EzCatDB: S00521
Related links:    PDB-formatted query search system Fasta-formatted query search system Fasta-formatted query search system

DB codeS00521
RLCP classification4.15.898500.454 : Addition
CATH domainDomain 13.40.1050.10 : Beta-carbonic Anhydrase; Chain ACatalytic domain
E.C.4.2.1.1

CATH domainRelated DB codes (homologues)
3.40.1050.10 : Beta-carbonic Anhydrase; Chain AS00424,D00474

Enzyme Name
UniProtKBKEGG

Q50565
Protein name
carbonate dehydratase
carbonic anhydrase
anhydrase
carbonate anhydrase
carbonic acid anhydrase
carboxyanhydrase
carbonic anhydrase A
carbonate hydro-lyase
SynonymsCarbonic anhydrase
RefSeqNP_276694.1 (Protein)
NC_000916.1 (DNA/RNA sequence)
PfamPF00484 (Pro_CA)
[Graphical view]

KEGG pathways
MAP codePathways
MAP00910Nitrogen metabolism

UniProtKB:Accession NumberQ50565
Entry nameQ50565_METTH
Activity
Subunit
Subcellular location
Cofactor

Compound table: links to PDB-related databases & PoSSuM

CofactorsSubstratesProducts
KEGG-idC00038C00011C00001C01353
CompoundZincCO2H2OCarbonic acid
Typeheavy metalothersH2Ocarboxyl group
ChEBI29105
16526
15377
28976
PubChem32051
280
962
22247451
767
3614646
22639876
            
1g5cABound:_ZNUnboundBound:HOH 1Unbound
1g5cBBound:_ZNUnboundBound:HOH 2Unbound
1g5cCBound:_ZNUnboundBound:HOH 3Unbound
1g5cDBound:_ZNUnboundBound:HOH 4Unbound
1g5cEBound:_ZNUnboundBound:HOH 6Unbound
1g5cFBound:_ZNUnboundBound:HOH 5Unbound

Active-site residues
resource
literature [4]
pdbCatalytic residuesCofactor-binding residuesMain-chain involved in catalysiscomment
            
1g5cAASP  34
CYS  32;       ;HIS  87;CYS  90(Zinc binding)
GLY 91
D34 sligtly away from zinc
1g5cBASP  34
CYS  32;       ;HIS  87;CYS  90(Zinc binding)
GLY 91
D34 sligtly away from zinc
1g5cCASP  34
CYS  32;ASP  34;HIS  87;CYS  90(Zinc binding)
GLY 91
 
1g5cDASP  34
CYS  32;       ;HIS  87;CYS  90(Zinc binding)
GLY 91
D34 sligtly away from zinc
1g5cEASP  34
CYS  32;       ;HIS  87;CYS  90(Zinc binding)
GLY 91
D34 sligtly away from zinc
1g5cFASP  34
CYS  32;       ;HIS  87;CYS  90(Zinc binding)
GLY 91
D34 sligtly away from zinc

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[4]Fig.4, p.1414-14154
[5]FIG.4, p.55264
[6]p.10305
[7]p.48615, p.48617
[8]p.919-920
[9]Fig.7, p.2085
[10]

[11]


