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Title :   CRYSTAL STRUCTURE OF DEPHOSPHO-COA KINASE

Authors :   Structural Genomix

Date :   01 Dec 03 (Deposition) - 30 Dec 03 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.89

Chains :   Asym./Biol. Unit : A,B,C

Keywords :   Structural Genomics, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Badger, J. M. Sauder, J. M. Adams, S. Antonysamy, K. Bain, M. G. Bergseid, S. G. Buchanan, M. D. Buchanan, Y. Batiyenko, J. A. Christopher, S. Emtage, A. Eroshkina, I. Feil, E. B. Furlong, K. S. Gajiwala, X. Gao, D. He, J. Hendle, A. Huber, K. Hoda, P. Kearins, C. Kissinger, B. Laubert, H. A. Lewis, J. Lin, K. Loomis, D. Lorimer, G. Louie, M. Maletic, C. D. Marsh, I. Miller, J. Molinari, H. J. Muller-Dieckmann, J. M. Newman, B. W. Noland, B. Pagarigan, F. Park, T. S. Peat, K. W. Post, S. Radojicic, A. Ramos, R. Romero, M. E. Rutter, W. E. Sanderson, K. D. Schwinn, J. Tresser, J. Winhoven, T. A. Wright, L. Wu, J. Xu, T. J. Harris
Structural Analysis Of A Set Of Proteins Resulting From A Bacterial Genomics Project
Proteins V. 60 787 2005
PubMed-ID: 16021622 | Reference-DOI: 10.1002/PROT.20541

Molecule 1 - DEPHOSPHO-COA KINASE
	Chains	:	A, B, C
	EC Number	:	2.7.1.24
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	COAE, B0103, Z0113, ECS0107
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	DEPHOSPHOCOENZYME A KINASE

		1	2	3
Asymmetric/Biological Unit	:	A	B	C

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 5)

No.	Name	Count	Type	Full Name
1	SO4	5	Ligand/Ion	SULFATE ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ILE A:11 , GLY A:12 , SER A:13 , GLY A:14 , LYS A:15 , HOH A:375 , HOH A:434	BINDING SITE FOR RESIDUE SO4 A 217
2	AC2	SOFTWARE	ILE B:11 , GLY B:12 , SER B:13 , GLY B:14 , LYS B:15	BINDING SITE FOR RESIDUE SO4 B 217
3	AC3	SOFTWARE	GLY C:10 , GLY C:12 , SER C:13 , GLY C:14 , LYS C:15 , ARG C:144 , HOH C:266	BINDING SITE FOR RESIDUE SO4 C 217
4	AC4	SOFTWARE	SER A:119 , TYR A:121 , LYS A:122 , SER B:119 , TYR B:121 , LYS B:122 , SER C:119 , TYR C:121 , LYS C:122	BINDING SITE FOR RESIDUE SO4 B 218
5	AC5	SOFTWARE	ARG A:68 , HOH A:313 , HOH A:341 , HOH A:396	BINDING SITE FOR RESIDUE SO4 A 218

(no "SS Bond" information available for 1VIY)

(no "Cis Peptide Bond" information available for 1VIY)

(no "SAP(SNP)/Variant" information available for 1VIY)

Asymmetric/Biological Unit (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DPCK	PS51219	Dephospho-CoA kinase (DPCK) domain profile.	COAE_ECOLI	4-200	3	A:4-200 B:4-200 C:4-200

(no "Exon" information available for 1VIY)

Asymmetric/Biological Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:208
 aligned with COAE_ECOLI | P0A6I9 from UniProtKB/Swiss-Prot  Length:206

    Alignment length:208
                             1                                                                                                                                                                                                          206 
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199      | 
           COAE_ECOLI     - -MRYIVALTGGIGSGKSTVANAFADLGINVIDADIIARQVVEPGAPALHAIADHFGANMIAADGTLQRRALRERIFANPEEKNWLNALLHPLIQQETQHQIQQATSPYVLWVVPLLVENSLYKKANRVLVVDVSPETQLKRTMQRDDVTREHVEQILAAQATREARLAVADDVIDNNGAPDAIASDVARLHAHYLQLASQFVSQEKP-   -
               SCOP domains d1viya_ A: Dephospho-CoA kinase                                                                                                                                                                                  SCOP domains
               CATH domains 1viyA00 A:0-207 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee.....hhhhhhhhhhhh...eeehhhhhhhh....hhhhhhhhhhhhhhhh......hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh...eeeee.......hhhhhh.eeeeee.hhhhhhhhhhhhhh.hhhhhhhhhhhh.hhhhhhhhh.eeee...hhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----DPCK  PDB: A:4-200 UniProt: 4-200                                                                                                                                                                    ------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1viy A   0 SLRYIVALTGGIGSGKSTVANAFADLGINVIDADIIARQVVEPGAPALHAIADHFGANMIAADGTLQRRALRERIFANPEEKNWLNALLHPLIQQETQHQIQQATSPYVLWVVPLLVENSLYKKANRVLVVDVSPETQLKRTMQRDDVTREHVEQILAAQATREARLAVADDVIDNNGAPDAIASDVARLHAHYLQLASQFVSQEKPE 207
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199

Chain B from PDB  Type:PROTEIN  Length:208
 aligned with COAE_ECOLI | P0A6I9 from UniProtKB/Swiss-Prot  Length:206

