1T3H - JenaLib

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Biological Unit 3 (Jmol Viewer)

Title :   X-RAY STRUCTURE OF DEPHOSPHO-COA KINASE FROM E. COLI NORTEAST STRUCTURAL GENOMICS CONSORTIUM TARGET ER57

Authors :   A. P. Kuzin, Y. Chen, F. Forouhar, W. Edstrom, J. Benach, S. Vorobiev, T. Acton, R. Shastry, L. -C. Ma, R. Xia, G. Montelione, L. Tong, J. Hunt, Northeast Structural Genomics Consortium (Nesg)

Date :   26 Apr 04 (Deposition) - 11 May 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

Chains :   Asym. Unit : A,B,C
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)

Keywords :   Structural Genomics, Psi, Protein Structure Initiative, Northeast Structural Genomics Consortium, Nesg, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. P. Kuzin, Y. Chen, F. Forouhar, W. Edstrom, J. Benach, S. Vorobiev, T. Acton, R. Shastry, L. -C. Ma, R. Xia, G. Montelione, L. Tong, J. Hunt
X-Ray Structure Of Dephospho-Coa Kinase From E. Coli Norteast Structural Genomics Consortium Target Er57
To Be Published
PubMed: search
(for further references see the PDB file header)

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
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	DEPHOSPHOCOENZYME A KINASE

		1	2	3
Asymmetric Unit	:	A	B	C
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:			C

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 11)

No.	Name	Count	Type	Full Name
1	MSE	9	Mod. Amino Acid	SELENOMETHIONINE
2	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 4)

No.	Name	Count	Type	Full Name
1	MSE	3	Mod. Amino Acid	SELENOMETHIONINE
2	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 4)

No.	Name	Count	Type	Full Name
1	MSE	3	Mod. Amino Acid	SELENOMETHIONINE
2	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 3 (1, 3)

No.	Name	Count	Type	Full Name
1	MSE	3	Mod. Amino Acid	SELENOMETHIONINE
2	SO4	-1	Ligand/Ion	SULFATE ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:12 , SER A:13 , GLY A:14 , LYS A:15 , ARG A:144	BINDING SITE FOR RESIDUE SO4 A 301
2	AC2	SOFTWARE	GLN B:137 , LEU B:156 , GLN B:159 , ALA B:160 , ARG B:165	BINDING SITE FOR RESIDUE SO4 B 302

(no "SS Bond" information available for 1T3H)

(no "Cis Peptide Bond" information available for 1T3H)

(no "SAP(SNP)/Variant" information available for 1T3H)

Asymmetric 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

Biological Unit 1 (1, 1)

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

Biological Unit 2 (1, 1)

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

Biological Unit 3 (1, 1)

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

(no "Exon" information available for 1T3H)

Asymmetric 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:207
 aligned with COAE_ECOLI | P0A6I9 from UniProtKB/Swiss-Prot  Length:206

    Alignment length:207
                                                                                                                                                                                                                                       206 
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200     | 
           COAE_ECOLI     1 MRYIVALTGGIGSGKSTVANAFADLGINVIDADIIARQVVEPGAPALHAIADHFGANMIAADGTLQRRALRERIFANPEEKNWLNALLHPLIQQETQHQIQQATSPYVLWVVPLLVENSLYKKANRVLVVDVSPETQLKRTMQRDDVTREHVEQILAAQATREARLAVADDVIDNNGAPDAIASDVARLHAHYLQLASQFVSQEKP-   -
               SCOP domains d1t3ha_ A: Dephospho-CoA kinase                                                                                                                                                                                 SCOP domains
               CATH domains -1t3hA00 A:2-207 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                           CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.....hhhhhhhhhhh....eeehhhhhhhh....hhhhhhhhhhhhhhhh......hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh...eeeee.......hhhhhh.eeeeee.hhhhhhhhhhhhh..hhhhhhhhhh...hhhhhhh...eeee......hhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---DPCK  PDB: A:4-200 UniProt: 4-200                                                                                                                                                                    ------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1t3h A   1 mRYIVALTGGIGSGKSTVANAFADLGINVIDADIIARQVVEPGAPALHAIADHFGANmIAADGTLQRRALRERIFANPEEKNWLNALLHPLIQQETQHQIQQATSPYVLWVVPLLVENSLYKKANRVLVVDVSPETQLKRTmQRDDVTREHVEQILAAQATREARLAVADDVIDNNGAPDAIASDVARLHAHYLQLASQFVSQEKPE 207
                            |       10        20        30        40        50       |60        70        80        90       100       110       120       130       140 |     150       160       170       180       190       200       
                            |                                                       58-MSE                                                                             142-MSE                                                             
                            1-MSE

Chain B from PDB  Type:PROTEIN  Length:207
 aligned with COAE_ECOLI | P0A6I9 from UniProtKB/Swiss-Prot  Length:206

