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PDBsum entry 1cvd

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protein metals links
Lyase(oxo-acid) PDB id
1cvd
Jmol
Contents
Protein chain
255 a.a. *
Metals
_ZN
Waters ×113
* Residue conservation analysis
PDB id:
1cvd
Name: Lyase(oxo-acid)
Title: Structural consequences of redesigning a protein-zinc binding site
Structure: Carbonic anhydrase ii. Chain: a. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606
Resolution:
2.20Å     R-factor:   0.184    
Authors: J.A.Ippolito,D.W.Christianson
Key ref:
J.A.Ippolito and D.W.Christianson (1994). Structural consequences of redesigning a protein-zinc binding site. Biochemistry, 33, 15241-15249. PubMed id: 7803386 DOI: 10.1021/bi00255a004
Date:
21-Jun-94     Release date:   20-Dec-94    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00918  (CAH2_HUMAN) -  Carbonic anhydrase 2
Seq:
Struc:
260 a.a.
255 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 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: 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   19 terms 
  Biochemical function     protein binding     5 terms  

 

 
    Added reference    
 
 
DOI no: 10.1021/bi00255a004 Biochemistry 33:15241-15249 (1994)
PubMed id: 7803386  
 
 
Structural consequences of redesigning a protein-zinc binding site.
J.A.Ippolito, D.W.Christianson.
 
  ABSTRACT  
 
In order to probe the structural importance of zinc ligands in the active site of human carbonic anhydrase II (CAII), we have determined the three-dimensional structures of H94C (in metal-bound form), H94C-BME (i.e., disulfide-linked with beta-mercaptoethanol), H94A, H96C, H119C, and H119D variants of CAII by X-ray crystallographic methods at resolutions of 2.2, 2.35, 2.25, 2.3, 2.2, and 2.25 A, respectively. Each variant crystallizes isomorphously with the wild-type enzyme, in which zinc is tetrahedrally coordinated by H94, H96, H119, and hydroxide ion. The structure of H94C CAII reveals the successful substitution of the naturally occurring histidine zinc ligand by a cysteine thiolate, and metal coordination by C94 is facilitated by the plastic structural response of the beta-sheet superstructure. Importantly, the resulting structure represents the catalytically active form of the enzyme reported previously [Alexander, R. S., Kiefer, L. L., Fierke, C. A., & Christianson, D. W. (1993) Biochemistry 32, 1510-1518]. Contrastingly, the structure of H96C CAII reveals that the engineered side chain does not coordinate to zinc; instead, zinc is tetrahedrally liganded by H94, H119, and two solvent molecules. Thus, the beta-sheet superstructure is not sufficiently plastic in this location to allow C96 to coordinate to the metal ion. Substitution of the thiolate or carboxylate group for wild-type histidine in H119C and H119D CAIIs reveals that tetrahedral metal coordination is maintained in each variant; however, since there is no plastic structural response of the corresponding beta-strand, a longer metal-ligand separation results.(ABSTRACT TRUNCATED AT 250 WORDS)
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
18648861 A.Tamilselvi, and G.Mugesh (2008).
Zinc and antibiotic resistance: metallo-beta-lactamases and their synthetic analogues.
  J Biol Inorg Chem, 13, 1039-1053.  
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.  
16932811 S.Schenk, J.Notni, U.Köhn, K.Wermann, and E.Anders (2006).
Carbon dioxide and related heterocumulenes at zinc and lithium cations: bioinspired reactions and principles.
  Dalton Trans, (), 4191-4206.  
12045104 A.Hudmon, and H.Schulman (2002).
Neuronal CA2+/calmodulin-dependent protein kinase II: the role of structure and autoregulation in cellular function.
  Annu Rev Biochem, 71, 473-510.  
10899934 I.Lengyel, S.Fieuw-Makaroff, A.L.Hall, A.T.Sim, J.A.Rostas, and P.R.Dunkley (2000).
Modulation of the phosphorylation and activity of calcium/calmodulin-dependent protein kinase II by zinc.
  J Neurochem, 75, 594-605.  
10872443 D.W.Christianson, and J.D.Cox (1999).
Catalysis by metal-activated hydroxide in zinc and manganese metalloenzymes.
  Annu Rev Biochem, 68, 33-57.  
9667939 J.E.Coleman (1998).
Zinc enzymes.
  Curr Opin Chem Biol, 2, 222-234.  
9252341 J.A.Hunt, and C.A.Fierke (1997).
Selection of carbonic anhydrase variants displayed on phage. Aromatic residues in zinc binding site enhance metal affinity and equilibration kinetics.
  J Biol Chem, 272, 20364-20372.  
9020770 J.Guo, and D.P.Giedroc (1997).
Zinc site redesign in T4 gene 32 protein: structure and stability of cobalt(II) complexes formed by wild-type and metal ligand substitution mutants.
  Biochemistry, 36, 730-742.  
9408951 L.M.Watkins, J.M.Kuo, M.Chen-Goodspeed, and F.M.Raushel (1997).
A combinatorial library for the binuclear metal center of bacterial phosphotriesterase.
  Proteins, 29, 553-561.  
9336012 S.Lindskog (1997).
Structure and mechanism of carbonic anhydrase.
  Pharmacol Ther, 74, 1.  
8639494 C.C.Huang,, C.A.Lesburg, L.L.Kiefer, C.A.Fierke, and D.W.Christianson (1996).
Reversal of the hydrogen bond to zinc ligand histidine-119 dramatically diminishes catalysis and enhances metal equilibration kinetics in carbonic anhydrase II.
  Biochemistry, 35, 3439-3446.
PDB codes: 1zsa 1zsb 1zsc
8626461 K.Thirstrup, C.E.Elling, S.A.Hjorth, and T.W.Schwartz (1996).
Construction of a high affinity zinc switch in the kappa-opioid receptor.
  J Biol Chem, 271, 7875-7878.  
8634241 L.S.Brinen, W.S.Willett, C.S.Craik, and R.J.Fletterick (1996).
X-ray structures of a designed binding site in trypsin show metal-dependent geometry.
  Biochemistry, 35, 5999-6009.
PDB codes: 1slu 1slv 1slw 1slx
7579651 D.Barrick (1995).
Depletion and replacement of protein metal ligands.
  Curr Opin Biotechnol, 6, 411-418.  
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.