EzCatDB: S00676

DB codeS00676
RLCP classification3.103.70035.364
CATH domainDomain 13.40.50.300Catalytic domain
E.C.2.7.1.24

CATH domainRelated DB codes (homologues)
3.40.50.300S00527,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

Enzyme Name
Swiss-protKEGG

O67792P0A6I9Q56416
Protein nameDephospho-CoA kinaseDephospho-CoA kinaseDephospho-CoA kinaseDephospho-CoA kinase
Dephosphocoenzyme A kinase (phosphorylating)
3'-Dephospho-CoA kinase
Dephosphocoenzyme A kinase
SynonymsEC 2.7.1.24
Dephosphocoenzyme A kinase
EC 2.7.1.24
Dephosphocoenzyme A kinase
EC 2.7.1.24
Dephosphocoenzyme A kinase

KEGG pathways
MAP codePathways
MAP00770Pantothenate and CoA biosynthesis

Swiss-prot:Accession NumberO67792P0A6I9Q56416
Entry nameCOAE_AQUAECOAE_ECOLICOAE_THET8
ActivityATP + 3'-dephospho-CoA = ADP + CoA.ATP + 3'-dephospho-CoA = ADP + CoA.ATP + 3'-dephospho-CoA = ADP + CoA.
Subunit
Monomer (Probable).
Subcellular locationCytoplasm (By similarity).Cytoplasm (Probable).Cytoplasm (By similarity).
Cofactor




CofactorsSubstratesProducts
KEGG-idC00305C00002C00882C00008C00010
CompoundMagnesiumATPdephospho-CoAADPCoA
Typedivalent metal (Ca2+, Mg2+)amine group,nucleotideamine group,carbohydrate,nucleotide,peptide/protein,sulfhydryl groupamine group,nucleotideamine group,carbohydrate,nucleotide,peptide/protein,sulfhydryl group
2if2A00UnboundUnboundUnboundUnboundUnbound
2if2B00UnboundUnboundUnboundUnboundUnbound
2if2C00UnboundUnboundUnboundUnboundUnbound
1n3bA00UnboundUnboundUnboundUnboundUnbound
1n3bB00UnboundUnboundUnboundUnboundUnbound
1n3bC00UnboundUnboundUnboundUnboundUnbound
1t3hA00UnboundUnboundUnboundUnboundUnbound
1t3hB00UnboundUnboundUnboundUnboundUnbound
1t3hC00UnboundUnboundUnboundUnboundUnbound
1vhlA00UnboundUnboundUnboundBound:ADPUnbound
1vhlB00UnboundUnboundUnboundUnboundUnbound
1vhlC00UnboundUnboundUnboundUnboundUnbound
1vhtA00UnboundAnalogue:BA3UnboundUnboundUnbound
1vhtB00UnboundAnalogue:BA3UnboundUnboundUnbound
1vhtC00UnboundAnalogue:BA3UnboundUnboundUnbound
1viyA00UnboundUnboundUnboundUnboundUnbound
1viyB00UnboundUnboundUnboundUnboundUnbound
1viyC00UnboundUnboundUnboundUnboundUnbound
1uf9A00UnboundUnboundUnboundUnboundUnbound
1uf9B00UnboundUnboundUnboundUnboundUnbound
1uf9C00UnboundBound:ATPUnboundUnboundUnbound

Active-site residues
resource
literature [1], [2], [4], [5]
pdbCatalytic residuesCofactor-binding residuesMain-chain involved in catalysiscomment
2if2A00LYS 14;ASP 32;ARG 144
SER 15;ASP 30(Magnesium binding)
GLY 11;GLY 13;LYS 14;SER 15;THR 16

2if2B00LYS 14;ASP 32;ARG 144
SER 15;ASP 30(Magnesium binding)
GLY 11;GLY 13;LYS 14;SER 15;THR 16

2if2C00LYS 14;ASP 32;ARG 144
SER 15;ASP 30(Magnesium binding)
GLY 11;GLY 13;LYS 14;SER 15;THR 16
invisible 51-81
1n3bA00LYS 15;ASP 33;ARG 144
SER 16;ASP 31(Magnesium binding)
GLY 12;GLY 14;LYS 15;SER 16;THR 17
invisible 50-77
1n3bB00LYS 15;ASP 33;ARG 144
SER 16;ASP 31(Magnesium binding)
GLY 12;GLY 14;LYS 15;SER 16;THR 17

1n3bC00LYS 15;ASP 33;ARG 144
SER 16;ASP 31(Magnesium binding)
GLY 12;GLY 14;LYS 15;SER 16;THR 17

