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Lyase PDB id
2esf
Jmol
Contents
Protein chains
213 a.a. *
Ligands
BCT ×2
Metals
_ZN ×2
Waters ×178
* Residue conservation analysis
PDB id:
2esf
Name: Lyase
Title: Identification of a novel non-catalytic bicarbonate binding eubacterial beta-carbonic anhydrase
Structure: Carbonic anhydrase 2. Chain: a, b. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Gene: can, cynt2. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: Tetramer (from PDB file)
Resolution:
2.25Å     R-factor:   0.198     R-free:   0.228
Authors: J.D.Cronk,R.S.Rowlett,K.Y.J.Zhang,C.Tu,J.A.Endrizzi,P.C.Gare
Key ref:
J.D.Cronk et al. (2006). Identification of a novel noncatalytic bicarbonate binding site in eubacterial beta-carbonic anhydrase. Biochemistry, 45, 4351-4361. PubMed id: 16584170 DOI: 10.1021/bi052272q
Date:
26-Oct-05     Release date:   18-Apr-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P61517  (CAN_ECOLI) -  Carbonic anhydrase 2
Seq:
Struc: 		220 a.a.
213 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)
Bound ligand (Het Group name = BCT)
corresponds exactly 		= CO(2)
 + H(2)O
      Cofactor: Zinc
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytosol   1 term 
  Biological process     carbon utilization   1 term 
  Biochemical function     protein binding     5 terms  

 

 
    Added reference    
 
 
DOI no: 10.1021/bi052272q Biochemistry 45:4351-4361 (2006)
PubMed id: 16584170  
 
 
Identification of a novel noncatalytic bicarbonate binding site in eubacterial beta-carbonic anhydrase.
J.D.Cronk, R.S.Rowlett, K.Y.Zhang, C.Tu, J.A.Endrizzi, J.Lee, P.C.Gareiss, J.R.Preiss.
 
  ABSTRACT  
 
The structures of beta class carbonic anhydrases (beta-CAs) determined so far fall into two distinct subclasses based on the observed coordination of the catalytic zinc (Zn2+) ion. The subclass of beta-CAs that coordinate Zn2+ tetrahedrally with four protein-derived ligands is represented by the structures of orthologues from Porphyridium purpureum, Escherichia coli, and Mycobacterium tuberculosis. Here we present the structure of an additional member of that subclass, that from Haemophilus influenzae, as well as detailed kinetic analysis, revealing the correspondence between structural classification and kinetic profile for this subclass. In addition, we identify a unique, noncatalytic binding mode for the substrate bicarbonate that occurs in both the H. influenzae and E. coli enzymes. The kinetic and structural analysis indicates that binding of bicarbonate in this site of the enzyme may modulate its activity by influencing a pH-dependent, cooperative transition between active and inactive forms. We hypothesize that the two structural subclasses of beta-CAs may provide models for the proposed active and inactive forms of the H. influenzae and E. coli enzymes.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21402476 F.Carta, A.Innocenti, R.A.Hall, F.A.Mühlschlegel, A.Scozzafava, and C.T.Supuran (2011).
Carbonic anhydrase inhibitors. Inhibition of the β-class enzymes from the fungal pathogens Candida albicans and Cryptococcus neoformans with branched aliphatic/aromatic carboxylates and their derivatives.
  Bioorg Med Chem Lett, 21, 2521-2526.  
21298147 F.Pannetier, G.Ohanessian, and G.Frison (2011).
Comparison between α- and β-carbonic anhydrases: can Zn(His)3(H2O) and Zn(His)(Cys)2(H2O) sites lead to equivalent enzymes?
  Dalton Trans, 40, 2696-2698.  
20659325 L.Syrjänen, M.Tolvanen, M.Hilvo, A.Olatubosun, A.Innocenti, A.Scozzafava, J.Leppiniemi, B.Niederhauser, V.P.Hytönen, T.A.Gorr, S.Parkkila, and C.T.Supuran (2010).
Characterization of the first beta-class carbonic anhydrase from an arthropod (Drosophila melanogaster) and phylogenetic analysis of beta-class carbonic anhydrases in invertebrates.
  BMC Biochem, 11, 28.  
20525828 P.Burghout, L.E.Cron, H.Gradstedt, B.Quintero, E.Simonetti, J.J.Bijlsma, H.J.Bootsma, and P.W.Hermans (2010).
Carbonic anhydrase is essential for Streptococcus pneumoniae growth in environmental ambient air.
  J Bacteriol, 192, 4054-4062.  
20359198 R.S.Rowlett, K.M.Hoffmann, H.Failing, M.M.Mysliwiec, and D.Samardzic (2010).
Evidence for a bicarbonate "escort" site in Haemophilus influenzae beta-carbonic anhydrase .
  Biochemistry, 49, 3640-3647.
PDB codes: 3e2x 3e31 3e3f 3e3g 3e3i
19459702 R.S.Rowlett, C.Tu, J.Lee, A.G.Herman, D.A.Chapnick, S.H.Shah, and P.C.Gareiss (2009).
Allosteric site variants of Haemophilus influenzae beta-carbonic anhydrase.
  Biochemistry, 48, 6146-6156.
PDB codes: 3e1v 3e1w 3e24 3e28 3e2a 3e2w
19852838 Y.B.Teng, Y.L.Jiang, Y.X.He, W.W.He, F.M.Lian, Y.Chen, and C.Z.Zhou (2009).
Structural insights into the substrate tunnel of Saccharomyces cerevisiae carbonic anhydrase Nce103.
  BMC Struct Biol, 9, 67.
PDB code: 3eyx
18931408 J.Jeyakanthan, S.Rangarajan, P.Mridula, S.P.Kanaujia, Y.Shiro, S.Kuramitsu, S.Yokoyama, and K.Sekar (2008).
Observation of a calcium-binding site in the gamma-class carbonic anhydrase from Pyrococcus horikoshii.
  Acta Crystallogr D Biol Crystallogr, 64, 1012-1019.
PDB codes: 1v3w 1v67 2fko
17993516 S.S.Cot, A.K.So, and G.S.Espie (2008).
A multiprotein bicarbonate dehydration complex essential to carboxysome function in cyanobacteria.
  J Bacteriol, 190, 936-945.  
18335973 V.M.Krishnamurthy, G.K.Kaufman, A.R.Urbach, I.Gitlin, K.L.Gudiksen, D.B.Weibel, and G.M.Whitesides (2008).
Carbonic anhydrase as a model for biophysical and physical-organic studies of proteins and protein-ligand binding.
  Chem Rev, 108, 946.  
18322527 Y.Xu, L.Feng, P.D.Jeffrey, Y.Shi, and F.M.Morel (2008).
Structure and metal exchange in the cadmium carbonic anhydrase of marine diatoms.
  Nature, 452, 56-61.
PDB codes: 3bob 3boc 3boe 3boh 3boj
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 codes are shown on the right.