PDBsum entry 1z97

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protein metals links
Lyase PDB id
Protein chain
263 a.a. *
Waters ×97
* Residue conservation analysis
PDB id:
Name: Lyase
Title: Human carbonic anhydrase iii: structural and kinetic study of catalysis and proton transfer.
Structure: Carbonic anhydrase iii. Chain: a. Synonym: carbonate dehydratase iii, ca- iii. Engineered: yes. Mutation: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: ca3. Expressed in: escherichia coli. Expression_system_taxid: 562.
2.10Å     R-factor:   0.186     R-free:   0.237
Authors: D.M.Duda,C.Tu,S.Z.Fisher,H.An,C.Yoshioka,L.Govindasamy, P.J.Laipis,M.Agbandje-Mckenna,D.N.Silverman,R.Mckenna
Key ref:
D.M.Duda et al. (2005). Human carbonic anhydrase III: structural and kinetic study of catalysis and proton transfer. Biochemistry, 44, 10046-10053. PubMed id: 16042381 DOI: 10.1021/bi050610h
31-Mar-05     Release date:   09-Aug-05    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P07451  (CAH3_HUMAN) -  Carbonic anhydrase 3
260 a.a.
263 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 4 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.  - Carbonate dehydratase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: H2CO3 = CO2 + H2O
= 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   2 terms 
  Biological process     small molecule metabolic process   5 terms 
  Biochemical function     lyase activity     5 terms  


    Added reference    
DOI no: 10.1021/bi050610h Biochemistry 44:10046-10053 (2005)
PubMed id: 16042381  
Human carbonic anhydrase III: structural and kinetic study of catalysis and proton transfer.
D.M.Duda, C.Tu, S.Z.Fisher, H.An, C.Yoshioka, L.Govindasamy, P.J.Laipis, M.Agbandje-McKenna, D.N.Silverman, R.McKenna.
The residue phenylalanine 198 (Phe 198) is a prominent cause of the lower activity of human carbonic anhydrase III (HCA III) compared with HCA II and other isozymes which have leucine at this site. We report the crystal structures of HCA III and the site-directed mutant F198L HCA III, both at 2.1 A resolution, and the enhancement of catalytic activity by exogenous proton donors containing imidazole rings. Both enzymes had a hexahistidine extension at the carboxy-terminal end, used to aid in purification, that was ordered in the crystal structures bound in the active site cavity of an adjacent symmetry-related enzyme. This observation allowed us to comment on a number of possible binding sites for imidazole and derivatives as exogenous proton donors/acceptors in catalysis by HCA III. Kinetic and structural evidence indicates that the phenyl side chain of Phe 198 in HCA III, about 5 A from the zinc, is a steric constriction in the active site, may cause altered interactions at the zinc-bound solvent, and is a binding site for the activation of catalysis by histidylhistidine. This suggests that sites of activation of the proton-transfer pathway in carbonic anhydrase are closer to the zinc than considered in previous studies.

Literature references that cite this PDB file's key reference

  PubMed id Reference
21282642 H.M.Becker, M.Klier, C.Schüler, R.McKenna, and J.W.Deitmer (2011).
Intramolecular proton shuttle supports not only catalytic but also noncatalytic function of carbonic anhydrase II.
  Proc Natl Acad Sci U S A, 108, 3071-3076.  
20945495 B.Kanbar, and E.Ozdemir (2010).
Thermal stability of carbonic anhydrase immobilized within polyurethane foam.
  Biotechnol Prog, 26, 1474-1480.  
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
19637848 S.E.Hill, J.N.Bandaria, M.Fox, E.Vanderah, A.Kohen, and C.M.Cheatum (2009).
Exploring the molecular origins of protein dynamics in the active site of human carbonic anhydrase II.
  J Phys Chem B, 113, 11505-11510.  
19805286 V.Alterio, M.Hilvo, A.Di Fiore, C.T.Supuran, P.Pan, S.Parkkila, A.Scaloni, J.Pastorek, S.Pastorekova, C.Pedone, A.Scozzafava, S.M.Monti, and G.De Simone (2009).
Crystal structure of the catalytic domain of the tumor-associated human carbonic anhydrase IX.
  Proc Natl Acad Sci U S A, 106, 16233-16238.
PDB code: 3iai
18551345 B.Wang, F.Li, W.Luan, Y.Xie, C.Zhang, Z.Luo, L.Gui, H.Yan, and J.Xiang (2008).
Comparison of gene expression profiles of Fenneropenaeus chinensis challenged with WSSV and Vibrio.
  Mar Biotechnol (NY), 10, 664-675.  
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.  
17427958 I.Elder, Z.Fisher, P.J.Laipis, C.Tu, R.McKenna, and D.N.Silverman (2007).
Structural and kinetic analysis of proton shuttle residues in the active site of human carbonic anhydrase III.
  Proteins, 68, 337-343.
PDB codes: 2hfw 2hfx 2hfy 3uyn 3uyq
17164835 J.M.Purkerson, and G.J.Schwartz (2007).
The role of carbonic anhydrases in renal physiology.
  Kidney Int, 71, 103-115.  
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.  
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 code is shown on the right.