PDBsum entry 1lgd

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Lyase PDB id
Protein chain
257 a.a. *
Waters ×161
* Residue conservation analysis
PDB id:
Name: Lyase
Title: Crystal structure analysis of hca ii mutant t199p in complex with bicarbonate
Structure: Carbonic anhydrase ii. Chain: a. Synonym: carbonate dehydratase ii, ca-ii. Engineered: yes. Mutation: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562
1.90Å     R-factor:   0.189     R-free:   0.214
Authors: S.Huang,B.Sjoblom,A.E.Sauer-Eriksson,B.-H.Jonsson
Key ref:
S.Huang et al. (2002). Organization of an efficient carbonic anhydrase: implications for the mechanism based on structure-function studies of a T199P/C206S mutant. Biochemistry, 41, 7628-7635. PubMed id: 12056894 DOI: 10.1021/bi020053o
15-Apr-02     Release date:   24-Jul-02    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P00918  (CAH2_HUMAN) -  Carbonic anhydrase 2
260 a.a.
257 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 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: Zinc
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular space   10 terms 
  Biological process     angiotensin-mediated signaling pathway   20 terms 
  Biochemical function     protein binding     5 terms  


    Added reference    
DOI no: 10.1021/bi020053o Biochemistry 41:7628-7635 (2002)
PubMed id: 12056894  
Organization of an efficient carbonic anhydrase: implications for the mechanism based on structure-function studies of a T199P/C206S mutant.
S.Huang, B.Sjöblom, A.E.Sauer-Eriksson, B.H.Jonsson.
Substitution of Pro for Thr199 in the active site of human carbonic anhydrase II (HCA II)(1) reduces its catalytic efficiency about 3000-fold. X-ray crystallographic structures of the T199P/C206S variant have been determined in complex with the substrate bicarbonate and with the inhibitors thiocyanate and beta-mercaptoethanol. The latter molecule is normally not an inhibitor of wild-type HCA II. All three ligands display novel binding interactions to the T199P/C206S mutant. The beta-mercaptoethanol molecule binds in the active site area with its sulfur atom tetrahedrally coordinated to the zinc ion. Thiocyanate binds tetrahedrally coordinated to the zinc ion in T199P/C206S, in contrast to its pentacoordinated binding to the zinc ion in wild-type HCA II. Bicarbonate binds to the mutant with two of its oxygens at the positions of the zinc water (Wat263) and Wat318 in wild-type HCA II. The environment of this area is more hydrophilic than the normal bicarbonate-binding site of HCA II situated in the hydrophobic part of the cavity normally occupied by the so-called deep water (Wat338). The observation of a new binding site for bicarbonate has implications for understanding the mechanism by which the main-chain amino group of Thr199 acquired an important role for orientation of the substrate during the evolution of the enzyme.

Literature references that cite this PDB file's key reference

  PubMed id Reference
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.  
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