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PDBsum entry 1rzb

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protein ligands metals links
Lyase(oxo-acid) PDB id
1rzb
Jmol
Contents
Protein chain
258 a.a. *
Ligands
SO4
Metals
_CO
Waters ×216
* Residue conservation analysis
PDB id:
1rzb
Name: Lyase(oxo-acid)
Title: X-ray analysis of metal substituted human carbonic anhydrase ii derivatives
Structure: Carbonic anhydrase ii. Chain: a. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606
Resolution:
1.80Å     R-factor:   0.155    
Authors: K.Hakansson,A.Wehnert,A.Liljas
Key ref:
K.Håkansson et al. (1994). X-ray analysis of metal-substituted human carbonic anhydrase II derivatives. Acta Crystallogr D Biol Crystallogr, 50, 93. PubMed id: 15299481 DOI: 10.1107/S0907444993008790
Date:
25-May-93     Release date:   31-Oct-93    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00918  (CAH2_HUMAN) -  Carbonic anhydrase 2
Seq:
Struc:
260 a.a.
258 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)
= 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     extracellular space   11 terms 
  Biological process     angiotensin-mediated signaling pathway   21 terms 
  Biochemical function     protein binding     5 terms  

 

 
    Added reference    
 
 
DOI no: 10.1107/S0907444993008790 Acta Crystallogr D Biol Crystallogr 50:93 (1994)
PubMed id: 15299481  
 
 
X-ray analysis of metal-substituted human carbonic anhydrase II derivatives.
K.Håkansson, A.Wehnert, A.Liljas.
 
  ABSTRACT  
 
Metal-substituted crystals of human carbonic anhydrase II belonging to space group P2(1) with cell dimensions a = 42.7, b = 41.7, c = 73.0 A and beta = 104.6 degrees were analyzed crystallographically. The resolution limit ranged from 1.82 to 1.92 A with high completeness (86.2-90.7%). Cobalt(II)-substituted carbonic anhydrase has a tetrahedral coordination around the metal both at pH 6 and pH 7.8, similar to the native zinc enzyme. In contrast, the catalytically inactive copper(II), nickel(II) and manganese(II) derivatives showed increased coordination number around the metal ion. Whereas the copper is best described as penta-coordinated, the nickel and manganese are best described as hexa-coordinated. The results are briefly compared with spectroscopic observations and our current view on carbonic anhydrase catalysis.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. The active-site structure of native human carbonic anhydrase II. The conformation of the peptide chain is the same in the native enzyme and all the metal-substituted derivatives described in this paper, but the solvent structure differs among the different substitutions. Waters 263 and 338 are sometimes referred to as the 'zinc water' and 'deep water', respectively. The structure was plotted using the coordinates of HD, ansson, Carlsson, Svensson & Liljas (1992).
Figure 3.
Fig. 3. The active site of cobalt(II)-substituted carbonic anhydrase at pit 6.0. Difference electron maps were calculated after refinement of native coordinates without waters 263, 338 and 339. Positive (continuous lines) and negative (broken lines) IFol - IFcI contours were drawn at +3e. The occupancy of the sulfate was refined to 0.6.
 
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (1994, 50, 93-0) copyright 1994.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19818877 T.K.Hurst, D.Wang, R.B.Thompson, and C.A.Fierke (2010).
Carbonic anhydrase II-based metal ion sensing: Advances and new perspectives.
  Biochim Biophys Acta, 1804, 393-403.  
15726624 M.Babor, H.M.Greenblatt, M.Edelman, and V.Sobolev (2005).
Flexibility of metal binding sites in proteins on a database scale.
  Proteins, 59, 221-230.  
  8535232 D.R.Holland, A.C.Hausrath, D.Juers, and B.W.Matthews (1995).
Structural analysis of zinc substitutions in the active site of thermolysin.
  Protein Sci, 4, 1955-1965.
PDB codes: 1lna 1lnb 1lnc 1lnd 1lne 1lnf
7796265 R.W.Strange, F.E.Dodd, Z.H.Abraham, J.G.Grossmann, T.Brüser, R.R.Eady, B.E.Smith, and S.S.Hasnain (1995).
The substrate-binding site in Cu nitrite reductase and its similarity to Zn carbonic anhydrase.
  Nat Struct Biol, 2, 287-292.  
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.