S00424
type: Enzyme
rlcp: p455
cath: Beta-carbonic Anhydrase; Chain A
ec: https://purl.uniprot.org/enzyme/4.2.1.1
csa: 1i6p
uniprot: P17067
uniprot: P61517
kegg enzyme: carbonate dehydratase
kegg enzyme: carbonic anhydrase
kegg enzyme: anhydrase
kegg enzyme: carbonate anhydrase
kegg enzyme: carbonic acid anhydrase
kegg enzyme: carboxyanhydrase
kegg enzyme: carbonic anhydrase A
kegg enzyme: carbonate hydro-lyase
kegg pathway: Nitrogen metabolism
kegg cofactor: Zinc
kegg substrate: H2O
kegg substrate: CO2
kegg product: Carbonic acid
pdb: 1ekjA
pdb: 1ekjB
pdb: 1ekjC
pdb: 1ekjD
pdb: 1ekjE
pdb: 1ekjF
pdb: 1ekjG
pdb: 1ekjH
pdb: 1t75A
pdb: 1t75B
pdb: 1t75D
pdb: 1t75E
pdb: 1i6oA
pdb: 1i6oB
pdb: 1i6pA
pdb bound state: Unbound
  compound: CO2
  pdb: 1ekjA
pdb bound state: Unbound
  compound: CO2
  pdb: 1ekjB
pdb bound state: Unbound
  compound: CO2
  pdb: 1ekjC
pdb bound state: Unbound
  compound: CO2
  pdb: 1ekjD
pdb bound state: Unbound
  compound: CO2
  pdb: 1ekjE
pdb bound state: Unbound
  compound: CO2
  pdb: 1ekjF
pdb bound state: Unbound
  compound: CO2
  pdb: 1ekjG
pdb bound state: Unbound
  compound: CO2
  pdb: 1ekjH
pdb bound state: Unbound
  compound: CO2
  pdb: 1t75A
pdb bound state: Unbound
  compound: CO2
  pdb: 1t75B
pdb bound state: Unbound
  compound: CO2
  pdb: 1t75D
pdb bound state: Unbound
  compound: CO2
  pdb: 1t75E
pdb bound state: Unbound
  compound: CO2
  pdb: 1i6oA
pdb bound state: Unbound
  compound: CO2
  pdb: 1i6oB
pdb bound state: Unbound
  compound: CO2
  pdb: 1i6pA
pdb bound state: Unbound
  compound: H2O
  pdb: 1ekjA
pdb bound state: Unbound
  compound: H2O
  pdb: 1ekjB
pdb bound state: Unbound
  compound: H2O
  pdb: 1ekjD
pdb bound state: Unbound
  compound: H2O
  pdb: 1ekjE
pdb bound state: Unbound
  compound: H2O
  pdb: 1ekjF
pdb bound state: Unbound
  compound: H2O
  pdb: 1ekjG
pdb bound state: Unbound
  compound: H2O
  pdb: 1ekjH
pdb bound state: Unbound
  compound: H2O
  pdb: 1i6oA
pdb bound state: Unbound
  compound: H2O
  pdb: 1i6oB
pdb bound state: Unbound
  compound: H2O
  pdb: 1i6pA
pdb bound state: Analogue
  compound: Carbonic acid
  pdb: 1ekjA
  ligand het code: ACT
pdb bound state: Analogue
  compound: Carbonic acid
  pdb: 1ekjB
  ligand het code: ACT
pdb bound state: Analogue
  compound: Carbonic acid
  pdb: 1ekjC
  ligand het code: ACT
pdb bound state: Analogue
  compound: Carbonic acid
  pdb: 1ekjD
  ligand het code: ACT
pdb bound state: Analogue
  compound: Carbonic acid
  pdb: 1ekjE
  ligand het code: ACT
pdb bound state: Analogue
  compound: Carbonic acid
  pdb: 1ekjF
  ligand het code: ACT
active site residues resources: X-ray structure of beta-carbonic anhydrase from the red alga, Porphyridium purpureum, reveals a novel catalytic site for CO(2) hydration.
references: Solvent hydrogen isotope effects and anion inhibition of CO2 hydration catalysed by carbonic anhydrase from Pisum sativum.
references: The sulfhydryl groups of Cys 269 and Cys 272 are critical for the oligomeric state of chloroplast carbonic anhydrase from Pisum sativum.
references: Structure and mechanism of carbonic anhydrase.
references: The active site architecture of Pisum sativum beta-carbonic anhydrase is a mirror image of that of alpha-carbonic anhydrases.
references: X-ray structure of beta-carbonic anhydrase from the red alga, Porphyridium purpureum, reveals a novel catalytic site for CO(2) hydration.
references: Crystal structure of the "cab"-type beta class carbonic anhydrase from the archaeon Methanobacterium thermoautotrophicum.
references: Carbonic anhydrase: new insights for an ancient enzyme.
references: Crystal structure of E. coli beta-carbonic anhydrase, an enzyme with an unusual pH-dependent activity.
references: Kinetic characterization of wild-type and proton transfer-impaired variants of beta-carbonic anhydrase from Arabidopsis thaliana.
references: Chemical rescue of proton transfer in catalysis by carbonic anhydrases in the beta- and gamma-class.
references: Roles of the conserved aspartate and arginine in the catalytic mechanism of an archaeal beta-class carbonic anhydrase.
references: Examination of the role of Gln-158 in the mechanism of CO(2) hydration catalyzed by beta-carbonic anhydrase from Arabidopsis thaliana.
comment: 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.

