spacer
spacer

PDBsum entry 2cab

Go to PDB code: 
protein metals links
Hydro-lyase PDB id
2cab
Jmol
Contents
Protein chain
256 a.a. *
Metals
_ZN
* Residue conservation analysis
PDB id:
2cab
Name: Hydro-lyase
Title: Structure, refinement and function of carbonic anhydrase isozymes. Refinement of human carbonic anhydrase i
Structure: Carbonic anhydrase form b. Chain: a. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606
Resolution:
2.00Å     R-factor:   0.193    
Authors: K.K.Kannan,M.Ramanadham,T.A.Jones
Key ref: K.K.Kannan et al. (1984). Structure, refinement, and function of carbonic anhydrase isozymes: refinement of human carbonic anhydrase I. Ann N Y Acad Sci, 429, 49-60. PubMed id: 6430186
Date:
05-Oct-83     Release date:   02-Feb-84    
Supersedes: 1cab
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00915  (CAH1_HUMAN) -  Carbonic anhydrase 1
Seq:
Struc:
261 a.a.
256 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.4.2.1.1  - Carbonate dehydratase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: H2CO3 = CO2 + H2O
H(2)CO(3)
= 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    
 
 
Ann N Y Acad Sci 429:49-60 (1984)
PubMed id: 6430186  
 
 
Structure, refinement, and function of carbonic anhydrase isozymes: refinement of human carbonic anhydrase I.
K.K.Kannan, M.Ramanadham, T.A.Jones.
 
  ABSTRACT  
 
The structure of human erythrocyte carbonic anhydrase I has been refined to a final R value of 19% to 2-A resolution by a combination of least squares refinement and model fitting in a three-dimensional graphics display. About 300 solvent atoms have been located bound to the protein molecule. An interesting hydrogen bond network involving Zn2+, the liganded solvent, side chain groups of Thr-199, Glu-106, Thr-7, and His-64 through two solvent molecules have been found that may be important for the catalytic mechanism of the carbonic anhydrase.
 

