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PDBsum entry 1h9q

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protein metals links
Lyase PDB id
1h9q
Jmol
Contents
Protein chain
255 a.a. *
Metals
_ZN
Waters ×38
* Residue conservation analysis
PDB id:
1h9q
Name: Lyase
Title: H119q carbonic anhydrase ii
Structure: Carbonic anhydrase ii. Chain: a. Synonym: caii, carbonic dehydratase. Engineered: yes. Mutation: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Cell_line: bl21. Gene: caii. Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: this caii variant was produced using oligonucleotide-directed mutagenesis of the cloned human
Resolution:
2.20Å     R-factor:   0.182     R-free:   0.249
Authors: C.A.Lesburg,D.W.Christianson
Key ref:
C.A.Lesburg et al. (1997). Histidine --> carboxamide ligand substitutions in the zinc binding site of carbonic anhydrase II alter metal coordination geometry but retain catalytic activity. Biochemistry, 36, 15780-15791. PubMed id: 9398308 DOI: 10.1021/bi971296x
Date:
29-May-97     Release date:   17-Sep-97    
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: 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: 10.1021/bi971296x Biochemistry 36:15780-15791 (1997)
PubMed id: 9398308  
 
 
Histidine --> carboxamide ligand substitutions in the zinc binding site of carbonic anhydrase II alter metal coordination geometry but retain catalytic activity.
C.A.Lesburg, C.Huang, D.W.Christianson, C.A.Fierke.
 