Beta-carbonic Anhydrase; Chain A
type: Cath
references: http://www.cathdb.info/version/latest/superfamily/3.40.1050.10
catalytic domain: index.html

Nitrogen metabolism
type: KeggPathway
references: KEGG:MAP00910

Zinc
type: KeggCofactor
references: KEGG:C00038
compound type: heavy metal
references: CHEBI:29105
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi

H2O
type: KeggSubstrate
references: KEGG:C00001
compound type: H2O
references: CHEBI:15377
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi

CO2
type: KeggSubstrate
references: KEGG:C00011
compound type: others
references: CHEBI:16526
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi

Carbonic acid
type: KeggProduct
references: KEGG:C01353
compound type: carboxyl group
references: CHEBI:28976
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi

1ekjA
type: Pdb
references: 1ekj
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1ekj
catalytic residue: GLN 151;ASP 162;TYR 205
cofactor binding residue: CYS 160; ;HIS 220;CYS 223(Zinc binding)
comment: D160 sligtly away from zinc

1ekjB
type: Pdb
references: 1ekj
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1ekj
catalytic residue: GLN 151;ASP 162;TYR 205
cofactor binding residue: CYS 160; ;HIS 220;CYS 223(Zinc binding)
comment: D160 sligtly away from zinc

1ekjC
type: Pdb
references: 1ekj
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1ekj
catalytic residue: GLN 151;ASP 162;TYR 205
cofactor binding residue: CYS 160;ASP 162;HIS 220;CYS 223(Zinc binding)

1ekjD
type: Pdb
references: 1ekj
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1ekj
catalytic residue: GLN 151;ASP 162;TYR 205
cofactor binding residue: CYS 160;ASP 162;HIS 220;CYS 223(Zinc binding)

1ekjE
type: Pdb
references: 1ekj
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1ekj
catalytic residue: GLN 151;ASP 162;TYR 205
cofactor binding residue: CYS 160; ;HIS 220;CYS 223(Zinc binding)
comment: D160 sligtly away from zinc

1ekjF
type: Pdb
references: 1ekj
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1ekj
catalytic residue: GLN 151;ASP 162;TYR 205
cofactor binding residue: CYS 160; ;HIS 220;CYS 223(Zinc binding)
comment: D160 sligtly away from zinc

1ekjG
type: Pdb
references: 1ekj
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1ekj
catalytic residue: GLN 151;ASP 162;TYR 205
cofactor binding residue: CYS 160;ASP 162;HIS 220;CYS 223(Zinc binding)

1ekjH
type: Pdb
references: 1ekj
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1ekj
catalytic residue: GLN 151;ASP 162;TYR 205
cofactor binding residue: CYS 160; ;HIS 220;CYS 223(Zinc binding)
comment: D160 sligtly away from zinc

1t75A
type: Pdb
references: 1t75
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1t75
catalytic residue: GLN 33;ASP 44;TYR 83
cofactor binding residue: CYS 42;ASP 44;HIS 98;CYS 101(Zinc binding)

1t75B
type: Pdb
references: 1t75
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1t75
catalytic residue: GLN 33;ASP 44;TYR 83
cofactor binding residue: CYS 42;ASP 44;HIS 98;CYS 101(Zinc binding)

1t75D
type: Pdb
references: 1t75
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1t75
catalytic residue: GLN 33;ASP 44;TYR 83
cofactor binding residue: CYS 42;ASP 44;HIS 98;CYS 101(Zinc binding)

1t75E
type: Pdb
references: 1t75
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1t75
catalytic residue: GLN 33;ASP 44;TYR 83
cofactor binding residue: CYS 42;ASP 44;HIS 98;CYS 101(Zinc binding)

1i6oA
type: Pdb
references: 1i6o
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1i6o
catalytic residue: GLN 33;ASP 44;TYR 83
cofactor binding residue: CYS 42;ASP 44;HIS 98;CYS 101(Zinc binding)

1i6oB
type: Pdb
references: 1i6o
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1i6o
catalytic residue: GLN 33;ASP 44;TYR 83
cofactor binding residue: CYS 42;ASP 44;HIS 98;CYS 101(Zinc binding)

1i6pA
type: Pdb
references: 1i6p
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1i6p
catalytic residue: GLN 33;ASP 44;TYR 83
cofactor binding residue: CYS 42;ASP 44;HIS 98;CYS 101(Zinc binding)

Solvent hydrogen isotope effects and anion inhibition of CO2 hydration catalysed by carbonic anhydrase from Pisum sativum.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/7925414
journal: Eur J Biochem
volume: 224
pages: 901-7
published year: 1994
authors:
  item: Johansson IM
  item: Forsman C