    Alignment length:207
                                                                                                                                                                                                                                       206 
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200     | 
           COAE_ECOLI     1 MRYIVALTGGIGSGKSTVANAFADLGINVIDADIIARQVVEPGAPALHAIADHFGANMIAADGTLQRRALRERIFANPEEKNWLNALLHPLIQQETQHQIQQATSPYVLWVVPLLVENSLYKKANRVLVVDVSPETQLKRTMQRDDVTREHVEQILAAQATREARLAVADDVIDNNGAPDAIASDVARLHAHYLQLASQFVSQEKP-   -
               SCOP domains d1t3hb_ B: Dephospho-CoA kinase                                                                                                                                                                                 SCOP domains
               CATH domains -1t3hB00 B:2-207 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                           CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.....hhhhhhhhhhh...eeeehhhhhhhh....hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee.......hhhhhh.eeeeee.hhhhhhhhhhhh...hhhhhhhhhhhh.hhhhhhhh..eeee......hhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---DPCK  PDB: B:4-200 UniProt: 4-200                                                                                                                                                                    ------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1t3h B   1 mRYIVALTGGIGSGKSTVANAFADLGINVIDADIIARQVVEPGAPALHAIADHFGANmIAADGTLQRRALRERIFANPEEKNWLNALLHPLIQQETQHQIQQATSPYVLWVVPLLVENSLYKKANRVLVVDVSPETQLKRTmQRDDVTREHVEQILAAQATREARLAVADDVIDNNGAPDAIASDVARLHAHYLQLASQFVSQEKPE 207
                            |       10        20        30        40        50       |60        70        80        90       100       110       120       130       140 |     150       160       170       180       190       200       
                            1-MSE                                                   58-MSE                                                                             142-MSE

Chain C from PDB  Type:PROTEIN  Length:187
 aligned with COAE_ECOLI | P0A6I9 from UniProtKB/Swiss-Prot  Length:206

    Alignment length:207
                                                                                                                                                                                                                                       206 
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200     | 
           COAE_ECOLI     1 MRYIVALTGGIGSGKSTVANAFADLGINVIDADIIARQVVEPGAPALHAIADHFGANMIAADGTLQRRALRERIFANPEEKNWLNALLHPLIQQETQHQIQQATSPYVLWVVPLLVENSLYKKANRVLVVDVSPETQLKRTMQRDDVTREHVEQILAAQATREARLAVADDVIDNNGAPDAIASDVARLHAHYLQLASQFVSQEKP-   -
               SCOP domains d1t3hc_ C: Dephospho-CoA kinase                                                                                                                                                                                 SCOP domains
               CATH domains -1t3hC00 C:2-207 P-loop containing nucleotide triphosphate                     hydrolases                                                                                                                       CATH domains
           Pfam domains (1) --CoaE-1t3hC01 C:3-181                                                                                                                                                               -------------------------- Pfam domains (1)
           Pfam domains (2) --CoaE-1t3hC02 C:3-181                                                                                                                                                               -------------------------- Pfam domains (2)
           Pfam domains (3) --CoaE-1t3hC03 C:3-181                                                                                                                                                               -------------------------- Pfam domains (3)
         Sec.struct. author ..eeeeee.....hhhhhhhhhhh....eeehhhhhhhh....hhhhhhhhhhh....--------------------.........hhhhhhhhhhhhhhhh...eeeee.......hhhhhh.eeeeee.hhhhhhhhhhhhh..hhhhhhhhhh...hhhhhhhhh.eeee.......hhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---DPCK  PDB: C:4-200 UniProt: 4-200                                                                                                                                                                    ------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1t3h C   1 mRYIVALTGGIGSGKSTVANAFADLGINVIDADIIARQVVEPGAPALHAIADHFGANm--------------------EEKNWLNALLHPLIQQETQHQIQQATSPYVLWVVPLLVENSLYKKANRVLVVDVSPETQLKRTmQRDDVTREHVEQILAAQATREARLAVADDVIDNNGAPDAIASDVARLHAHYLQLASQFVSQEKPE 207
                            |       10        20        30        40        50       | -         -        80        90       100       110       120       130       140 |     150       160       170       180       190       200       
                            1-MSE                                                   58-MSE               79                                                            142-MSE

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 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	d1t3ha_	A:
1b	d1t3hb_	B:
1c	d1t3hc_	C:

Asymmetric 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. (35)

1a	1t3hA00	A:2-207
1b	1t3hB00	B:2-207
1c	1t3hC00	C:2-207

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: P-loop_NTPase (1112)

Family: CoaE (7)

Escherichia coli (strain K12) (5)

1a	CoaE-1t3hC01	C:3-181
1b	CoaE-1t3hC02	C:3-181
1c	CoaE-1t3hC03	C:3-181

Asymmetric 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 Unit
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	COAE_ECOLI \| P0A6I9	:	1n3b 1vhl 1vht 1viy

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Ligands, Modified Residues, Ions (2, 11)

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SS Bonds (0, 0)

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