DB code: S00222

RLCP classification 6.10.400200.114 : Double-bonded atom exchange
5.111.552000.6100 : Elimination
6.20.8000.6100 : Double-bonded atom exchange
CATH domain 3.20.20.70 : TIM Barrel Catalytic domain
E.C. 4.1.2.14 4.1.3.16
CSA 1fq0
M-CSA 1fq0
MACiE

CATH domain Related DB codes (homologues)
3.20.20.70 : TIM Barrel S00215 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

Uniprot Enzyme Name
UniprotKB Protein name Synonyms Includes RefSeq Pfam
P0A955 KHG/KDPG aldolase
None 4-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)
NP_416364.1 (Protein)
NC_000913.2 (DNA/RNA sequence)
YP_490112.1 (Protein)
NC_007779.1 (DNA/RNA sequence)
PF01081 (Aldolase)
[Graphical View]

KEGG enzyme name
2-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 )

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P0A955 ALKH_ECOLI 4-hydroxy-2-oxoglutarate = pyruvate + glyoxylate. 2-dehydro-3-deoxy-D-gluconate 6-phosphate = pyruvate + D-glyceraldehyde 3-phosphate. Homotrimer. Cytoplasm.

KEGG Pathways
Map code Pathways E.C.
MAP00030 Pentose phosphate pathway 4.1.2.14 4.1.3.16
MAP00040 Pentose and glucuronate interconversions 4.1.2.14 4.1.3.16
MAP00330 Arginine and proline metabolism 4.1.2.14 4.1.3.16
MAP00630 Glyoxylate and dicarboxylate metabolism 4.1.3.16

Compound table
Substrates Products Intermediates
KEGG-id C04442 C01127 C00022 C00118 C00048
E.C. 4.1.2.14
4.1.3.16
4.1.2.14
4.1.3.16
4.1.2.14
4.1.3.16
Compound 2-Dehydro-3-deoxy-D-gluconate 6-phosphate 4-Hydroxy-2-oxoglutarate Pyruvate D-Glyceraldehyde 3-phosphate Glyoxylate
Type carbohydrate,carboxyl group,phosphate group/phosphate ion carbohydrate,carboxyl group carbohydrate,carboxyl group carbohydrate,phosphate group/phosphate ion carbohydrate,carboxyl group
ChEBI 15925
30923
32816
29052
16891
PubChem 3080745
46
599
1060
439168
760
1euaA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Bound:PYR Unbound Unbound
1euaB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Bound:PYR Unbound Unbound
1euaC Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Bound:PYR Unbound Unbound
1eunA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1eunB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1eunC Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1fq0A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Analogue:CIT Unbound Unbound Unbound
1fq0B Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Analogue:CIT Unbound Unbound Unbound
1fq0C Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Analogue:CIT Unbound Unbound Unbound
1fwrA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Analogue:CIT Unbound Unbound Unbound
1fwrB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Analogue:CIT Unbound Unbound Unbound
1fwrC Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Analogue:CIT Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
Swiss-prot;P0A955 & literature [8]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1euaA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 45;ARG 49;LYS 133
1euaB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 45;ARG 49;LYS 133
1euaC Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 45;ARG 49;LYS 133
1eunA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 45;ARG 49;LYS 133
1eunB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 45;ARG 49;LYS 133
1eunC Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 45;ARG 49;LYS 133
1fq0A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 45;ARG 49;LYS 133
1fq0B Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 45;ARG 49;LYS 133
1fq0C Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 45;ARG 49;LYS 133
1fwrA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 45;ARG 49; mutant K133Q;T161K
1fwrB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 45;ARG 49; mutant K133Q;T161K
1fwrC Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 45;ARG 49; mutant K133Q;T161K

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[4]
Fig.1, p.4411 5
[8]
SCHEME I, SCHEME II, p.20387-20389
[12]
Scheme 1, p.3682-3684 6

