EzCatDB: S00914
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DB codeS00914
RLCP classification3.103.70035.366 : Transfer
CATH domainDomain 13.40.50.300 : Rossmann foldCatalytic domain
E.C.2.7.1.24

CATH domainRelated DB codes (homologues)
3.40.50.300 : Rossmann foldS00527,S00547,S00548,S00550,S00554,S00555,S00671,S00672,S00676,S00680,S00682,S00913,S00301,S00302,S00303,S00304,S00307,S00308,S00305,S00306,S00309,S00310,S00311,M00114,M00199,D00129,D00130,D00540,M00186

Enzyme Name
UniProtKBKEGG

Q9X1A7
Protein nameDephospho-CoA kinaseDephospho-CoA kinase
Dephosphocoenzyme A kinase (phosphorylating)
3'-Dephospho-CoA kinase
Dephosphocoenzyme A kinase
SynonymsEC 2.7.1.24
Dephosphocoenzyme A kinase
RefSeqNP_229188.1 (Protein)
NC_000853.1 (DNA/RNA sequence)
PfamPF01121 (CoaE)
[Graphical view]

KEGG pathways
MAP codePathways
MAP00770Pantothenate and CoA biosynthesis

UniProtKB:Accession NumberQ9X1A7
Entry nameCOAE_THEMA
ActivityATP + 3'-dephospho-CoA = ADP + CoA.
Subunit
Subcellular locationCytoplasm (By similarity).
Cofactor

Compound table: links to PDB-related databases & PoSSuM

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
ChEBI18420
15422
15468
16761
15346
PubChem888
5957
444485
6022
87642
6816
             
2grjA00UnboundUnboundBound:CODBound:ADPUnbound
2grjB00UnboundUnboundBound:CODBound:ADPUnbound
2grjC00UnboundUnboundBound:CODBound:ADPUnbound
2grjD00UnboundUnboundBound:CODBound:ADPUnbound
2grjE00UnboundUnboundBound:CODBound:ADPUnbound
2grjF00UnboundUnboundBound:CODBound:ADPUnbound
2grjG00UnboundUnboundBound:CODBound:ADPUnbound
2grjH00UnboundUnboundBound:CODBound:ADPUnbound

Active-site residues
resource
literature [1], [2], [4], [5]
pdbCatalytic residuesCofactor-binding residuesMain-chain involved in catalysis
           
2grjA00LYS 13;ASP 32
SER 14;ASN 30(Magnesium binding)
GLY 10;GLY 12;LYS 13;SER 14;THR 15
2grjB00LYS 13;ASP 32
SER 14;ASN 30(Magnesium binding)
GLY 10;GLY 12;LYS 13;SER 14;THR 15
2grjC00LYS 13;ASP 32
SER 14;ASN 30(Magnesium binding)
GLY 10;GLY 12;LYS 13;SER 14;THR 15
2grjD00LYS 13;ASP 32
SER 14;ASN 30(Magnesium binding)
GLY 10;GLY 12;LYS 13;SER 14;THR 15
2grjE00LYS 13;ASP 32
SER 14;ASN 30(Magnesium binding)
GLY 10;GLY 12;LYS 13;SER 14;THR 15
2grjF00LYS 13;ASP 32
SER 14;ASN 30(Magnesium binding)
GLY 10;GLY 12;LYS 13;SER 14;THR 15
2grjG00LYS 13;ASP 32
SER 14;ASN 30(Magnesium binding)
GLY 10;GLY 12;LYS 13;SER 14;THR 15
2grjH00LYS 13;ASP 32
SER 14;ASN 30(Magnesium binding)
GLY 10;GLY 12;LYS 13;SER 14;THR 15

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 closely related to the counterpart enzyme from E. coli and other bacteria (S00676 in EzCatDB), but has got a slightly different catalytic site. Particularly, an arginine residue on the LID region is missing in this enzyme.
This enzyme is also 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 Ser14 and Asn30, stabilizes the negative charge on beta- and gamma-phosphate groups of ATP. Mainchain amide groups on P-loop along with sidechain of Lys13 also stabilize the negative charge of ATP.
(1) Asp30 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 sidechain of Lys14.
(4) The transfer reaction completes.

createdupdated
2009-12-092012-03-06


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