    Alignment length:208
                             1                                                                                                                                                                                                          206 
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199      | 
           COAE_ECOLI     - -MRYIVALTGGIGSGKSTVANAFADLGINVIDADIIARQVVEPGAPALHAIADHFGANMIAADGTLQRRALRERIFANPEEKNWLNALLHPLIQQETQHQIQQATSPYVLWVVPLLVENSLYKKANRVLVVDVSPETQLKRTMQRDDVTREHVEQILAAQATREARLAVADDVIDNNGAPDAIASDVARLHAHYLQLASQFVSQEKP-   -
               SCOP domains d1viyb_ B: Dephospho-CoA kinase                                                                                                                                                                                  SCOP domains
               CATH domains 1viyB00 B:0-207 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee.....hhhhhhhhhhhh..eeeehhhhhhhh....hhhhhhhhhhhhhhhh......hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh....eeee.......hhhhhh.eeeeee.hhhhhhhhhhhhhh.hhhhhhhhhhhh.hhhhhhhhh.eeee...hhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----DPCK  PDB: B:4-200 UniProt: 4-200                                                                                                                                                                    ------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1viy B   0 SLRYIVALTGGIGSGKSTVANAFADLGINVIDADIIARQVVEPGAPALHAIADHFGANMIAADGTLQRRALRERIFANPEEKNWLNALLHPLIQQETQHQIQQATSPYVLWVVPLLVENSLYKKANRVLVVDVSPETQLKRTMQRDDVTREHVEQILAAQATREARLAVADDVIDNNGAPDAIASDVARLHAHYLQLASQFVSQEKPE 207
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199

Chain C from PDB  Type:PROTEIN  Length:208
 aligned with COAE_ECOLI | P0A6I9 from UniProtKB/Swiss-Prot  Length:206

    Alignment length:208
                             1                                                                                                                                                                                                          206 
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199      | 
           COAE_ECOLI     - -MRYIVALTGGIGSGKSTVANAFADLGINVIDADIIARQVVEPGAPALHAIADHFGANMIAADGTLQRRALRERIFANPEEKNWLNALLHPLIQQETQHQIQQATSPYVLWVVPLLVENSLYKKANRVLVVDVSPETQLKRTMQRDDVTREHVEQILAAQATREARLAVADDVIDNNGAPDAIASDVARLHAHYLQLASQFVSQEKP-   -
               SCOP domains d1viyc_ C: Dephospho-CoA kinase                                                                                                                                                                                  SCOP domains
               CATH domains 1viyC00 C:0-207 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                             CATH domains
           Pfam domains (1) ---CoaE-1viyC01 C:3-181                                                                                                                                                               -------------------------- Pfam domains (1)
           Pfam domains (2) ---CoaE-1viyC02 C:3-181                                                                                                                                                               -------------------------- Pfam domains (2)
           Pfam domains (3) ---CoaE-1viyC03 C:3-181                                                                                                                                                               -------------------------- Pfam domains (3)
         Sec.struct. author ...eeeeee.....hhhhhhhhhhh...eeeehhhhhhhhh...hhhhhhhhhhhhhhhh......hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee.......hhhhhh.eeeeee.hhhhhhhhhhhhh..hhhhhhhhhhhh.hhhhhhhhh.eeee...hhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----DPCK  PDB: C:4-200 UniProt: 4-200                                                                                                                                                                    ------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1viy C   0 SLRYIVALTGGIGSGKSTVANAFADLGINVIDADIIARQVVEPGAPALHAIADHFGANMIAADGTLQRRALRERIFANPEEKNWLNALLHPLIQQETQHQIQQATSPYVLWVVPLLVENSLYKKANRVLVVDVSPETQLKRTMQRDDVTREHVEQILAAQATREARLAVADDVIDNNGAPDAIASDVARLHAHYLQLASQFVSQEKPE 207
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: P-loop containing nucleoside triphosphate hydrolases (2083)

Superfamily: P-loop containing nucleoside triphosphate hydrolases (2083)

Family: Nucleotide and nucleoside kinases (231)

Protein domain: Dephospho-CoA kinase (8)

Escherichia coli [TaxId: 562] (5)

1a	d1viya_	A:
1b	d1viyb_	B:
1c	d1viyc_	C:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: P-loop containing nucleotide triphosphate hydrolases (1378)

Escherichia coli. Organism_taxid: 562. (54)

1a	1viyA00	A:0-207
1b	1viyB00	B:0-207
1c	1viyC00	C:0-207

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: P-loop_NTPase (1112)

Family: CoaE (7)

Escherichia coli (strain K12) (5)

1a	CoaE-1viyC01	C:3-181
1b	CoaE-1viyC02	C:3-181
1c	CoaE-1viyC03	C:3-181

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C (COAE_ECOLI | P0A6I9)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0004140	dephospho-CoA kinase activity	Catalysis of the reaction: 3'-dephospho-CoA + ATP = ADP + CoA + 2 H(+).
	GO:0016301	kinase activity	Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
	GO:0015937	coenzyme A biosynthetic process	The chemical reactions and pathways resulting in the formation of coenzyme A, 3'-phosphoadenosine-(5')diphospho(4')pantatheine, an acyl carrier in many acylation and acyl-transfer reactions in which the intermediate is a thiol ester.
	GO:0016310	phosphorylation	The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric/Biological Unit
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(no "Related Entries Specified in the PDB File" available for 1VIY)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 5)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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