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PDBsum entry 1j9w

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protein ligands metals links
Lyase PDB id
1j9w
Jmol
Contents
Protein chains
257 a.a. *
Ligands
EDO ×2
Metals
_ZN ×2
Waters ×321
* Residue conservation analysis
PDB id:
1j9w
Name: Lyase
Title: Solution structure of the cai michigan 1 variant
Structure: Carbonic anhydrase i. Chain: a, b. Synonym: carbonate dehydratase i. Engineered: yes. Mutation: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.60Å     R-factor:   0.205     R-free:   0.311
Authors: F.Briganti,M Ferraroni,W.R.Chedwiggen,A.Scozzafava,C.T.Supur S.Tilli
Key ref:
M.Ferraroni et al. (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. PubMed id: 12009884 DOI: 10.1021/bi0120446
Date:
29-May-01     Release date:   13-Jun-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P00915  (CAH1_HUMAN) -  Carbonic anhydrase 1
Seq:
Struc:
261 a.a.
257 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)
Bound ligand (Het Group name = EDO)
matches with 40.00% similarity
+ 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    
 
 
DOI no: 10.1021/bi0120446 Biochemistry 41:6237-6244 (2002)
PubMed id: 12009884  
 
 
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.
M.Ferraroni, S.Tilli, F.Briganti, W.R.Chegwidden, C.T.Supuran, K.E.Wiebauer, R.E.Tashian, A.Scozzafava.
 
  ABSTRACT  
 
The human genetic variant carbonic anhydrase I (CA I) Michigan 1 results from a single point mutation that changes His 67 to Arg in a critical region of the active site. This variant of the zinc metalloenzyme appears to be unique in that it possesses an esterase activity that is specifically enhanced by added free zinc ions. We have determined the three-dimensional structure of human CA I Michigan 1 by X-ray crystallography to a resolution of 2.6 A. In the absence of added zinc ions, the mutated residue, Arg 67, points out of the active site, hydrogen bonding with the carboxylate of Asn 69. This contrasts with the orientation of His 67, in the native isozyme, which points into the active site. The orientations of His 94, His 96, and His 119, that coordinate the catalytic zinc ion, and of the catalytically critical Thr 199-Glu 106 hydrogen bonding system, are largely unchanged in the mutant. The structure of an enzyme adduct with a second zinc bound was determined to a resolution of 2.0 A. The second zinc ion is coordinated to His 64, His 200, and Arg 67. This arginine residue reverses its orientation on zinc binding and turns into the active site. The residues at these three positions have been implicated in determining the specific kinetic properties of native CA I. This is, to our knowledge, the first example of a zinc ion coordinating with an arginine residue in a Zn(II) enzyme.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
19768473 M.G.Fuchs, F.Meyer, and U.Ryde (2010).
A combined computational and experimental investigation of the [2Fe-2S] cluster in biotin synthase.
  J Biol Inorg Chem, 15, 203-212.  
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.  
  18443360 Z.Ma, K.Y.Wong, and F.T.Horrigan (2008).
An extracellular Cu2+ binding site in the voltage sensor of BK and Shaker potassium channels.
  J Gen Physiol, 131, 483-502.  
16981206 L.Di Costanzo, L.V.Flores, and D.W.Christianson (2006).
Stereochemistry of guanidine-metal interactions: implications for L-arginine-metal interactions in protein structure and function.
  Proteins, 65, 637-642.  
15613631 L.Giachini, F.Francia, A.Mallardi, G.Palazzo, E.Carpenè, F.Boscherini, and G.Venturoli (2005).
Multiple scattering x-ray absorption studies of Zn2+ binding sites in bacterial photosynthetic reaction centers.
  Biophys J, 88, 2038-2046.  
14600151 J.Lehtonen, B.Shen, M.Vihinen, A.Casini, A.Scozzafava, C.T.Supuran, A.K.Parkkila, J.Saarnio, A.J.Kivelä, A.Waheed, W.S.Sly, and S.Parkkila (2004).
Characterization of CA XIII, a novel member of the carbonic anhydrase isozyme family.
  J Biol Chem, 279, 2719-2727.  
15220411 J.N.Bragg, D.M.Lawrence, and A.O.Jackson (2004).
The N-terminal 85 amino acids of the barley stripe mosaic virus gammab pathogenesis protein contain three zinc-binding motifs.
  J Virol, 78, 7379-7391.  
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.  
12500287 C.T.Supuran, A.Scozzafava, and A.Casini (2003).
Carbonic anhydrase inhibitors.
  Med Res Rev, 23, 146-189.  
12644179 R.E.Tashian, and J.Neel (2003).
A colleague's personal account of J.V. Neel's early incorporation of isozymes and isoforms into his research on the causes and consequences of mutations.
  Mutat Res, 543, 105-113.  
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.