references
[1]
PubMed ID7925414
JournalEur J Biochem
Year1994
Volume224
Pages901-7
AuthorsJohansson IM, Forsman C
TitleSolvent hydrogen isotope effects and anion inhibition of CO2 hydration catalysed by carbonic anhydrase from Pisum sativum.
[2]
PubMed ID9100024
JournalBiochemistry
Year1997
Volume36
Pages4287-94
AuthorsBjorkbacka H, Johansson IM, Skarfstad E, Forsman C
TitleThe sulfhydryl groups of Cys 269 and Cys 272 are critical for the oligomeric state of chloroplast carbonic anhydrase from Pisum sativum.
[3]
PubMed ID9336012
JournalPharmacol Ther
Year1997
Volume74
Pages1-20
AuthorsLindskog S
TitleStructure and mechanism of carbonic anhydrase.
[4]
CommentsX-RAY CRYSTALLOGRAPHY (1.93 ANGSTROMS) OF 108-328.
Medline ID20211383
PubMed ID10747009
JournalEMBO J
Year2000
Volume19
Pages1407-18
AuthorsKimber MS, Pai EF
TitleThe active site architecture of Pisum sativum beta-carbonic anhydrase is a mirror image of that of alpha-carbonic anhydrases.
Related PDB1ekj
Related UniProtKBP17067
[5]
CommentsX-ray crystallography
PubMed ID10681531
JournalJ Biol Chem
Year2000
Volume275
Pages5521-6
AuthorsMitsuhashi S, Mizushima T, Yamashita E, Yamamoto M, Kumasaka T, Moriyama H, Ueki T, Miyachi S, Tsukihara T
TitleX-ray structure of beta-carbonic anhydrase from the red alga, Porphyridium purpureum, reveals a novel catalytic site for CO(2) hydration.
Related PDB1ddz
[6]
CommentsX-ray crystallography
PubMed ID11096105
JournalJ Biol Chem
Year2001
Volume276
Pages10299-305
AuthorsStrop P, Smith KS, Iverson TM, Ferry JG, Rees DC
TitleCrystal structure of the "cab"-type beta class carbonic anhydrase from the archaeon Methanobacterium thermoautotrophicum.
Related PDB1g5c
[7]
PubMed ID11696553
JournalJ Biol Chem
Year2001
Volume276
Pages48615-8
AuthorsTripp BC, Smith K, Ferry JG
TitleCarbonic anhydrase: new insights for an ancient enzyme.
[8]
PubMed ID11316870
JournalProtein Sci
Year2001
Volume10
Pages911-22
AuthorsCronk JD, Endrizzi JA, Cronk MR, O'neill JW, Zhang KY
TitleCrystal structure of E. coli beta-carbonic anhydrase, an enzyme with an unusual pH-dependent activity.
Related PDB1i6o,1i6p
[9]
PubMed ID12147257
JournalArch Biochem Biophys
Year2002
Volume404
Pages197-209
AuthorsRowlett RS, Tu C, McKay MM, Preiss JR, Loomis RJ, Hicks KA, Marchione RJ, Strong JA, Donovan GS Jr, Chamberlin JE
TitleKinetic characterization of wild-type and proton transfer-impaired variants of beta-carbonic anhydrase from Arabidopsis thaliana.
[10]
PubMed ID12484784
JournalBiochemistry
Year2002
Volume41
Pages15429-35
AuthorsTu C, Rowlett RS, Tripp BC, Ferry JG, Silverman DN
TitleChemical rescue of proton transfer in catalysis by carbonic anhydrases in the beta- and gamma-class.
[11]
PubMed ID12107142
JournalJ Bacteriol
Year2002
Volume184
Pages4240-5
AuthorsSmith KS, Ingram-Smith C, Ferry JG
TitleRoles of the conserved aspartate and arginine in the catalytic mechanism of an archaeal beta-class carbonic anhydrase.
[12]
PubMed ID15081890
JournalArch Biochem Biophys
Year2004
Volume425
Pages25-32
AuthorsRowlett RS, Tu C, Murray PS, Chamberlin JE
TitleExamination of the role of Gln-158 in the mechanism of CO(2) hydration catalyzed by beta-carbonic anhydrase from Arabidopsis thaliana.

comments
Although this enzyme belongs to the beta-carbonic anhydrase family, it seems to have a slightly different mechanism from that of other beta-carbonic anhydrase enzymes (see [6], [7]).
The catalytic zinc ion is ligated by two conserved cysteine residues and a conserved histidine, together with a conserved aspartate residue (Asp34).
According to the literature [6] & [7], the catalytic reaction proceeds as follows:
(1) A water molecule is bound to the cofactor zinc.
(2) A proton of the substrate water is abstracted by a solvent water, to generate the hydroxide. Asp34 may act as a general base or a proton shuttle, which transfer a proton from the water bound to the cofactor zinc ion.
(3) The hydroxide bound to zinc makes a nucleophilic attack on the carbon atom of another substrate, carbon dioxide (CO2), which is stabilized by Gly91. The nucleophile, the hydroxide, is also stabilized by Asp34. This reaction leads to the formation of the product, bicarbonate anion.

createdupdated
2004-07-152009-02-26


Copyright: Nozomi Nagano, JST & CBRC-AIST
Funded by PRESTO/Japan Science and Technology Corporation (JST) (December 2001 - November 2004)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2006)
Funded by Grant-in-Aid for Scientific Research (B)/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (September 2005 - September 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (October 2007 - September 2010)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2011 - March 2012)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2012 - March 2013)
Supported by the commission for the Development of Artificial Gene Synthesis Technology for Creating Innovative Biomaterial from the Ministry of Economy, Trade and Industry (METI) (October 2012 - )
© Biotechnology Research Institute for Drug Discovery, AIST, 2015-2016 All Rights Reserved.
© Computational Biology Research Center, AIST, 2004-2016 All Rights Reserved.