PDBsum entry 1v3w

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protein ligands metals links
Transferase PDB id
Protein chain
173 a.a. *
EDO ×3
_CA ×4
Waters ×193
* Residue conservation analysis
PDB id:
Name: Transferase
Title: Structure of ferripyochelin binding protein from pyrococcus ot3
Structure: Ferripyochelin binding protein. Chain: a. Engineered: yes
Source: Pyrococcus horikoshii. Organism_taxid: 70601. Strain: ot3. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Trimer (from PDB file)
1.50Å     R-factor:   0.185     R-free:   0.203
Authors: J.Jeyakanthan,T.H.Tahirov,Riken Structural Genomics/proteomi Initiative (Rsgi)
Key ref:
J.Jeyakanthan et al. (2008). Observation of a calcium-binding site in the gamma-class carbonic anhydrase from Pyrococcus horikoshii. Acta Crystallogr D Biol Crystallogr, 64, 1012-1019. PubMed id: 18931408 DOI: 10.1107/S0907444908024323
07-Nov-03     Release date:   18-Nov-03    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
O59257  (O59257_PYRHO) -  173aa long hypothetical ferripyochelin binding protein
173 a.a.
173 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     metal ion binding     1 term  


DOI no: 10.1107/S0907444908024323 Acta Crystallogr D Biol Crystallogr 64:1012-1019 (2008)
PubMed id: 18931408  
Observation of a calcium-binding site in the gamma-class carbonic anhydrase from Pyrococcus horikoshii.
J.Jeyakanthan, S.Rangarajan, P.Mridula, S.P.Kanaujia, Y.Shiro, S.Kuramitsu, S.Yokoyama, K.Sekar.
Carbonic anhydrases are zinc-containing metalloenzymes that catalyze the interconversion of carbon dioxide and bicarbonate. Three crystal structures of gamma-class carbonic anhydrase (one of which is bound to a bicarbonate molecule) from the aerobic OT3 strain of the hyperthermophilic archeon Pyrococcus horikoshii have been solved by molecular replacement in space group F4(1)32. The asymmetric unit contains a monomer of 173 amino acids and a catalytic Zn2+ ion. The protein fold is a regular prism formed by a left-handed beta-helix, similar to previously reported structures. The active-site Zn2+ ion located at the interface between the two monomers is bound to three histidyl residues and a water molecule in a tetrahedral fashion. In addition to the 20 beta-strands comprising the beta-helix, there is also a long C-terminal alpha-helix. For the first time, Ca2+ ions have been observed in addition to the catalytic Zn2+ ion. It is hypothesized that Tyr159 (which corresponds to the catalytically important Asn202 in previously reported structures) utilizes C-H...pi interactions to fulfill its functions. This study may shed light on the catalytic mechanism of the enzyme and throw open new questions on the mechanism of product removal in carbonic anhydrases.
  Selected figure(s)  
Figure 3.
Figure 3 In this representation of the Zn-Cap trimer (generated from 1v67 ), metal ions are shown as spheres. The central Ca^2+ ion is in magenta, the Zn^2+ ions in brick red and the positions of the Cl^- ions from a 1v3w trimer are shown as green circles.
Figure 4.
Figure 4 Metal-ion coordination. (a) Zn^2+ is coordinated to His65A ND1, His87A NE2, His82B NE2, HOH44 and Tyr159B OH. The OH is at a distance of 2.71 Å from Zn^2+. (b) The Ca^2+ ion is coordinated to Ser40 OG and Asn61 OD1 from all three chains.
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2008, 64, 1012-1019) copyright 2008.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19747990 J.G.Ferry (2010).
The gamma class of carbonic anhydrases.
  Biochim Biophys Acta, 1804, 374-381.  
20023030 S.A.Zimmerman, J.F.Tomb, and J.G.Ferry (2010).
Characterization of CamH from Methanosarcina thermophila, founding member of a subclass of the {gamma} class of carbonic anhydrases.
  J Bacteriol, 192, 1353-1360.  
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