2IF2 - JenaLib

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Title :   CRYSTAL STRUCTURE OF THE PUTATIVE DEPHOSPHO-COA KINASE FROM AQUIFEX AEOLICUS, NORTHEAST STRUCTURAL GENOMICS TARGET QR72.

Authors :   F. Forouhar, M. Hussain, J. Seetharaman, A. Hussain, M. Wu, Y. Fang, K. Cunningham, L. C. Ma, R. Xiao, J. Liu, M. Baran, B. Rost, T. B. Acton, G. T. Montelione, J. F. Hunt, L. Tong, Northeast Structural Genomic Consortium (Nesg)

Date :   19 Sep 06 (Deposition) - 03 Oct 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.00

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

Keywords :   Alpha-Beta Protein, Structural Genomics, Psi-2, Protein Structure Initiative, Northeast Structural Genomics Consortium, Nesg, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :

PubMed: search

Molecule 1 - DEPHOSPHO-COA KINASE
	Chains	:	A, B, C
	EC Number	:	2.7.1.24
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET21,JM109
	Expression System Strain	:	BL21(DE3)+MAGIC
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	COAE
	Organism Scientific	:	AQUIFEX AEOLICUS
	Organism Taxid	:	224324
	Strain	:	VF5
	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 (3, 16)

No.	Name	Count	Type	Full Name
1	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
2	MSE	12	Mod. Amino Acid	SELENOMETHIONINE
3	SO4	3	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 5)

No.	Name	Count	Type	Full Name
1	EDO	-1	Ligand/Ion	1,2-ETHANEDIOL
2	MSE	4	Mod. Amino Acid	SELENOMETHIONINE
3	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 2 (3, 6)

No.	Name	Count	Type	Full Name
1	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
2	MSE	4	Mod. Amino Acid	SELENOMETHIONINE
3	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 3 (2, 5)

No.	Name	Count	Type	Full Name
1	EDO	-1	Ligand/Ion	1,2-ETHANEDIOL
2	MSE	4	Mod. Amino Acid	SELENOMETHIONINE
3	SO4	1	Ligand/Ion	SULFATE ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:9 , ILE A:10 , GLY A:11 , CYS A:12 , GLY A:13 , LYS A:14 , SER A:15 , ARG A:144	BINDING SITE FOR RESIDUE SO4 A 301
2	AC2	SOFTWARE	GLY B:11 , CYS B:12 , GLY B:13 , LYS B:14 , ARG B:144	BINDING SITE FOR RESIDUE SO4 B 302
3	AC3	SOFTWARE	ASN C:9 , GLY C:11 , CYS C:12 , GLY C:13 , LYS C:14 , SER C:15 , ARG C:144	BINDING SITE FOR RESIDUE SO4 C 303
4	AC4	SOFTWARE	ASP B:32 , HIS B:88 , LYS B:118	BINDING SITE FOR RESIDUE EDO B 304

(no "SS Bond" information available for 2IF2)

(no "Cis Peptide Bond" information available for 2IF2)

(no "SAP(SNP)/Variant" information available for 2IF2)

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_AQUAE	3-196	3	A:3-194 B:3-194 C:3-194

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_AQUAE	3-196	1	A:3-194 - -

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_AQUAE	3-196	1	- B:3-194 -

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_AQUAE	3-196	1	- - C:3-194

(no "Exon" information available for 2IF2)

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:194
 aligned with COAE_AQUAE | O67792 from UniProtKB/Swiss-Prot  Length:196

    Alignment length:194
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190    
           COAE_AQUAE     1 MKRIGLTGNIGCGKSTVAQMFRELGAYVLDADKLIHSFYRKGHPVYEEVVKTFGKGILDEEGNIDRKKLADIVFKDEEKLRKLEEITHRALYKEIEKITKNLSEDTLFILEASLLVEKGTYKNYDKLIVVYAPYEVCKERAIKRGMSEEDFERRWKKQMPIEEKVKYADYVIDNSGSIEETYKQVKKVYEELTR 194
               SCOP domains d2if2a_ A: automated matches                                                                                                                                                                       SCOP domains
               CATH domains -2if2A00 A:2-194 P-loop containing nucleotide triphosphate hydrolases                                                                                                                              CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee....hhhhhhhhhhhh..eeeehhhhhhhhhh..hhhhhhhhhhhh....ee..eehhhhhhhh...hhhhhhhhhhhhhhhhh.hhhhhhhhh.....eeee........hhhhh.eeeee..hhhhhhhhhhhh..hhhhhhhhhh...hhhhhhhhh.ee.....hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --DPCK  PDB: A:3-194 UniProt: 3-196                                                                                                                                                                PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2if2 A   1 mKRIGLTGNIGCGKSTVAQmFRELGAYVLDADKLIHSFYRKGHPVYEEVVKTFGKGILDEEGNIDRKKLADIVFKDEEKLRKLEEITHRALYKEIEKITKNLSEDTLFILEASLLVEKGTYKNYDKLIVVYAPYEVCKERAIKRGmSEEDFERRWKKQmPIEEKVKYADYVIDNSGSIEETYKQVKKVYEELTR 194
                            |       10        20        30        40        50        60        70        80        90       100       110       120       130       140     | 150       160       170       180       190    
                            |                 20-MSE                                                                                                                       146-MSE      159-MSE                               
                            1-MSE