1t3hA00LYS 15;ASP 33;ARG 144
SER 16;ASP 31(Magnesium binding)
GLY 12;GLY 14;LYS 15;SER 16;THR 17

1t3hB00LYS 15;ASP 33;ARG 144
SER 16;ASP 31(Magnesium binding)
GLY 12;GLY 14;LYS 15;SER 16;THR 17

1t3hC00LYS 15;ASP 33;ARG 144
SER 16;ASP 31(Magnesium binding)
GLY 12;GLY 14;LYS 15;SER 16;THR 17
invisible 59-78
1vhlA00LYS 15;ASP 33;ARG 144
SER 16;ASP 31(Magnesium binding)
GLY 12;GLY 14;LYS 15;SER 16;THR 17

1vhlB00LYS 15;ASP 33;ARG 144
SER 16;ASP 31(Magnesium binding)
GLY 12;GLY 14;LYS 15;SER 16;THR 17

1vhlC00LYS 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
1vhtA00LYS 15;ASP 33;ARG 144
SER 16;ASP 31(Magnesium binding)
GLY 12;GLY 14;LYS 15;SER 16;THR 17

1vhtB00LYS 15;ASP 33;ARG 144
SER 16;ASP 31(Magnesium binding)
GLY 12;GLY 14;LYS 15;SER 16;THR 17

1vhtC00LYS 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
1viyA00LYS 15;ASP 33;ARG 144
SER 16;ASP 31(Magnesium binding)
GLY 12;GLY 14;LYS 15;SER 16;THR 17

1viyB00LYS 15;ASP 33;ARG 144
SER 16;ASP 31(Magnesium binding)
GLY 12;GLY 14;LYS 15;SER 16;THR 17

1viyC00LYS 15;ASP 33;ARG 144
SER 16;ASP 31(Magnesium binding)
GLY 12;GLY 14;LYS 15;SER 16;THR 17

1uf9A00LYS 21;ASP 39;ARG 145
SER 22;ASP 37(Magnesium binding)
GLY 18;GLY 20;LYS 21;SER 22;THR 23

1uf9B00LYS 21;ASP 39;ARG 145
SER 22;ASP 37(Magnesium binding)
GLY 18;GLY 20;LYS 21;SER 22;THR 23

1uf9C00LYS 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
ReferencesSectionsNo. of steps in catalysis
[1]Fig.4, p2697-2698
[2]p.123
[4]p.785

references
[1]
PubMed ID10835366
JournalEMBO J
Year2000
Volume19
Pages2690-700
AuthorsIzard T, Ellis J
TitleThe crystal structures of chloramphenicol phosphotransferase reveal a novel inactivation mechanism.
Related PDB1qhn,1qhs,1qhx,1qhy
[2]
PubMed ID11886213
JournalJ Struct Biol
Year2001
Volume136
Pages119-25
AuthorsObmolova G, Teplyakov A, Bonander N, Eisenstein E, Howard AJ, Gilliland GL
TitleCrystal structure of dephospho-coenzyme A kinase from Haemophilus influenzae.
Related PDB1jjv
[3]
PubMed ID12054870
JournalJ Mol Biol
Year2002
Volume319
Pages779-89
AuthorsGu Y, Reshetnikova L, Li Y, Wu Y, Yan H, Singh S, Ji X
TitleCrystal structure of shikimate kinase from Mycobacterium tuberculosis reveals the dynamic role of the LID domain in catalysis.
Related PDB1l4u,1l4y
[4]
PubMed ID14568537
JournalJ Mol Biol
Year2003
Volume333
Pages781-815
AuthorsLeipe DD, Koonin EV, Aravind L
TitleEvolution and classification of P-loop kinases and related proteins.
[5]
PubMed ID12538896
JournalProtein Sci
Year2003
Volume12
Pages327-36
AuthorsO'Toole N, Barbosa JA, Li Y, Hung LW, Matte A, Cygler M
TitleCrystal structure of a trimeric form of dephosphocoenzyme A kinase from Escherichia coli.
Related PDB1n3b
[6]
PubMed ID16021622
JournalProteins
Year2005
Volume60
Pages787-96
AuthorsBadger 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
TitleStructural analysis of a set of proteins resulting from a bacterial genomics project.
Related PDB1vhl,1vht,1viy
[7]
PubMed ID15526298
JournalProteins
Year2005
Volume58
Pages235-42
AuthorsSeto A, Murayama K, Toyama M, Ebihara A, Nakagawa N, Kuramitsu S, Shirouzu M, Yokoyama S
TitleATP-induced structural change of dephosphocoenzyme A kinase from Thermus thermophilus HB8.
Related PDB1uf9

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.

createdupdated
2009-12-092012-03-06
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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