2Q5R - JenaLib

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Title :   STRUCTURE OF APO STAPHYLOCOCCUS AUREUS D-TAGATOSE-6-PHOSPHATE KINASE

Authors :   T. E. Mcgrath, M. Soloveychik, V. Romanov, D. Thambipillai, A. Dharams C. Virag, M. Domagala, E. F. Pai, A. M. Edwards, K. Battaile, N. Y. Chirg

Date :   01 Jun 07 (Deposition) - 12 Jun 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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

Keywords :   Transferase, D-Tagatose-6-Phosphate Kinase, Phosphoryl Transfer, Conformational Change, Kinase, Lactose Metabolism (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. E. Mcgrath, M. Soloveychik, V. Romanov, D. Thambipillai, A. Dharamsi, C. Virag, M. Domagala, E. F. Pai, A. M. Edwards, K. Battaile, N. Y. Chirgadze
Structure Of Apo Staphylococcus Aureus D-Tagatose-6-Phosphate Kinase
To Be Published
PubMed: search

Molecule 1 - TAGATOSE-6-PHOSPHATE KINASE
	Chains	:	A, B, C, D
	EC Number	:	2.7.1.144
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET15B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	LACC
	Organism Scientific	:	STAPHYLOCOCCUS AUREUS
	Organism Taxid	:	1280
	Strain	:	COLA
	Synonym	:	PHOSPHOTAGATOKINASE

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 8)

No.	Name	Count	Type	Full Name
1	MSE	8	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (1, 4)

No.	Name	Count	Type	Full Name
1	MSE	4	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (1, 4)

No.	Name	Count	Type	Full Name
1	MSE	4	Mod. Amino Acid	SELENOMETHIONINE

(no "Site" information available for 2Q5R)

(no "SS Bond" information available for 2Q5R)

(no "Cis Peptide Bond" information available for 2Q5R)

(no "SAP(SNP)/Variant" information available for 2Q5R)

Asymmetric Unit (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PFKB_KINASES_1	PS00583	pfkB family of carbohydrate kinases signature 1.	LACC_STAAC	36-60	4	A:36-60 B:36-60 C:36-60 D:36-60
2	PFKB_KINASES_2	PS00584	pfkB family of carbohydrate kinases signature 2.	LACC_STAAC	248-261	4	A:248-261 B:248-261 C:249-261 D:249-261

Biological Unit 1 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PFKB_KINASES_1	PS00583	pfkB family of carbohydrate kinases signature 1.	LACC_STAAC	36-60	2	A:36-60 B:36-60 - -
2	PFKB_KINASES_2	PS00584	pfkB family of carbohydrate kinases signature 2.	LACC_STAAC	248-261	2	A:248-261 B:248-261 - -

Biological Unit 2 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PFKB_KINASES_1	PS00583	pfkB family of carbohydrate kinases signature 1.	LACC_STAAC	36-60	2	- - C:36-60 D:36-60
2	PFKB_KINASES_2	PS00584	pfkB family of carbohydrate kinases signature 2.	LACC_STAAC	248-261	2	- - C:249-261 D:249-261

(no "Exon" information available for 2Q5R)

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:318
 aligned with LACC_STAAC | Q5HE12 from UniProtKB/Swiss-Prot  Length:310

    Alignment length:318
                                    1                                                                                                                                                                                                                                                                                                                     
                                    |2        12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302        
           LACC_STAAC     - --------MILTLTLNPSVDISYPLTALKLDDVNRVQEVSKTAGGKGLNVTRVLAQVGEPVLASGFIGGELGQFIAKKLDHADIKHAFYNIKGETRNCIAILHEGQQTEILEQGPEIDNQEAAGFIKHFEQLLEKVEAVAISGSLPKGLNQDYYAQIIERCQNKGVPVILDCSGATLQTVLENPYKPTVIKPNISELYQLLNQPLDESLESLKQAVSQPLFEGIEWIIVSLGAQGAFAKHNHTFYRVNIPTISVLNPVGSGDSTVAGITSAILNHENDHDLLKKANTLGMLNAQEAQTGYVNLNNYDDLFNQIEVLEV 310
               SCOP domains d2q5ra_ A: automated matches                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........eeeee...eeeeeeee.......eeee...eeeeehhhhhhhhhhhhhh..eeeeeeehhhhhhhhhhhhhhh......ee.....eeeeeeee..eeeeeee.....hhhhhhhhhhhhhhhhh...eeeee.........hhhhhhhhhhhhhh..eeee.hhhhhhhhhhh.....ee..hhhhhhhhhh.....hhhhhhhhhhhhhhh...eeeee.....eeeee..eeeeee..........hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.......hhhhhhhhhh..eeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------PFKB_KINASES_1           -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PFKB_KINASES_2------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2q5r A  -7 GLVPRGSHmILTLTLNPSVDISYPLTALKLDDVNRVQEVSKTAGGKGLNVTRVLAQVGEPVLASGFIGGELGQFIAKKLDHADIKHAFYNIKGETRNCIAILHEGQQTEILEQGPEIDNQEAAGFIKHFEQLLEKVEAVAISGSLPKGLNQDYYAQIIERCQNKGVPVILDCSGATLQTVLENPYKPTVIKPNISELYQLLNQPLDESLESLKQAVSQPLFEGIEWIIVSLGAQGAFAKHNHTFYRVNIPTISVLNPVGSGDSTVAGITSAILNHENDHDLLKKANTLGmLNAQEAQTGYVNLNNYDDLFNQIEVLEV 310
                                    |2        12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302        
                                    1-MSE                                                                                                                                                                                                                                                                                  282-MSE