  ABSTRACT  
 
The catalytic zinc ion of human carbonic anhydrase II (CAII) is coordinated by three histidine ligands (H94, H96, and H119) and a hydroxide ion with tetrahedral geometry. Structural and functional analysis of variants in which the zinc ligands H94 and H119 are substituted with asparagine and glutamine, and comparison with results obtained with aspartate and glutamate substitutions indicate that the neutral ligand field provided by the protein optimizes the electrostatic environment for the catalytic function of the metal ion, including stabilization of bound anions. This is demonstrated by catalytic activity measurements for ester hydrolysis and CO2 hydration, as well as sulfonamide inhibitor affinity assays. High-resolution X-ray crystal structure determinations of H94N, H119N, and H119Q CAIIs reveal that the engineered carboxamide side chains coordinate to zinc with optimal stereochemistry. However, zinc coordination geometry remains tetrahedral only in H119Q CAII. Metal geometry changes to trigonal bipyramidal in H119N CAII due to the addition of a second water molecule to the zinc coordination polyhedron and also in H94N CAII due to the displacement of zinc-bound hydroxide by the bidentate coordination of a Tris molecule. Possibly, the bulky histidine imidazole ligands of the native enzyme play a role in disfavoring trigonal bipyramidal coordination geometry for zinc. Protein-metal affinity is significantly compromised by all histidine --> carboxamide ligand substitutions. Diminished affinity may result from significant movements (up to 1 A) of the metal ion from its position in the wild-type enzyme, as well as the associated, minor conformational changes of metal ligands and their neighboring residues.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21212893 O.Amata, T.Marino, N.Russo, and M.Toscano (2011).
Catalytic activity of a ΞΆ-class zinc and cadmium containing carbonic anhydrase. Compared work mechanisms.
  Phys Chem Chem Phys, 13, 3468-3477.  
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.  
  19851004 K.H.Sippel, A.H.Robbins, J.Domsic, C.Genis, M.Agbandje-McKenna, and R.McKenna (2009).
High-resolution structure of human carbonic anhydrase II complexed with acetazolamide reveals insights into inhibitor drug design.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 65, 992-995.
PDB code: 3hs4
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.  
17665409 G.E.Höst, J.Razkin, L.Baltzer, and B.H.Jonsson (2007).
Combined enzyme and substrate design: grafting of a cooperative two-histidine catalytic motif into a protein targeted at the scissile bond in a designed ester substrate.
  Chembiochem, 8, 1570-1576.  
17594033 J.Banerjee, M.K.Haldar, S.Manokaran, S.Mallik, and D.K.Srivastava (2007).
New fluorescent probes for carbonic anhydrases.
  Chem Commun (Camb), (), 2723-2725.  
17473007 L.Zhang, J.Shen, M.T.Guarnieri, A.Heroux, K.Yang, and R.Zhao (2007).
Crystal structure of the C-terminal domain of splicing factor Prp8 carrying retinitis pigmentosa mutants.
  Protein Sci, 16, 1024-1031.
PDB codes: 2p87 2p8r
18020665 M.V.Inamdar, C.M.Lastoskie, C.A.Fierke, and A.M.Sastry (2007).
Mobile trap algorithm for zinc detection using protein sensors.
  J Chem Phys, 127, 185102.  
16416502 K.Okrasa, and R.J.Kazlauskas (2006).
Manganese-substituted carbonic anhydrase as a new peroxidase.
  Chemistry, 12, 1587-1596.  
16428608 P.Bellare, A.K.Kutach, A.K.Rines, C.Guthrie, and E.J.Sontheimer (2006).
Ubiquitin binding by a variant Jab1/MPN domain in the essential pre-mRNA splicing factor Prp8p.
  RNA, 12, 292-302.  
16538615 P.J.Lyons, N.R.Mattatall, and H.S.Ro (2006).
Modeling and functional analysis of AEBP1, a transcriptional repressor.
  Proteins, 63, 1069-1083.  
16737955 S.Soundar, M.O'hagan, K.S.Fomulu, and R.F.Colman (2006).
Identification of Mn2+-binding aspartates from alpha, beta, and gamma subunits of human NAD-dependent isocitrate dehydrogenase.
  J Biol Chem, 281, 21073-21081.  
15604675 G.Parisi, M.Perales, M.S.Fornasari, A.Colaneri, N.González-Schain, D.Gómez-Casati, S.Zimmermann, A.Brennicke, A.Araya, J.G.Ferry, J.Echave, and E.Zabaleta (2004).
Gamma carbonic anhydrases in plant mitochondria.
  Plant Mol Biol, 55, 193-207.  
15821992 M.Perales, G.Parisi, M.S.Fornasari, A.Colaneri, F.Villarreal, N.González-Schain, J.Echave, D.Gómez-Casati, H.P.Braun, A.Araya, and E.Zabaleta (2004).
Gamma carbonic anhydrase like complex interact with plant mitochondrial complex I.
  Plant Mol Biol, 56, 947-957.  
14567693 B.V.Alvarez, F.B.Loiselle, C.T.Supuran, G.J.Schwartz, and J.R.Casey (2003).
Direct extracellular interaction between carbonic anhydrase IV and the human NBC1 sodium/bicarbonate co-transporter.
  Biochemistry, 42, 12321-12329.  
12740384 S.T.Nevin, B.A.Cromer, J.L.Haddrill, C.J.Morton, M.W.Parker, and J.W.Lynch (2003).
Insights into the structural basis for zinc inhibition of the glycine receptor.
  J Biol Chem, 278, 28985-28992.  
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.  
11148046 J.E.Jackman, C.R.Raetz, and C.A.Fierke (2001).
Site-directed mutagenesis of the bacterial metalloamidase UDP-(3-O-acyl)-N-acetylglucosamine deacetylase (LpxC). Identification of the zinc binding site.
  Biochemistry, 40, 514-523.  
10821857 P.Karhumaa, S.Parkkila, A.Waheed, A.K.Parkkila, K.Kaunisto, P.W.Tucker, C.J.Huang, W.S.Sly, and H.Rajaniemi (2000).
Nuclear NonO/p54(nrb) protein is a nonclassical carbonic anhydrase.
  J Biol Chem, 275, 16044-16049.  
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.  
10353848 H.Teng, and C.Grubmeyer (1999).
Mutagenesis of histidinol dehydrogenase reveals roles for conserved histidine residues.
  Biochemistry, 38, 7363-7371.  
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.  
10347149 P.M.Cummins, A.Pabon, E.H.Margulies, and M.J.Glucksman (1999).
Zinc coordination and substrate catalysis within the neuropeptide processing enzyme endopeptidase EC 3.4.24.15. Identification of active site histidine and glutamate residues.
  J Biol Chem, 274, 16003-16009.  
9521766 H.W.Fu, L.S.Beese, and P.J.Casey (1998).
Kinetic analysis of zinc ligand mutants of mammalian protein farnesyltransferase.
  Biochemistry, 37, 4465-4472.  
9628737 S.L.Clugston, J.F.Barnard, R.Kinach, D.Miedema, R.Ruman, E.Daub, and J.F.Honek (1998).
Overproduction and characterization of a dimeric non-zinc glyoxalase I from Escherichia coli: evidence for optimal activation by nickel ions.
  Biochemistry, 37, 8754-8763.  
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.