DB code: S00676

RLCP classification 3.103.70035.364 : Transfer
CATH domain 3.40.50.300 : Rossmann fold Catalytic domain
E.C. 2.7.1.24
CSA
M-CSA
MACiE

CATH domain Related DB codes (homologues)
3.40.50.300 : Rossmann fold S00527 S00547 S00548 S00550 S00554 S00555 S00671 S00672 S00680 S00682 S00913 S00914 S00301 S00302 S00303 S00304 S00307 S00308 S00305 S00306 S00309 S00310 S00311 M00114 M00199 D00129 D00130 D00540 M00186

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq Pfam
O67792 Dephospho-CoA kinase
EC 2.7.1.24
Dephosphocoenzyme A kinase
NP_214361.1 (Protein)
NC_000918.1 (DNA/RNA sequence)
PF01121 (CoaE)
[Graphical View]
P0A6I9 Dephospho-CoA kinase
EC 2.7.1.24
Dephosphocoenzyme A kinase
NP_414645.1 (Protein)
NC_000913.2 (DNA/RNA sequence)
YP_488407.1 (Protein)
NC_007779.1 (DNA/RNA sequence)
PF01121 (CoaE)
[Graphical View]
Q56416 Dephospho-CoA kinase
EC 2.7.1.24
Dephosphocoenzyme A kinase
YP_144192.1 (Protein)
NC_006461.1 (DNA/RNA sequence)
PF01121 (CoaE)
[Graphical View]

KEGG enzyme name
Dephospho-CoA kinase
Dephosphocoenzyme A kinase (phosphorylating)
3'-Dephospho-CoA kinase
Dephosphocoenzyme A kinase

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
O67792 COAE_AQUAE ATP + 3'-dephospho-CoA = ADP + CoA. Cytoplasm (By similarity).
P0A6I9 COAE_ECOLI ATP + 3'-dephospho-CoA = ADP + CoA. Monomer (Probable). Cytoplasm (Probable).
Q56416 COAE_THET8 ATP + 3'-dephospho-CoA = ADP + CoA. Cytoplasm (By similarity).

KEGG Pathways
Map code Pathways E.C.
MAP00770 Pantothenate and CoA biosynthesis

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C00305 C00002 C00882 C00008 C00010
E.C.
Compound Magnesium ATP dephospho-CoA ADP CoA
Type divalent metal (Ca2+, Mg2+) amine group,nucleotide amine group,carbohydrate,nucleotide ,peptide/protein,sulfhydryl group amine group,nucleotide amine group,carbohydrate,nucleotide ,peptide/protein,sulfhydryl group
ChEBI 18420
15422
15468
16761
15346
PubChem 888
5957
444485
6022
6816
87642
2if2A00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
2if2B00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
2if2C00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1n3bA00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1n3bB00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1n3bC00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1t3hA00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1t3hB00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1t3hC00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1vhlA00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Bound:ADP Unbound
1vhlB00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1vhlC00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1vhtA00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Analogue:BA3 Unbound Unbound Unbound
1vhtB00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Analogue:BA3 Unbound Unbound Unbound
1vhtC00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Analogue:BA3 Unbound Unbound Unbound
1viyA00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1viyB00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1viyC00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1uf9A00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1uf9B00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1uf9C00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:ATP Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
literature [1], [2], [4], [5]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
2if2A00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 14;ASP 32;ARG 144 SER 15;ASP 30(Magnesium binding) GLY 11;GLY 13;LYS 14;SER 15;THR 16
2if2B00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 14;ASP 32;ARG 144 SER 15;ASP 30(Magnesium binding) GLY 11;GLY 13;LYS 14;SER 15;THR 16
2if2C00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 14;ASP 32;ARG 144 SER 15;ASP 30(Magnesium binding) GLY 11;GLY 13;LYS 14;SER 15;THR 16 invisible 51-81
1n3bA00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 15;ASP 33;ARG 144 SER 16;ASP 31(Magnesium binding) GLY 12;GLY 14;LYS 15;SER 16;THR 17 invisible 50-77
1n3bB00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 15;ASP 33;ARG 144 SER 16;ASP 31(Magnesium binding) GLY 12;GLY 14;LYS 15;SER 16;THR 17
1n3bC00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 15;ASP 33;ARG 144 SER 16;ASP 31(Magnesium binding) GLY 12;GLY 14;LYS 15;SER 16;THR 17
1t3hA00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 15;ASP 33;ARG 144 SER 16;ASP 31(Magnesium binding) GLY 12;GLY 14;LYS 15;SER 16;THR 17
1t3hB00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 15;ASP 33;ARG 144 SER 16;ASP 31(Magnesium binding) GLY 12;GLY 14;LYS 15;SER 16;THR 17
1t3hC00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 15;ASP 33;ARG 144 SER 16;ASP 31(Magnesium binding) GLY 12;GLY 14;LYS 15;SER 16;THR 17 invisible 59-78
1vhlA00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 15;ASP 33;ARG 144 SER 16;ASP 31(Magnesium binding) GLY 12;GLY 14;LYS 15;SER 16;THR 17
1vhlB00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 15;ASP 33;ARG 144 SER 16;ASP 31(Magnesium binding) GLY 12;GLY 14;LYS 15;SER 16;THR 17
1vhlC00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 15;ASP 33;ARG 144 SER 16;ASP 31(Magnesium binding) GLY 12;GLY 14;LYS 15;SER 16;THR 17 invisible 49-55, 66-82
1vhtA00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 15;ASP 33;ARG 144 SER 16;ASP 31(Magnesium binding) GLY 12;GLY 14;LYS 15;SER 16;THR 17
1vhtB00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 15;ASP 33;ARG 144 SER 16;ASP 31(Magnesium binding) GLY 12;GLY 14;LYS 15;SER 16;THR 17
1vhtC00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 15;ASP 33;ARG 144 SER 16;ASP 31(Magnesium binding) GLY 12;GLY 14;LYS 15;SER 16;THR 17 invisible 54-55, 66-82
1viyA00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 15;ASP 33;ARG 144 SER 16;ASP 31(Magnesium binding) GLY 12;GLY 14;LYS 15;SER 16;THR 17
1viyB00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 15;ASP 33;ARG 144 SER 16;ASP 31(Magnesium binding) GLY 12;GLY 14;LYS 15;SER 16;THR 17
1viyC00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 15;ASP 33;ARG 144 SER 16;ASP 31(Magnesium binding) GLY 12;GLY 14;LYS 15;SER 16;THR 17
1uf9A00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 21;ASP 39;ARG 145 SER 22;ASP 37(Magnesium binding) GLY 18;GLY 20;LYS 21;SER 22;THR 23
1uf9B00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 21;ASP 39;ARG 145 SER 22;ASP 37(Magnesium binding) GLY 18;GLY 20;LYS 21;SER 22;THR 23
1uf9C00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 21;ASP 39;ARG 145 SER 22;ASP 37(Magnesium binding) GLY 18;GLY 20;LYS 21;SER 22;THR 23

