PDBsum entry 1hcb

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Lyase(oxo-acid) PDB id
Protein chain
258 a.a. *
Waters ×254
* Residue conservation analysis
PDB id:
Name: Lyase(oxo-acid)
Title: Enzyme-substrate interactions: structure of human carbonic anhydrase i complexed with bicarbonate
Structure: Carbonic anhydrase i. Chain: a. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606
1.60Å     R-factor:   0.177    
Authors: V.Kumar,K.K.Kannan
Key ref: V.Kumar and K.K.Kannan (1994). Enzyme-substrate interactions. Structure of human carbonic anhydrase I complexed with bicarbonate. J Mol Biol, 241, 226-232. PubMed id: 8057362
07-Jan-94     Release date:   30-Apr-94    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P00915  (CAH1_HUMAN) -  Carbonic anhydrase 1
261 a.a.
258 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - Carbonate dehydratase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: H2CO3 = CO2 + H2O
Bound ligand (Het Group name = BCT)
corresponds exactly
= CO(2)
+ 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   3 terms 
  Biological process     small molecule metabolic process   3 terms 
  Biochemical function     lyase activity     4 terms  


    Added reference    
J Mol Biol 241:226-232 (1994)
PubMed id: 8057362  
Enzyme-substrate interactions. Structure of human carbonic anhydrase I complexed with bicarbonate.
V.Kumar, K.K.Kannan.
The structure of HCAI-HCO3- complex has been refined with 10-1.6A X-ray diffraction data to an R-value of 17.7%. The structure reveals monodentate binding of the HCO3- anion at an apical tetrahedral position to the zinc ion. The binding mode and interactions of HCO3- in HCAI differ from that in HCAII. The activity linked H2O/OH- group in the free HCAI is replaced by the hydroxyl group of the bicarbonate anion. This result rules out the rearrangement of the bound HCO3- advocated earlier to explain the microscopic reversibility of the catalysed reaction. From the geometry of the H-bonds between Glu106-Thr199 pair and Glu117-His119 couple, the glutamic acids are expected to be ionized and accept H-bonds from their partners. The product-inhibiton by HCO3- anion is explained on the basis of proton localization on His119 in the Glu117-His119 couple. These results are consistent with the hypothesis that Glu117-His119 tunes the ionicity of the Zn2+ and the binding strength of HCO3- anion. A pi hydrogen bond is observed between a water and phenyl ring of the Tyr114 residue.

Literature references that cite this PDB file's key reference

  PubMed id Reference
20505865 V.Alterio, S.M.Monti, E.Truppo, C.Pedone, C.T.Supuran, and G.De Simone (2010).
The first example of a significant active site conformational rearrangement in a carbonic anhydrase-inhibitor adduct: the carbonic anhydrase I-topiramate complex.
  Org Biomol Chem, 8, 3528-3533.
PDB code: 3lxe
19520834 B.Sjöblom, M.Polentarutti, and K.Djinovic-Carugo (2009).
Structural study of X-ray induced activation of carbonic anhydrase.
  Proc Natl Acad Sci U S A, 106, 10609-10613.
PDB codes: 2vva 2vvb
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.  
17607683 A.Thiry, B.Masereel, J.M.Dogné, C.T.Supuran, J.Wouters, and C.Michaux (2007).
Exploration of the Binding Mode of Indanesulfonamides as Selective Inhibitors of Human Carbonic Anhydrase Type VII by Targeting Lys 91.
  ChemMedChem, 2, 1273-1280.  
17573429 S.Marino, K.Hayakawa, K.Hatada, M.Benfatto, A.Rizzello, M.Maffia, and L.Bubacco (2007).
Structural features that govern enzymatic activity in carbonic anhydrase from a low-temperature adapted fish, Chionodraco hamatus.
  Biophys J, 93, 2781-2790.  
16506782 K.M.Jude, A.L.Banerjee, M.K.Haldar, S.Manokaran, B.Roy, S.Mallik, D.K.Srivastava, and D.W.Christianson (2006).
Ultrahigh resolution crystal structures of human carbonic anhydrases I and II complexed with "two-prong" inhibitors reveal the molecular basis of high affinity.
  J Am Chem Soc, 128, 3011-3018.
PDB codes: 2foq 2fos 2fou 2fov 2foy
9241431 C.Chothia, T.Hubbard, S.Brenner, H.Barns, and A.Murzin (1997).
Protein folds in the all-beta and all-alpha classes.
  Annu Rev Biophys Biomol Struct, 26, 597-627.  
9336012 S.Lindskog (1997).
Structure and mechanism of carbonic anhydrase.
  Pharmacol Ther, 74, 1.  
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