References
[1]
Resource
Comments
Medline ID
PubMed ID 5561473
Journal J Biol Chem
Year 1971
Volume 246
Pages 4028-35
Authors Barran LR, Wood WA
Title The mechanism of 2-keto-3-deoxy-6-phosphogluconate aldolase. 3. Nature of the inactivation by fluorodinitrobenzene.
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID 5576072
Journal J Biol Chem
Year 1971
Volume 246
Pages 2084-90
Authors Robertson DC, Altekar WW, Wood WA
Title Structure of 2-keto-3-deoxy-6-phosphogluconate aldolase. 3. Sequence of a hexadecapeptide containing the azomethine-forming lysine residue.
Related PDB
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID 5044518
Journal Arch Biochem Biophys
Year 1972
Volume 151
Pages 251-60
Authors Mohler H, Decker K, Wood WA
Title Structure of 2-keto-3-deoxy-6-phosphogluconate aldolase. IV. Structural features revealed by treatment with urea and Ellman's reagent.
Related PDB
Related UniProtKB
[4]
Resource
Comments
Medline ID
PubMed ID 974067
Journal Biochemistry
Year 1976
Volume 15
Pages 4410-7
Authors Mavridis IM, Tulinsky A
Title The folding and quaternary structure of trimeric 2-keto-3-deoxy-6-phosphogluconic aldolase at 3.5-A resolution.
Related PDB
Related UniProtKB
[5]
Resource
Comments
Medline ID
PubMed ID 496979
Journal Biochem Biophys Res Commun
Year 1979
Volume 90
Pages 285-90
Authors Richardson JS
Title The singly-wound parallel beta barrel: a proposed structure for 2-keto-3-deoxy-6-phosphogluconate aldolase.
Related PDB
Related UniProtKB
[6]
Resource
Comments
Medline ID
PubMed ID 7161802
Journal J Mol Biol
Year 1982
Volume 162
Pages 445-58
Authors Lebioda L, Hatada MH, Tulinsky A, Mavridis IM
Title Comparison of the folding of 2-keto-3-deoxy-6-phosphogluconate aldolase, triosephosphate isomerase and pyruvate kinase. Implications in molecular evolution.
Related PDB
Related UniProtKB
[7]
Resource
Comments
Medline ID
PubMed ID 7161801
Journal J Mol Biol
Year 1982
Volume 162
Pages 419-44
Authors Mavridis IM, Hatada MH, Tulinsky A, Lebioda L
Title Structure of 2-keto-3-deoxy-6-phosphogluconate aldolase at 2 . 8 A resolution.
Related PDB
Related UniProtKB
[8]
Resource
Comments ACTIVE SITE.
Medline ID 91056084
PubMed ID 1978721
Journal J Biol Chem
Year 1990
Volume 265
Pages 20384-9
Authors Vlahos CJ, Dekker EE
Title Active-site residues of 2-keto-4-hydroxyglutarate aldolase from Escherichia coli. Bromopyruvate inactivation and labeling of glutamate 45.
Related PDB
Related UniProtKB P0A955
[9]
Resource
Comments
Medline ID
PubMed ID 8166720
Journal Biochem Biophys Res Commun
Year 1994
Volume 200
Pages 459-66
Authors Taha TS, Deits TL
Title Purification 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.
Related PDB
Related UniProtKB
[10]
Resource
Comments
Medline ID
PubMed ID 10531504
Journal Acta Crystallogr D Biol Crystallogr
Year 1999
Volume 55
Pages 1946-8
Authors Buchanan LV, Mehta N, Pocivavsek L, Niranjanakumari S, Toone EJ, Naismith JH
Title Initiating a structural study of 2-keto-3-deoxy-6-phosphogluconate aldolase from Escherichia coli.
Related PDB
Related UniProtKB
[11]
Resource
Comments
Medline ID
PubMed ID 11094340
Journal Chem Biol
Year 2000
Volume 7
Pages 873-83
Authors Fong S, Machajewski TD, Mak CC, Wong C
Title Directed evolution of D-2-keto-3-deoxy-6-phosphogluconate aldolase to new variants for the efficient synthesis of D- and L-sugars.
Related PDB
Related UniProtKB
[12]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.95 ANGSTROMS).
Medline ID 21173617
PubMed ID 11274385
Journal Proc Natl Acad Sci U S A
Year 2001
Volume 98
Pages 3679-84
Authors Allard J, Grochulski P, Sygusch J
Title Covalent intermediate trapped in 2-keto-3-deoxy-6- phosphogluconate (KDPG) aldolase structure at 1.95-A resolution.
Related PDB 1eua 1eun
Related UniProtKB P0A955
[13]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS).
Medline ID 21340757
PubMed ID 11342129
Journal Structure (Camb)
Year 2001
Volume 9
Pages 1-9
Authors Wymer N, Buchanan LV, Henderson D, Mehta N, Botting CH, Pocivavsek L, Fierke CA, Toone EJ, Naismith JH
Title Directed evolution of a new catalytic site in 2-keto-3-deoxy-6-phosphogluconate aldolase from Escherichia coli.
Related PDB 1fq0 1fwr
Related UniProtKB P0A955

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.

Created Updated
2004-05-26 2009-02-26