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[1]
Fig.4, p2697-2698
[2]
p.123
[4]
p.785

References
[1]
Resource
Comments
Medline ID
PubMed ID 10835366
Journal EMBO J
Year 2000
Volume 19
Pages 2690-700
Authors Izard T, Ellis J
Title The crystal structures of chloramphenicol phosphotransferase reveal a novel inactivation mechanism.
Related PDB 1qhn 1qhs 1qhx 1qhy
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID 11886213
Journal J Struct Biol
Year 2001
Volume 136
Pages 119-25
Authors Obmolova G, Teplyakov A, Bonander N, Eisenstein E, Howard AJ, Gilliland GL
Title Crystal structure of dephospho-coenzyme A kinase from Haemophilus influenzae.
Related PDB 1jjv
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID 12054870
Journal J Mol Biol
Year 2002
Volume 319
Pages 779-89
Authors Gu Y, Reshetnikova L, Li Y, Wu Y, Yan H, Singh S, Ji X
Title Crystal structure of shikimate kinase from Mycobacterium tuberculosis reveals the dynamic role of the LID domain in catalysis.
Related PDB 1l4u 1l4y
Related UniProtKB
[4]
Resource
Comments
Medline ID
PubMed ID 14568537
Journal J Mol Biol
Year 2003
Volume 333
Pages 781-815
Authors Leipe DD, Koonin EV, Aravind L
Title Evolution and classification of P-loop kinases and related proteins.
Related PDB
Related UniProtKB
[5]
Resource
Comments
Medline ID
PubMed ID 12538896
Journal Protein Sci
Year 2003
Volume 12
Pages 327-36
Authors O'Toole N, Barbosa JA, Li Y, Hung LW, Matte A, Cygler M
Title Crystal structure of a trimeric form of dephosphocoenzyme A kinase from Escherichia coli.
Related PDB 1n3b
Related UniProtKB
[6]
Resource
Comments
Medline ID
PubMed ID 16021622
Journal Proteins
Year 2005
Volume 60
Pages 787-96
Authors Badger J, Sauder JM, Adams JM, Antonysamy S, Bain K, Bergseid MG, Buchanan SG, Buchanan MD, Batiyenko Y, Christopher JA, Emtage S, Eroshkina A, Feil I, Furlong EB, Gajiwala KS, Gao X, He D, Hendle J, Huber A, Hoda K, Kearins P, Kissinger C, Laubert B, Lewis HA, Lin J, Loomis K, Lorimer D, Louie G, Maletic M, Marsh CD, Miller I, Molinari J, Muller-Dieckmann HJ, Newman JM, Noland BW, Pagarigan B, Park F, Peat TS, Post KW, Radojicic S, Ramos A, Romero R, Rutter ME, Sanderson WE, Schwinn KD, Tresser J, Winhoven J, Wright TA, Wu L, Xu J, Harris TJ
Title Structural analysis of a set of proteins resulting from a bacterial genomics project.
Related PDB 1vhl 1vht 1viy
Related UniProtKB
[7]
Resource
Comments
Medline ID
PubMed ID 15526298
Journal Proteins
Year 2005
Volume 58
Pages 235-42
Authors Seto A, Murayama K, Toyama M, Ebihara A, Nakagawa N, Kuramitsu S, Shirouzu M, Yokoyama S
Title ATP-induced structural change of dephosphocoenzyme A kinase from Thermus thermophilus HB8.
Related PDB 1uf9
Related UniProtKB

Comments
This enzyme is homologous to shikimate kinase (EC 2.7.1.71;S00304 in EzCatDB)(see [4]).
This enzyme catalyzes phosphoryl transfer from ATP to 3'-OH of dephospho-CoA, as follows:
(0) Magnesium ion, bound to Ser15 and Asp30, stabilizes the negative charge on beta- and gamma-phosphate groups of ATP. Mainchain amide groups on P-loop along with sidechains of Lys14 and Arg144 from LID region also stabilize the negative charge of ATP.
(1) Asp32 acts as a general base to deprotonate 3'-OH of dephospho-CoA.
(2) The activated hydroxyl group makes a nucleophilic attack on gamma-phosphate group on ATP. (SN2-like reaction)
(3) During the transition state, the transferred gamma-phosphate and the leaving beta-phosphate must be stabilized by the magnesium ion and mainchain amide groups and sidechains of Lys14 and Arg144.
(4) The transfer reaction completes.

Created Updated
2009-12-09 2012-03-06