EzCatDB: S00424
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DB codeS00424
RLCP classification4.15.898520.455 : Addition
CATH domainDomain 13.40.1050.10 : Beta-carbonic Anhydrase; Chain ACatalytic domain
E.C.4.2.1.1
CSA1i6p

CATH domainRelated DB codes (homologues)
3.40.1050.10 : Beta-carbonic Anhydrase; Chain AS00521,D00474

Enzyme Name
UniProtKBKEGG

P17067P61517
Protein nameCarbonic anhydrase, chloroplasticCarbonic anhydrase 2carbonate dehydratase
carbonic anhydrase
anhydrase
carbonate anhydrase
carbonic acid anhydrase
carboxyanhydrase
carbonic anhydrase A
carbonate hydro-lyase
SynonymsEC 4.2.1.1
Carbonate dehydratase
EC 4.2.1.1
Carbonate dehydratase 2
ContainsCarbonic anhydrase, 27 kDa isoform
Carbonic anhydrase, 25 kDa isoform
None
RefSeq
NP_414668.1 (Protein)
NC_000913.2 (DNA/RNA sequence)
YP_488429.1 (Protein)
NC_007779.1 (DNA/RNA sequence)
PfamPF00484 (Pro_CA)
[Graphical view]
PF00484 (Pro_CA)
[Graphical view]

KEGG pathways
MAP codePathways
MAP00910Nitrogen metabolism

UniProtKB:Accession NumberP17067P61517
Entry nameCAHC_PEACAN_ECOLI
ActivityH(2)CO(3) = CO(2) + H(2)O.H(2)CO(3) = CO(2) + H(2)O.
SubunitHomohexamer.Homodimer.
Subcellular locationPlastid, chloroplast stroma.
Cofactor
Binds 1 zinc ion per subunit.

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
            
1ekjABound:_ZNUnboundUnboundAnalogue:ACT
1ekjBBound:_ZNUnboundUnboundAnalogue:ACT
1ekjCBound:_ZNUnboundBound:HOH 1001Analogue:ACT
1ekjDBound:_ZNUnboundUnboundAnalogue:ACT
1ekjEBound:_ZNUnboundUnboundAnalogue:ACT
1ekjFBound:_ZNUnboundUnboundAnalogue:ACT
1ekjGBound:_ZNUnboundUnboundAnalogue:ACT
1ekjHBound:_ZNUnboundUnboundAnalogue:ACT
1t75ABound:_ZNUnbound Unbound
1t75BBound:_ZNUnbound Unbound
1t75DBound:_ZNUnbound Unbound
1t75EBound:_ZNUnbound Unbound
1i6oABound:_ZNUnboundUnboundUnbound
1i6oBBound:_ZNUnboundUnboundUnbound
1i6pABound:_ZNUnboundUnboundUnbound

Active-site residues
resource
literature [4]
pdbCatalytic residuesCofactor-binding residuescomment
           
1ekjAGLN 151;ASP 162;TYR 205
CYS 160;       ;HIS 220;CYS 223(Zinc binding)
D160 sligtly away from zinc
1ekjBGLN 151;ASP 162;TYR 205
CYS 160;       ;HIS 220;CYS 223(Zinc binding)
D160 sligtly away from zinc
1ekjCGLN 151;ASP 162;TYR 205
CYS 160;ASP 162;HIS 220;CYS 223(Zinc binding)
 
1ekjDGLN 151;ASP 162;TYR 205
CYS 160;ASP 162;HIS 220;CYS 223(Zinc binding)
 
1ekjEGLN 151;ASP 162;TYR 205
CYS 160;       ;HIS 220;CYS 223(Zinc binding)
D160 sligtly away from zinc
1ekjFGLN 151;ASP 162;TYR 205
CYS 160;       ;HIS 220;CYS 223(Zinc binding)
D160 sligtly away from zinc
1ekjGGLN 151;ASP 162;TYR 205
CYS 160;ASP 162;HIS 220;CYS 223(Zinc binding)
 
1ekjHGLN 151;ASP 162;TYR 205
CYS 160;       ;HIS 220;CYS 223(Zinc binding)
D160 sligtly away from zinc
1t75AGLN  33;ASP  44;TYR  83
CYS  42;ASP  44;HIS  98;CYS 101(Zinc binding)
 
1t75BGLN  33;ASP  44;TYR  83
CYS  42;ASP  44;HIS  98;CYS 101(Zinc binding)
 
1t75DGLN  33;ASP  44;TYR  83
CYS  42;ASP  44;HIS  98;CYS 101(Zinc binding)
 
1t75EGLN  33;ASP  44;TYR  83
CYS  42;ASP  44;HIS  98;CYS 101(Zinc binding)
 
1i6oAGLN  33;ASP  44;TYR  83
CYS  42;ASP  44;HIS  98;CYS 101(Zinc binding)
 
1i6oBGLN  33;ASP  44;TYR  83
CYS  42;ASP  44;HIS  98;CYS 101(Zinc binding)
 
1i6pAGLN  33;ASP  44;TYR  83
CYS  42;ASP  44;HIS  98;CYS 101(Zinc binding)
 

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
This enzyme belongs to the beta-carbonic anhydrase family.
The catalytic zinc ion is ligated by two conserved cysteine residues and a conserved histidine, together with a conserved aspartate residue (Asp162 of 1ekj). However, in some structures, the aspartate residue is displaced, suggesting that this residue function as a switch of catalytic reaction (see [8]).
According to the literature [4], [7], [8], [9] & [12], 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 general base or proton shuttle residue (which transfers a proton to the solvent), or solvent, to generate the hydroxide. This role is probably played by Tyr205' from the adjacent chain (of 1ekj). (Asp162 may act as a general base, which deprotonates 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 Gln151' from the adjacent chain (of 1ekj). The nucleophile, the hydroxide, is also stabilized by Asp162. This reaction leads to the formation of the product, bicarbonate anion.

createdupdated
2004-07-152009-02-26
Copyright: Nozomi Nagano, JST & CBRC-AIST
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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 - )
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