The sulfhydryl groups of Cys 269 and Cys 272 are critical for the oligomeric state of chloroplast carbonic anhydrase from Pisum sativum.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/9100024
journal: Biochemistry
volume: 36
pages: 4287-94
published year: 1997
authors:
  item: Bjorkbacka H
  item: Johansson IM
  item: Skarfstad E
  item: Forsman C

Structure and mechanism of carbonic anhydrase.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/9336012
journal: Pharmacol Ther
volume: 74
pages: 1-20
published year: 1997
authors:
  item: Lindskog S

The active site architecture of Pisum sativum beta-carbonic anhydrase is a mirror image of that of alpha-carbonic anhydrases.
type: BibliographicResource
comment: X-RAY CRYSTALLOGRAPHY (1.93 ANGSTROMS) OF 108-328.
medline id: 20211383
references: http://www.ncbi.nlm.nih.gov/pubmed/10747009
journal: EMBO J
volume: 19
pages: 1407-18
published year: 2000
authors:
  item: Kimber MS
  item: Pai EF
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: P17067

X-ray structure of beta-carbonic anhydrase from the red alga, Porphyridium purpureum, reveals a novel catalytic site for CO(2) hydration.
type: BibliographicResource
comment: X-ray crystallography
references: http://www.ncbi.nlm.nih.gov/pubmed/10681531
journal: J Biol Chem
volume: 275
pages: 5521-6
published year: 2000
authors:
  item: Mitsuhashi S
  item: Mizushima T
  item: Yamashita E
  item: Yamamoto M
  item: Kumasaka T
  item: Moriyama H
  item: Ueki T
  item: Miyachi S
  item: Tsukihara T
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl

Crystal structure of the "cab"-type beta class carbonic anhydrase from the archaeon Methanobacterium thermoautotrophicum.
type: BibliographicResource
comment: X-ray crystallography
references: http://www.ncbi.nlm.nih.gov/pubmed/11096105
journal: J Biol Chem
volume: 276
pages: 10299-305
published year: 2001
authors:
  item: Strop P
  item: Smith KS
  item: Iverson TM
  item: Ferry JG
  item: Rees DC
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl

Carbonic anhydrase: new insights for an ancient enzyme.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/11696553
journal: J Biol Chem
volume: 276
pages: 48615-8
published year: 2001
authors:
  item: Tripp BC
  item: Smith K
  item: Ferry JG

Crystal structure of E. coli beta-carbonic anhydrase, an enzyme with an unusual pH-dependent activity.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/11316870
journal: Protein Sci
volume: 10
pages: 911-22
published year: 2001
authors:
  item: Cronk JD
  item: Endrizzi JA
  item: Cronk MR
  item: O'neill JW
  item: Zhang KY
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl

Kinetic characterization of wild-type and proton transfer-impaired variants of beta-carbonic anhydrase from Arabidopsis thaliana.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/12147257
journal: Arch Biochem Biophys
volume: 404
pages: 197-209
published year: 2002
authors:
  item: Rowlett RS
  item: Tu C
  item: McKay MM
  item: Preiss JR
  item: Loomis RJ
  item: Hicks KA
  item: Marchione RJ
  item: Strong JA
  item: Donovan GS Jr
  item: Chamberlin JE

Chemical rescue of proton transfer in catalysis by carbonic anhydrases in the beta- and gamma-class.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/12484784
journal: Biochemistry
volume: 41
pages: 15429-35
published year: 2002
authors:
  item: Tu C
  item: Rowlett RS
  item: Tripp BC
  item: Ferry JG
  item: Silverman DN

Roles of the conserved aspartate and arginine in the catalytic mechanism of an archaeal beta-class carbonic anhydrase.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/12107142
journal: J Bacteriol
volume: 184
pages: 4240-5
published year: 2002
authors:
  item: Smith KS
  item: Ingram-Smith C
  item: Ferry JG

Examination of the role of Gln-158 in the mechanism of CO(2) hydration catalyzed by beta-carbonic anhydrase from Arabidopsis thaliana.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/15081890
journal: Arch Biochem Biophys
volume: 425
pages: 25-32
published year: 2004
authors:
  item: Rowlett RS
  item: Tu C
  item: Murray PS
  item: Chamberlin JE

Analogue
compound: Carbonic acid
pdb: 1ekjG
ligand het code: ACT

Analogue
compound: Carbonic acid
pdb: 1ekjH
ligand het code: ACT

ReferenceForCatalyticMechanism
reference index: 4
reference section: Fig.4, p.1414-1415
reference step: 4

ReferenceForCatalyticMechanism
reference index: 5
reference section: FIG.4, p.5526
reference step: 4

ReferenceForCatalyticMechanism
reference index: 6
reference section: p.10305

ReferenceForCatalyticMechanism
reference index: 7
reference section: p.48615, p.48617

ReferenceForCatalyticMechanism
reference index: 8
reference section: p.919-920

ReferenceForCatalyticMechanism
reference index: 9
reference section: Fig.7, p.208
reference step: 5

ReferenceForCatalyticMechanism
reference index: 10

ReferenceForCatalyticMechanism
reference index: 11