EzCatDB: S00222

DB codeS00222
RLCP classification6.10.400200.114
5.111.552000.6100
6.20.8000.6100
CATH domainDomain 13.20.20.70Catalytic domain
E.C.4.1.2.14,4.1.3.16
CSA1fq0

CATH domainRelated DB codes (homologues)
3.20.20.70S00215,S00217,S00218,S00219,S00532,S00198,S00220,S00745,S00537,S00538,S00539,S00826,S00841,S00235,S00239,S00240,S00243,S00244,S00199,S00200,S00201,S00221,S00847,S00224,S00225,S00226,D00014,D00029,M00141,T00015,T00239,D00664,D00665,D00804,D00863,T00089

Enzyme Name
Swiss-protKEGG

P0A955
Protein nameKHG/KDPG aldolase2-dehydro-3-deoxy-phosphogluconate aldolase
   (EC 4.1.2.14)
phospho-2-keto-3-deoxygluconate aldolase
   (EC 4.1.2.14)
KDPG aldolase
   (EC 4.1.2.14)
phospho-2-keto-3-deoxygluconic aldolase
   (EC 4.1.2.14)
2-keto-3-deoxy-6-phosphogluconic aldolase
   (EC 4.1.2.14)
2-keto-3-deoxy-6-phosphogluconate aldolase
   (EC 4.1.2.14)
6-phospho-2-keto-3-deoxygluconate aldolase
   (EC 4.1.2.14)
ODPG aldolase
   (EC 4.1.2.14)
2-oxo-3-deoxy-6-phosphogluconate aldolase
   (EC 4.1.2.14)
2-keto-3-deoxygluconate-6-P-aldolase
   (EC 4.1.2.14)
2-keto-3-deoxygluconate-6-phosphate aldolase
   (EC 4.1.2.14)
2-dehydro-3-deoxy-D-gluconate-6-phosphateD-glyceraldehyde-3-phosphate-lyase
   (EC 4.1.2.14)
4-hydroxy-2-oxoglutarate aldolase
   (EC 4.1.3.16)
2-oxo-4-hydroxyglutarate aldolase
   (EC 4.1.3.16)
hydroxyketoglutaric aldolase
   (EC 4.1.3.16)
4-hydroxy-2-ketoglutaric aldolase
   (EC 4.1.3.16)
2-keto-4-hydroxyglutaric aldolase
   (EC 4.1.3.16)
4-hydroxy-2-ketoglutarate aldolase
   (EC 4.1.3.16)
2-keto-4-hydroxyglutarate aldolase
   (EC 4.1.3.16)
2-oxo-4-hydroxyglutaric aldolase
   (EC 4.1.3.16)
DL-4-hydroxy-2-ketoglutarate aldolase
   (EC 4.1.3.16)
hydroxyketoglutarate aldolase
   (EC 4.1.3.16)
2-keto-4-hydroxybutyrate aldolase
   (EC 4.1.3.16)
4-hydroxy-2-oxoglutarate glyoxylate-lyase
   (EC 4.1.3.16)
SynonymsNone
Includes4-hydroxy-2-oxoglutarate aldolase
   EC 4.1.3.16
2-keto-4-hydroxyglutarate aldolase
(KHG-aldolase)
2-dehydro-3-deoxy-phosphogluconate aldolase
   EC 4.1.2.14
Phospho-2-dehydro-3-deoxygluconate aldolase Phospho-2-keto-3-deoxygluconate aldolase 2-keto-3-deoxy-6-phosphogluconate aldolase
(KDPG-aldolase)

KEGG pathways
MAP codePathwaysE.C.
MAP00030Pentose phosphate pathway4.1.2.14,4.1.3.16
MAP00040Pentose and glucuronate interconversions4.1.2.14,4.1.3.16
MAP00330Arginine and proline metabolism4.1.2.14,4.1.3.16
MAP00630Glyoxylate and dicarboxylate metabolism4.1.3.16

Swiss-prot:Accession NumberP0A955
Entry nameALKH_ECOLI
Activity4-hydroxy-2-oxoglutarate = pyruvate + glyoxylate.,2-dehydro-3-deoxy-D-gluconate 6-phosphate = pyruvate + D-glyceraldehyde 3-phosphate.
SubunitHomotrimer.
Subcellular locationCytoplasm.
Cofactor


