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PDBsum entry 2fko

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protein ligands metals links
Lyase PDB id
2fko
Jmol
Contents
Protein chain
173 a.a. *
Ligands
EDO ×2
Metals
_ZN
Waters ×189
* Residue conservation analysis
PDB id:
2fko
Name: Lyase
Title: Structure of ph1591 from pyrococcus horikoshii ot3
Structure: 173aa long hypothetical ferripyochelin binding pr chain: a. Synonym: carbonic anhydrases. Engineered: yes
Source: Pyrococcus horikoshii. Organism_taxid: 70601. Strain: ot3. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
1.85Å     R-factor:   0.192     R-free:   0.207
Authors: J.Jeyakanthan,T.H.Tahirov,S.Yokoyama,Y.Shiro,Riken Structura Genomics/proteomics 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
Date:
05-Jan-06     Release date:   16-Jan-07    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
O59257  (O59257_PYRHO) -  173aa long hypothetical ferripyochelin binding protein
Seq:
Struc:
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.
 
  ABSTRACT  
 
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.  
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.