DB code: S00914

RLCP classification 3.103.70035.366 : 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 S00676 S00680 S00682 S00913 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
Q9X1A7 Dephospho-CoA kinase
EC 2.7.1.24
Dephosphocoenzyme A kinase
NP_229188.1 (Protein)
NC_000853.1 (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
Q9X1A7 COAE_THEMA 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
 18420
 		15422
 15422
 		15468
 15468
 		16761
 16761
 		15346
 15346
PubChem 888
 888
 		5957
 5957
 		444485
 444485
 		6022
 6022
 		6816
 87642
 6816
 87642
2grjA00 Unbound Unbound Bound:COD Bound:ADP Unbound
2grjB00 Unbound Unbound Bound:COD Bound:ADP Unbound
2grjC00 Unbound Unbound Bound:COD Bound:ADP Unbound
2grjD00 Unbound Unbound Bound:COD Bound:ADP Unbound
2grjE00 Unbound Unbound Bound:COD Bound:ADP Unbound
2grjF00 Unbound Unbound Bound:COD Bound:ADP Unbound
2grjG00 Unbound Unbound Bound:COD Bound:ADP Unbound
2grjH00 Unbound Unbound Bound:COD Bound:ADP 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
2grjA00 LYS 13;ASP 32 SER 14;ASN 30(Magnesium binding) GLY 10;GLY 12;LYS 13;SER 14;THR 15
2grjB00 LYS 13;ASP 32 SER 14;ASN 30(Magnesium binding) GLY 10;GLY 12;LYS 13;SER 14;THR 15
2grjC00 LYS 13;ASP 32 SER 14;ASN 30(Magnesium binding) GLY 10;GLY 12;LYS 13;SER 14;THR 15
2grjD00 LYS 13;ASP 32 SER 14;ASN 30(Magnesium binding) GLY 10;GLY 12;LYS 13;SER 14;THR 15
2grjE00 LYS 13;ASP 32 SER 14;ASN 30(Magnesium binding) GLY 10;GLY 12;LYS 13;SER 14;THR 15
2grjF00 LYS 13;ASP 32 SER 14;ASN 30(Magnesium binding) GLY 10;GLY 12;LYS 13;SER 14;THR 15
2grjG00 LYS 13;ASP 32 SER 14;ASN 30(Magnesium binding) GLY 10;GLY 12;LYS 13;SER 14;THR 15
2grjH00 LYS 13;ASP 32 SER 14;ASN 30(Magnesium binding) GLY 10;GLY 12;LYS 13;SER 14;THR 15

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 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.

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