Chain B from PDB  Type:PROTEIN  Length:312
 aligned with LACC_STAAC | Q5HE12 from UniProtKB/Swiss-Prot  Length:310

    Alignment length:312
                              1                                                                                                                                                                                                                                                                                                                     
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308  
           LACC_STAAC     - --MILTLTLNPSVDISYPLTALKLDDVNRVQEVSKTAGGKGLNVTRVLAQVGEPVLASGFIGGELGQFIAKKLDHADIKHAFYNIKGETRNCIAILHEGQQTEILEQGPEIDNQEAAGFIKHFEQLLEKVEAVAISGSLPKGLNQDYYAQIIERCQNKGVPVILDCSGATLQTVLENPYKPTVIKPNISELYQLLNQPLDESLESLKQAVSQPLFEGIEWIIVSLGAQGAFAKHNHTFYRVNIPTISVLNPVGSGDSTVAGITSAILNHENDHDLLKKANTLGMLNAQEAQTGYVNLNNYDDLFNQIEVLEV 310
               SCOP domains d2q5rb_ B: automated matches                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeee...eeeeeeee.......eeee...eeeeehhhhhhhhhhhhhh..eeeeeeeehhhhhhhhhhhhhh..ee..eee....eeeeeeee..eeeeeee.....hhhhhhhhhhhhhhhhhhh.eeeee.........hhhhhhhhhhhhh...eeee.hhhhhhhhhh......ee..hhhhhhhhh......hhhhhhhhhhhhhhh...eeeee....eeeeee..eeeeee..........hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh..........hhhhhhhh.eeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------PFKB_KINASES_1           -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PFKB_KINASES_2------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2q5r B  -1 SHmILTLTLNPSVDISYPLTALKLDDVNRVQEVSKTAGGKGLNVTRVLAQVGEPVLASGFIGGELGQFIAKKLDHADIKHAFYNIKGETRNCIAILHEGQQTEILEQGPEIDNQEAAGFIKHFEQLLEKVEAVAISGSLPKGLNQDYYAQIIERCQNKGVPVILDCSGATLQTVLENPYKPTVIKPNISELYQLLNQPLDESLESLKQAVSQPLFEGIEWIIVSLGAQGAFAKHNHTFYRVNIPTISVLNPVGSGDSTVAGITSAILNHENDHDLLKKANTLGmLNAQEAQTGYVNLNNYDDLFNQIEVLEV 310
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278   |   288       298       308  
                              1-MSE                                                                                                                                                                                                                                                                                  282-MSE

Chain C from PDB  Type:PROTEIN  Length:303
 aligned with LACC_STAAC | Q5HE12 from UniProtKB/Swiss-Prot  Length:310

    Alignment length:311
                             1                                                                                                                                                                                                                                                                                                                     
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309 
           LACC_STAAC     - -MILTLTLNPSVDISYPLTALKLDDVNRVQEVSKTAGGKGLNVTRVLAQVGEPVLASGFIGGELGQFIAKKLDHADIKHAFYNIKGETRNCIAILHEGQQTEILEQGPEIDNQEAAGFIKHFEQLLEKVEAVAISGSLPKGLNQDYYAQIIERCQNKGVPVILDCSGATLQTVLENPYKPTVIKPNISELYQLLNQPLDESLESLKQAVSQPLFEGIEWIIVSLGAQGAFAKHNHTFYRVNIPTISVLNPVGSGDSTVAGITSAILNHENDHDLLKKANTLGMLNAQEAQTGYVNLNNYDDLFNQIEVLEV 310
               SCOP domains d2q5rc_ C: automated matches                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...eeeeeeee.......eeee...eeeeehhhhhhhhhhhhhh..eeeeeeehhhhhhhhhhhhhhh..ee..ee.....eeeeeeee..eeeeeee.....hhhhhhhhhhhhhhhhh...eeeee.........hhhhhhhhhhhhh...eeee.hhhhhhhhhhh.....ee..hhhhhhhh.......hhhhhhhhhhhhhhh...eeeee....eeeeee..eeeeee....----..hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh----....hhhhhhhhhh..eeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------PFKB_KINASES_1           -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PFKB_KINASES_2------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2q5r C   0 HmILTLTLNPSVDISYPLTALKLDDVNRVQEVSKTAGGKGLNVTRVLAQVGEPVLASGFIGGELGQFIAKKLDHADIKHAFYNIKGETRNCIAILHEGQQTEILEQGPEIDNQEAAGFIKHFEQLLEKVEAVAISGSLPKGLNQDYYAQIIERCQNKGVPVILDCSGATLQTVLENPYKPTVIKPNISELYQLLNQPLDESLESLKQAVSQPLFEGIEWIIVSLGAQGAFAKHNHTFYRVNIPTI----PVGSGDSTVAGITSAILNHENDHDLLKKANTLGmLNA----TGYVNLNNYDDLFNQIEVLEV 310
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239    |  249       259       269       279  |  |   -|      299       309 
                             1-MSE                                                                                                                                                                                                                                            244  249                              282-MSE 290                    
                                                                                                                                                                                                                                                                                                                       285