Chain B from PDB  Type:PROTEIN  Length:194
 aligned with COAE_AQUAE | O67792 from UniProtKB/Swiss-Prot  Length:196

    Alignment length:194
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190    
           COAE_AQUAE     1 MKRIGLTGNIGCGKSTVAQMFRELGAYVLDADKLIHSFYRKGHPVYEEVVKTFGKGILDEEGNIDRKKLADIVFKDEEKLRKLEEITHRALYKEIEKITKNLSEDTLFILEASLLVEKGTYKNYDKLIVVYAPYEVCKERAIKRGMSEEDFERRWKKQMPIEEKVKYADYVIDNSGSIEETYKQVKKVYEELTR 194
               SCOP domains d2if2b_ B: automated matches                                                                                                                                                                       SCOP domains
               CATH domains -2if2B00 B:2-194 P-loop containing nucleotide triphosphate hydrolases                                                                                                                              CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee....hhhhhhhhhhhhh.eeeehhhhhhh.....hhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeee.......hhhhhh.eeeeee.hhhhhhhhhhhh..hhhhhhhhhhhh.hhhhhh....eeee...hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --DPCK  PDB: B:3-194 UniProt: 3-196                                                                                                                                                                PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2if2 B   1 mKRIGLTGNIGCGKSTVAQmFRELGAYVLDADKLIHSFYRKGHPVYEEVVKTFGKGILDEEGNIDRKKLADIVFKDEEKLRKLEEITHRALYKEIEKITKNLSEDTLFILEASLLVEKGTYKNYDKLIVVYAPYEVCKERAIKRGmSEEDFERRWKKQmPIEEKVKYADYVIDNSGSIEETYKQVKKVYEELTR 194
                            |       10        20        30        40        50        60        70        80        90       100       110       120       130       140     | 150       160       170       180       190    
                            1-MSE             20-MSE                                                                                                                       146-MSE      159-MSE

Chain C from PDB  Type:PROTEIN  Length:163
 aligned with COAE_AQUAE | O67792 from UniProtKB/Swiss-Prot  Length:196

    Alignment length:194
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190    
           COAE_AQUAE     1 MKRIGLTGNIGCGKSTVAQMFRELGAYVLDADKLIHSFYRKGHPVYEEVVKTFGKGILDEEGNIDRKKLADIVFKDEEKLRKLEEITHRALYKEIEKITKNLSEDTLFILEASLLVEKGTYKNYDKLIVVYAPYEVCKERAIKRGMSEEDFERRWKKQMPIEEKVKYADYVIDNSGSIEETYKQVKKVYEELTR 194
               SCOP domains d2if2c_ C: automated matches                                                                                                                                                                       SCOP domains
               CATH domains -2if2C00 C:2-194 P-loop containing nucleotide trip                               hosphate hydrolases                                                                                               CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee....hhhhhhhhhhhh..eeeehhhhhhh.............-------------------------------.hhhhhhhhhhhhhhhhhhhh.....eeee..hhhhhh......eeeeee.hhhhhhhhhhh....hhhhhhhhhh..hhhhhhhhh.eeee...hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --DPCK  PDB: C:3-194 UniProt: 3-196                                                                                                                                                                PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2if2 C   1 mKRIGLTGNIGCGKSTVAQmFRELGAYVLDADKLIHSFYRKGHPVYEEVV-------------------------------KLEEITHRALYKEIEKITKNLSEDTLFILEASLLVEKGTYKNYDKLIVVYAPYEVCKERAIKRGmSEEDFERRWKKQmPIEEKVKYADYVIDNSGSIEETYKQVKKVYEELTR 194
                            |       10        20        30        40        50         -         -         - |      90       100       110       120       130       140     | 150       160       170       180       190    
                            1-MSE             20-MSE                        50                              82                                                             146-MSE      159-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(

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Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

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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: automated matches (303)

Protein domain: automated matches (303)

Aquifex aeolicus [TaxId: 224324] (4)

1a	d2if2a_	A:
1b	d2if2b_	B:
1c	d2if2c_	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)

Aquifex aeolicus vf5. Organism_taxid: 224324. Strain: vf5. (1)

1a	2if2A00	A:2-194
1b	2if2B00	B:2-194
1c	2if2C00	C:2-194

(no "Pfam Domain" information available for 2IF2)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (COAE_AQUAE | O67792)

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.

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Description

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Ligands, Modified Residues, Ions (3, 16)

Sites (4, 4)

SS Bonds (0, 0)

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