tunnel of Saccharomyces cerevisiae carbonic anhydrase Nce103. BMC Struct Biol, 9, 67. PubMed id: 19852838
Date:
22-Oct-08     Release date:   15-Sep-09    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P53615  (CAN_YEAST) -  Carbonic anhydrase
Seq:
Struc:
221 a.a.
197 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.4.2.1.1  - Carbonate dehydratase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: H2CO3 = CO2 + H2O
H(2)CO(3)
=
CO(2)
Bound ligand (Het Group name = ACT)
matches with 75.00% similarity
+ H(2)O
      Cofactor: Zn(2+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   4 terms 
  Biological process     metabolic process   4 terms 
  Biochemical function     lyase activity     4 terms  

 

 
    Added reference    
 
 
BMC Struct Biol 9:67 (2009)
PubMed id: 19852838  
 
 
Structural insights into the substrate tunnel of Saccharomyces cerevisiae carbonic anhydrase Nce103.
Y.B.Teng, Y.L.Jiang, Y.X.He, W.W.He, F.M.Lian, Y.Chen, C.Z.Zhou.
 
  ABSTRACT  
 
BACKGROUND: The carbonic anhydrases (CAs) are involved in inorganic carbon utilization. They have been classified into six evolutionary and structural families: alpha-, beta-, gamma-, delta-, epsilon-, zeta- CAs, with beta-CAs present in higher plants, algae and prokaryotes. The yeast Saccharomyces cerevisiae encodes a single copy of beta-CA Nce103/YNL036W. RESULTS: We determined the crystal structure of Nce103 in complex with a substrate analog at 2.04 A resolution. It assembles as a homodimer, with the active site located at the interface between two monomers. At the bottom of the substrate pocket, a zinc ion is coordinated by the three highly conserved residues Cys57, His112 and Cys115 in addition to a water molecule. Residues Asp59, Arg61, Gly111, Leu102, Val80, Phe75 and Phe97 form a tunnel to the bottom of the active site which is occupied by a molecule of the substrate analog acetate. Activity assays of full length and two truncated versions of Nce103 indicated that the N-terminal arm is indispensable. CONCLUSION: The quaternary structure of Nce103 resembles the typical plant type beta-CAs of known structure, with an N-terminal arm indispensable for the enzymatic activity. Comparative structure analysis enables us to draw a possible tunnel for the substrate to access the active site which is located at the bottom of a funnel-shaped substrate pocket.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
22012399 M.J.Smeulders, T.R.Barends, A.Pol, A.Scherer, M.H.Zandvoort, A.Udvarhelyi, A.F.Khadem, A.Menzel, J.Hermans, R.L.Shoeman, H.J.Wessels, L.P.van den Heuvel, L.Russ, I.Schlichting, M.S.Jetten, and H.J.Op den Camp (2011).
Evolution of a new enzyme for carbon disulphide conversion by an acidothermophilic archaeon.
  Nature, 478, 412-416.
PDB codes: 3ten 3teo
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