PDBsum entry 1hva

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protein links
Lyase(oxo-acid) PDB id
Protein chain
255 a.a. *
Waters ×38
* Residue conservation analysis
PDB id:
Name: Lyase(oxo-acid)
Title: Engineering the zinc binding site of human carbonic anhydrase ii: structure of the his-94-> cys apoenzyme in a new crystalline form
Structure: Carbonic anhydrase ii. Chain: a. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606
2.30Å     R-factor:   0.155    
Authors: R.S.Alexander,D.W.Christianson
Key ref:
R.S.Alexander et al. (1993). Engineering the zinc binding site of human carbonic anhydrase II: structure of the His-94-->Cys apoenzyme in a new crystalline form. Biochemistry, 32, 1510-1518. PubMed id: 8431430 DOI: 10.1021/bi00057a015
27-Oct-92     Release date:   31-Oct-93    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P00918  (CAH2_HUMAN) -  Carbonic anhydrase 2
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.  - Carbonate dehydratase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: H2CO3 = CO2 + H2O
= 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/bi00057a015 Biochemistry 32:1510-1518 (1993)
PubMed id: 8431430  
Engineering the zinc binding site of human carbonic anhydrase II: structure of the His-94-->Cys apoenzyme in a new crystalline form.
R.S.Alexander, L.L.Kiefer, C.A.Fierke, D.W.Christianson.
The structure of the His-94-->Cys variant of human carbonic anhydrase II (CAII) has been determined by X-ray crystallographic methods to a resolution of 2.3 A with a final crystallographic R factor of 0.155. This variant of CAII crystallizes in orthorhombic space group P2(1)2(1)2(1) which is the first example of a new crystal form for this important zinc hydrase (the wild-type enzyme crystallizes in monoclinic space group P21 under similar crystallization conditions). Although the overall structure of the enzyme in the orthorhombic crystal form is similar to that of the wild-type protein in the monoclinic crystal form, the rms deviation of C alpha atoms between the two structures is 0.5 A. Larger structural deviations occur in regions of the protein molecule involved in crystal lattice contacts, and significant structural changes are found in the polypeptide strand containing Cys-94. Surprisingly, no electron density corresponding to a zinc ion is found in the active site of crystalline His-94-->Cys CAII, even though the stoichiometry of zinc binding to this variant in solution is confirmed by atomic absorption spectroscopy. However, the KD for zinc dissociation from the variant is increased 10(4)-fold compared with wild-type enzyme; furthermore, under the crystallization conditions of high ionic strength (1.75-2.5 M ammonium sulfate), the observed KD is increased further, which leads to zinc dissociation. Spectroscopic analysis of Co(2+)-substituted His-94-->Cys CAII indicates that the metal binds in a tetrahedral geometry with a new thiolate bond.(ABSTRACT TRUNCATED AT 250 WORDS)

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.  
18461940 J.A.Aaron, J.M.Chambers, K.M.Jude, L.Di Costanzo, I.J.Dmochowski, and D.W.Christianson (2008).
Structure of a 129Xe-cryptophane biosensor complexed with human carbonic anhydrase II.
  J Am Chem Soc, 130, 6942-6943.
PDB code: 3cyu
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.  
15747135 W.Kou, H.S.Kolla, A.Ortiz-Acevedo, D.C.Haines, M.Junker, and G.R.Dieckmann (2005).
Modulation of zinc- and cobalt-binding affinities through changes in the stability of the zinc ribbon protein L36.
  J Biol Inorg Chem, 10, 167-180.  
12218024 N.Shapir, J.P.Osborne, G.Johnson, M.J.Sadowsky, and L.P.Wackett (2002).
Purification, substrate range, and metal center of AtzC: the N-isopropylammelide aminohydrolase involved in bacterial atrazine metabolism.
  J Bacteriol, 184, 5376-5384.  
11330997 C.A.DiTusa, K.A.McCall, T.Christensen, M.Mahapatro, C.A.Fierke, and E.J.Toone (2001).
Thermodynamics of metal ion binding. 2. Metal ion binding by carbonic anhydrase variants.
  Biochemistry, 40, 5345-5351.  
11330996 C.A.DiTusa, T.Christensen, K.A.McCall, C.A.Fierke, and E.J.Toone (2001).
Thermodynamics of metal ion binding. 1. Metal ion binding by wild-type carbonic anhydrase.
  Biochemistry, 40, 5338-5344.  
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.  
10413479 J.A.Hunt, M.Ahmed, and C.A.Fierke (1999).
Metal binding specificity in carbonic anhydrase is influenced by conserved hydrophobic core residues.
  Biochemistry, 38, 9054-9062.  
10354450 J.Gao, Q.Wu, J.Carbeck, Q.P.Lei, R.D.Smith, and G.M.Whitesides (1999).
Probing the energetics of dissociation of carbonic anhydrase-ligand complexes in the gas phase.
  Biophys J, 76, 3253-3260.  
  9865962 M.Cai, Y.Huang, M.Caffrey, R.Zheng, R.Craigie, G.M.Clore, and A.M.Gronenborn (1998).
Solution structure of the His12 --> Cys mutant of the N-terminal zinc binding domain of HIV-1 integrase complexed to cadmium.
  Protein Sci, 7, 2669-2674.
PDB codes: 1wje 1wjf
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
8987974 L.R.Scolnick, and D.W.Christianson (1996).
X-ray crystallographic studies of alanine-65 variants of carbonic anhydrase II reveal the structural basis of compromised proton transfer in catalysis.
  Biochemistry, 35, 16429-16434.
PDB codes: 1uga 1ugb 1ugc 1ugd 1uge 1ugf 1ugg
8810919 M.W.Crowder, Z.Wang, S.L.Franklin, E.P.Zovinka, and S.J.Benkovic (1996).
Characterization of the metal-binding sites of the beta-lactamase from Bacteroides fragilis.
  Biochemistry, 35, 12126-12132.  
7761440 J.A.Ippolito, T.T.Baird, S.A.McGee, D.W.Christianson, and C.A.Fierke (1995).
Structure-assisted redesign of a protein-zinc-binding site with femtomolar affinity.
  Proc Natl Acad Sci U S A, 92, 5017-5021.
PDB codes: 1ccs 1cct 1ccu
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.