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
19438233 C.M.Maupin, R.McKenna, D.N.Silverman, and G.A.Voth (2009).
Elucidation of the proton transport mechanism in human carbonic anhydrase II.
  J Am Chem Soc, 131, 7598-7608.  
19891498 D.J.Sindhikara, A.E.Roitberg, and K.M.Merz (2009).
Apo and nickel-bound forms of the Pyrococcus horikoshii species of the metalloregulatory protein: NikR characterized by molecular dynamics simulations.
  Biochemistry, 48, 12024-12033.  
19140795 J.M.Chambers, P.A.Hill, J.A.Aaron, Z.Han, D.W.Christianson, N.N.Kuzma, and I.J.Dmochowski (2009).
Cryptophane xenon-129 nuclear magnetic resonance biosensors targeting human carbonic anhydrase.
  J Am Chem Soc, 131, 563-569.  
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
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
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.  
17319695 C.M.Maupin, and G.A.Voth (2007).
Preferred orientations of His64 in human carbonic anhydrase II.
  Biochemistry, 46, 2938-2947.  
17407288 D.K.Srivastava, K.M.Jude, A.L.Banerjee, M.Haldar, S.Manokaran, J.Kooren, S.Mallik, and D.W.Christianson (2007).
Structural analysis of charge discrimination in the binding of inhibitors to human carbonic anhydrases I and II.
  J Am Chem Soc, 129, 5528-5537.
PDB codes: 2nmx 2nn1 2nn7 2nng 2nno 2nns 2nnv
17429993 J.M.Swanson, C.M.Maupin, H.Chen, M.K.Petersen, J.Xu, Y.Wu, and G.A.Voth (2007).
Proton solvation and transport in aqueous and biomolecular systems: insights from computer simulations.
  J Phys Chem B, 111, 4300-4314.  
12009884 M.Ferraroni, S.Tilli, F.Briganti, W.R.Chegwidden, C.T.Supuran, K.E.Wiebauer, R.E.Tashian, and A.Scozzafava (2002).
Crystal structure of a zinc-activated variant of human carbonic anhydrase I, CA I Michigan 1: evidence for a second zinc binding site involving arginine coordination.
  Biochemistry, 41, 6237-6244.
PDB codes: 1j9w 1jv0
11493685 D.A.Whittington, A.Waheed, B.Ulmasov, G.N.Shah, J.H.Grubb, W.S.Sly, and D.W.Christianson (2001).
Crystal structure of the dimeric extracellular domain of human carbonic anhydrase XII, a bitopic membrane protein overexpressed in certain cancer tumor cells.
  Proc Natl Acad Sci U S A, 98, 9545-9550.
PDB codes: 1jcz 1jd0
10924115 T.M.Iverson, B.E.Alber, C.Kisker, J.G.Ferry, and D.C.Rees (2000).
A closer look at the active site of gamma-class carbonic anhydrases: high-resolution crystallographic studies of the carbonic anhydrase from Methanosarcina thermophila.
  Biochemistry, 39, 9222-9231.
PDB codes: 1qq0 1qre 1qrf 1qrg 1qrl 1qrm
  8655508 B.E.Alber, and J.G.Ferry (1996).
Characterization of heterologously produced carbonic anhydrase from Methanosarcina thermophila.
  J Bacteriol, 178, 3270-3274.  
8942978 T.Stams, S.K.Nair, T.Okuyama, A.Waheed, W.S.Sly, and D.W.Christianson (1996).
Crystal structure of the secretory form of membrane-associated human carbonic anhydrase IV at 2.8-A resolution.
  Proc Natl Acad Sci U S A, 93, 13589-13594.
PDB code: 1znc
  8003972 C.L.Borders, J.A.Broadwater, P.A.Bekeny, J.E.Salmon, A.S.Lee, A.M.Eldridge, and V.B.Pett (1994).
A structural role for arginine in proteins: multiple hydrogen bonds to backbone carbonyl oxygens.
  Protein Sci, 3, 541-548.  
7925414 I.M.Johansson, and C.Forsman (1994).
Solvent hydrogen isotope effects and anion inhibition of CO2 hydration catalysed by carbonic anhydrase from Pisum sativum.
  Eur J Biochem, 224, 901-907.  
7866410 W.R.Chegwidden, L.E.Wagner, P.J.Venta, N.C.Bergenhem, Y.S.Yu, and R.E.Tashian (1994).
Marked zinc activation of ester hydrolysis by a mutation, 67-His (CAT) to Arg (CGT), in the active site of human carbonic anhydrase I.
  Hum Mutat, 4, 294-296.  
8269932 I.M.Johansson, and C.Forsman (1993).
Kinetic studies of pea carbonic anhydrase.
  Eur J Biochem, 218, 439-446.  
  1303752 M.E.Karpen, P.L.de Haseth, and K.E.Neet (1992).
Differences in the amino acid distributions of 3(10)-helices and alpha-helices.
  Protein Sci, 1, 1333-1342.  
  1678690 H.T.Wright (1991).
Nonenzymatic deamidation of asparaginyl and glutaminyl residues in proteins.
  Crit Rev Biochem Mol Biol, 26, 1.  
2166604 M.Nilges, G.M.Clore, and A.M.Gronenborn (1990).
1H-NMR stereospecific assignments by conformational data-base searches.
  Biopolymers, 29, 813-822.  
3151019 A.E.Eriksson, T.A.Jones, and A.Liljas (1988).
Refined structure of human carbonic anhydrase II at 2.0 A resolution.
  Proteins, 4, 274-282.
PDB codes: 1ca2 4cac 5cac
6430173 D.Hewett-Emmett, P.J.Hopkins, R.E.Tashian, and J.Czelusniak (1984).
Origins and molecular evolution of the carbonic anhydrase isozymes.
  Ann N Y Acad Sci, 429, 338-358.  
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.