SubstratesProducts
KEGG-idC04442C01127C00022C00118C00048
E.C.4.1.2.144.1.3.164.1.2.14,4.1.3.164.1.2.144.1.3.16
Compound2-Dehydro-3-deoxy-D-gluconate 6-phosphate4-Hydroxy-2-oxoglutaratePyruvateD-Glyceraldehyde 3-phosphateGlyoxylate
Typecarbohydrate,carboxyl group,phosphate group/phosphate ioncarbohydrate,carboxyl groupcarbohydrate,carboxyl groupcarbohydrate,phosphate group/phosphate ioncarbohydrate,carboxyl group
1euaAUnboundUnboundBound:PYRUnboundUnbound
1euaBUnboundUnboundBound:PYRUnboundUnbound
1euaCUnboundUnboundBound:PYRUnboundUnbound
1eunAUnboundUnboundUnboundUnboundUnbound
1eunBUnboundUnboundUnboundUnboundUnbound
1eunCUnboundUnboundUnboundUnboundUnbound
1fq0AUnboundAnalogue:CITUnboundUnboundUnbound
1fq0BUnboundAnalogue:CITUnboundUnboundUnbound
1fq0CUnboundAnalogue:CITUnboundUnboundUnbound
1fwrAUnboundAnalogue:CITUnboundUnboundUnbound
1fwrBUnboundAnalogue:CITUnboundUnboundUnbound
1fwrCUnboundAnalogue:CITUnboundUnboundUnbound

Active-site residues
resource
Swiss-prot;P0A955 & literature [8]
pdbCatalytic residuescomment
1euaAGLU 45;ARG 49;LYS 133

1euaBGLU 45;ARG 49;LYS 133

1euaCGLU 45;ARG 49;LYS 133

1eunAGLU 45;ARG 49;LYS 133

1eunBGLU 45;ARG 49;LYS 133

1eunCGLU 45;ARG 49;LYS 133

1fq0AGLU 45;ARG 49;LYS 133

1fq0BGLU 45;ARG 49;LYS 133

1fq0CGLU 45;ARG 49;LYS 133

1fwrAGLU 45;ARG 49;       
mutant K133Q;T161K
1fwrBGLU 45;ARG 49;       
mutant K133Q;T161K
1fwrCGLU 45;ARG 49;       
mutant K133Q;T161K

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[4]Fig.1, p.44115
[8]SCHEME I, SCHEME II, p.20387-20389
[12]Scheme 1, p.3682-36846

references
[1]
PubMed ID5561473
JournalJ Biol Chem
Year1971
Volume246
Pages4028-35
AuthorsBarran LR, Wood WA
TitleThe mechanism of 2-keto-3-deoxy-6-phosphogluconate aldolase. 3. Nature of the inactivation by fluorodinitrobenzene.
[2]
PubMed ID5576072
JournalJ Biol Chem
Year1971
Volume246
Pages2084-90
AuthorsRobertson DC, Altekar WW, Wood WA
TitleStructure of 2-keto-3-deoxy-6-phosphogluconate aldolase. 3. Sequence of a hexadecapeptide containing the azomethine-forming lysine residue.
[3]
PubMed ID5044518
JournalArch Biochem Biophys
Year1972
Volume151
Pages251-60
AuthorsMohler H, Decker K, Wood WA
TitleStructure of 2-keto-3-deoxy-6-phosphogluconate aldolase. IV. Structural features revealed by treatment with urea and Ellman's reagent.
[4]
PubMed ID974067
JournalBiochemistry
Year1976
Volume15
Pages4410-7
AuthorsMavridis IM, Tulinsky A
TitleThe folding and quaternary structure of trimeric 2-keto-3-deoxy-6-phosphogluconic aldolase at 3.5-A resolution.
[5]
PubMed ID496979
JournalBiochem Biophys Res Commun
Year1979
Volume90
Pages285-90
AuthorsRichardson JS
TitleThe singly-wound parallel beta barrel: a proposed structure for 2-keto-3-deoxy-6-phosphogluconate aldolase.
[6]
PubMed ID7161802
JournalJ Mol Biol
Year1982
Volume162
Pages445-58
AuthorsLebioda L, Hatada MH, Tulinsky A, Mavridis IM
TitleComparison of the folding of 2-keto-3-deoxy-6-phosphogluconate aldolase, triosephosphate isomerase and pyruvate kinase. Implications in molecular evolution.
[7]
PubMed ID7161801
JournalJ Mol Biol
Year1982
Volume162
Pages419-44
AuthorsMavridis IM, Hatada MH, Tulinsky A, Lebioda L
TitleStructure of 2-keto-3-deoxy-6-phosphogluconate aldolase at 2 . 8 A resolution.
[8]
CommentsACTIVE SITE.
Medline ID91056084
PubMed ID1978721
JournalJ Biol Chem
Year1990
Volume265
Pages20384-9
AuthorsVlahos CJ, Dekker EE
TitleActive-site residues of 2-keto-4-hydroxyglutarate aldolase from Escherichia coli. Bromopyruvate inactivation and labeling of glutamate 45.
Related Swiss-protP0A955
[9]
PubMed ID8166720
JournalBiochem Biophys Res Commun
Year1994
Volume200
Pages459-66
AuthorsTaha TS, Deits TL
TitlePurification and characterization of 2-keto-3-deoxy-6-phosphogluconate aldolase from Azotobacter vinelandii: evidence that the enzyme is bifunctional towards 2-keto-4-hydroxy glutarate cleavage.
[10]
PubMed ID10531504
JournalActa Crystallogr D Biol Crystallogr
Year1999
Volume55
Pages1946-8
AuthorsBuchanan LV, Mehta N, Pocivavsek L, Niranjanakumari S, Toone EJ, Naismith JH
TitleInitiating a structural study of 2-keto-3-deoxy-6-phosphogluconate aldolase from Escherichia coli.
[11]
PubMed ID11094340
JournalChem Biol
Year2000
Volume7
Pages873-83
AuthorsFong S, Machajewski TD, Mak CC, Wong C
TitleDirected evolution of D-2-keto-3-deoxy-6-phosphogluconate aldolase to new variants for the efficient synthesis of D- and L-sugars.
[12]
CommentsX-RAY CRYSTALLOGRAPHY (1.95 ANGSTROMS).
Medline ID21173617
PubMed ID11274385
JournalProc Natl Acad Sci U S A
Year2001
Volume98
Pages3679-84
AuthorsAllard J, Grochulski P, Sygusch J
TitleCovalent intermediate trapped in 2-keto-3-deoxy-6- phosphogluconate (KDPG) aldolase structure at 1.95-A resolution.
Related PDB1eua,1eun
Related Swiss-protP0A955
[13]
CommentsX-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS).
Medline ID21340757
PubMed ID11342129
JournalStructure (Camb)
Year2001
Volume9
Pages1-9
AuthorsWymer N, Buchanan LV, Henderson D, Mehta N, Botting CH, Pocivavsek L, Fierke CA, Toone EJ, Naismith JH
TitleDirected evolution of a new catalytic site in 2-keto-3-deoxy-6-phosphogluconate aldolase from Escherichia coli.
Related PDB1fq0,1fwr
Related Swiss-protP0A955