Chain D from PDB  Type:PROTEIN  Length:310
 aligned with LACC_STAAC | Q5HE12 from UniProtKB/Swiss-Prot  Length:310

    Alignment length:318
                                    1                                                                                                                                                                                                                                                                                                                     
                                    |2        12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302        
           LACC_STAAC     - --------MILTLTLNPSVDISYPLTALKLDDVNRVQEVSKTAGGKGLNVTRVLAQVGEPVLASGFIGGELGQFIAKKLDHADIKHAFYNIKGETRNCIAILHEGQQTEILEQGPEIDNQEAAGFIKHFEQLLEKVEAVAISGSLPKGLNQDYYAQIIERCQNKGVPVILDCSGATLQTVLENPYKPTVIKPNISELYQLLNQPLDESLESLKQAVSQPLFEGIEWIIVSLGAQGAFAKHNHTFYRVNIPTISVLNPVGSGDSTVAGITSAILNHENDHDLLKKANTLGMLNAQEAQTGYVNLNNYDDLFNQIEVLEV 310
               SCOP domains d2q5rd_ D: automated matches                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........eeeee...eeeeeeee.......eeee...eeeeehhhhhhhhhhhhhh..eeeeeeeehhhhhhhhhhhhhh......eee....eeeeeeee..eeeeeee.....hhhhhhhhhhhhhhhhhhh.eeeee.........hhhhhhhhhhhhh...eeee.hhhhhhhhhhh.....ee..hhhhhhhhh......hhhhhhhhhhhhhhh...eeeee.hhh.eeeee..eeeeee...-----..hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh..---..hhhhhhhhhh..eeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------PFKB_KINASES_1           -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PFKB_KINASES_2------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2q5r D  -7 GLVPRGSHmILTLTLNPSVDISYPLTALKLDDVNRVQEVSKTAGGKGLNVTRVLAQVGEPVLASGFIGGELGQFIAKKLDHADIKHAFYNIKGETRNCIAILHEGQQTEILEQGPEIDNQEAAGFIKHFEQLLEKVEAVAISGSLPKGLNQDYYAQIIERCQNKGVPVILDCSGATLQTVLENPYKPTVIKPNISELYQLLNQPLDESLESLKQAVSQPLFEGIEWIIVSLGAQGAFAKHNHTFYRVNIPT-----PVGSGDSTVAGITSAILNHENDHDLLKKANTLGmLNAQEA---YVNLNNYDDLFNQIEVLEV 310
                                    |2        12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242|     |252       262       272       282     | 292       302        
                                    1-MSE                                                                                                                                                                                                                                           243   249                              282-MSE88 292

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: Ribokinase-like (226)

Superfamily: Ribokinase-like (189)

Family: automated matches (88)

Protein domain: automated matches (88)

Staphylococcus aureus [TaxId: 1280] (3)

1a	d2q5ra_	A:
1b	d2q5rb_	B:
1c	d2q5rc_	C:
1d	d2q5rd_	D:

(no "CATH Domain" information available for 2Q5R)

(no "Pfam Domain" information available for 2Q5R)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (LACC_STAAC | Q5HE12)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	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:0016773	phosphotransferase activity, alcohol group as acceptor	Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to an alcohol group (acceptor).
	GO:0009024	tagatose-6-phosphate kinase activity	Catalysis of the reaction: ATP + D-tagatose 6-phosphate = ADP + D-tagatose 1,6-bisphosphate.
	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:2001059	D-tagatose 6-phosphate catabolic process	The chemical reactions and pathways resulting in the breakdown of a D-tagatose 6-phosphate.
	GO:0005975	carbohydrate metabolic process	The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
	GO:0019512	lactose catabolic process via tagatose-6-phosphate	The chemical reactions and pathways resulting in the breakdown of lactose, via the intermediate tagatose-6-phosphate.
	GO:0005988	lactose metabolic process	The chemical reactions and pathways involving lactose, the disaccharide galactopyranosyl-glucose.
	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.

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2jg1	STRUCTURE OF STAPHYLOCOCCUS AUREUS D-TAGATOSE-6-PHOSPHATE KINASE WITH COFACTOR AND SUBSTRATE
2jgv	STRUCTURE OF STAPHYLOCOCCUS AUREUS D-TAGATOSE-6-PHOSPHATE KINASE IN COMPLEX WITH ADP

Description

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Ligands, Modified Residues, Ions (1, 8)

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