comments
This enzyme belongs to the KDPG aldolase family.
This enzyme catalyzes three successive reactions;
(A) Schiff-base formation (elimination of hydroxyl group),
(B) Elimination of methylene (next to double-bonded carbon; sp2 carbon) from sp3 carbon with hydroxyl group, leading to formation of aldehyde,
(C) Schiff-base deformation (water addition or hydration).
These reactions proceeds in the followin way.
(A) The Schiff-base forming reaction is actually composed of addition reaction and elimination reaction. The Schiff-base forming reaction proceeds as follows (see [12]):
(A1) The sidechain of Lys133 is protonated at the initial stage. Glu45 probably acts as the first general base, which deprotonates Lys133 so that its sidechain can be neutral form.
(A2) The neutral sidechain of Lys133 makes a nucleophilic attack on the carbonyl carbon (of KDPG substrate, C04442), forming a tetrahedral intermediate.
(A3) A proton atom on the amine of Lys133 moves to the oxygen on the tetrahedral intermediate, leading to a hydroxyl group (Formation of carbinolamine intermediate). (Lys133 plays a dual role as nucleophile-acid.) Here, Glu45 stabilizes the hydroxyl oxygen (see [12]).
(A4) The lone pair on the nitrogen atom of Lys133 attacks on the tetrahedral carbon atom. The hydroxyl group is protonated by the second general acid, leading to the elimination of a water and the Schiff-base formation. According to the literature [12], Glu45 might act as the second general acid.
(B) The next elimination reaction proceeds as follows (see [8] & [12]):
(B1) Glu45 acts as a general base, to abstract a proton from C4 hydroxyl group (deprotonation site of leaving group), forming an enamine intermediate covalently-bound to Lys133. This reaction leads to the cleavage of the C3-C4 bond of KDPG and the release of G3P (aldehyde product).
(B2) Glu45 probably acts as a general acid, to protonate to the C3 atom of the enamine intermediate, leading to the Schiff-base (imine) intermediate.
(C) The Schiff-base deforming reaction is also composed of addition reaction and elimination reaction. This reaction is the reverse one of the first Schiff-base forming reaction (A). The Shciff-base deforming reaction proceeds as follows (see [12]):
(C1) The first general base activates a water, by abstracting a proton from the water. This activated water makes a nucleophilic attack on the Schiff-base carbon, to form a tetrahedral (carbinolamine) intermediate, again. (Glu45 probably acts as the general base.)
(C2) The amine group of Lys133 deprotonates the hydroxyl group, forming an oxygen anion. This anion makes an attack on the tetrahedral carbon atom, leading to the formation of the carbonyl group and the release of Lys133 from the carbon atom.
(C3) Glu45 probably protonates the neutral sidechain of the released Lys133.

createdupdated
2004-05-262009-02-26
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 2010)
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)

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