1V6S - JenaLib

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Title :   CRYSTAL STRUCTURE OF PHOSPHOGLYCERATE KINASE FROM THERMUS THERMOPHILUS HB8

Authors :   H. Mizutani, N. Kunishima, Riken Structural Genomics/Proteomics Initiative (Rsgi)

Date :   04 Dec 03 (Deposition) - 23 Dec 03 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.50

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

Keywords :   Phosphoglycerate Kinase, Thermus Thermophilus, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Mizutani, N. Kunishima
Crystal Structure Of Phosphoglycerate Kinase From Thermus Thermophilus Hb8
To Be Published
PubMed: search

Molecule 1 - PHOSPHOGLYCERATE KINASE
	Chains	:	A, B
	EC Number	:	2.7.2.3
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET11A
	Expression System Strain	:	BL21 (DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	THERMUS THERMOPHILUS
	Organism Taxid	:	274

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 7)

No.	Name	Count	Type	Full Name
1	GOL	4	Ligand/Ion	GLYCEROL
2	NA	3	Ligand/Ion	SODIUM ION

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL
2	NA	-1	Ligand/Ion	SODIUM ION

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL
2	NA	-1	Ligand/Ion	SODIUM ION

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:204 , GLU A:378 , HOH A:1569 , HOH A:1755 , HOH A:1756 , HOH A:1757	BINDING SITE FOR RESIDUE NA A 1405
2	AC2	SOFTWARE	SER B:204 , GLU B:378 , HOH B:1595 , HOH B:1717 , HOH B:1718 , HOH B:1748	BINDING SITE FOR RESIDUE NA B 1406
3	AC3	SOFTWARE	HOH B:1484 , HOH B:1496 , HOH B:1545 , HOH B:1547 , HOH B:1668 , HOH B:1746	BINDING SITE FOR RESIDUE NA B 1407
4	AC4	SOFTWARE	GLU A:126 , ARG A:130 , HOH A:1435 , HOH A:1506 , GLY B:92 , SER B:93 , GLU B:117 , ARG B:130	BINDING SITE FOR RESIDUE GOL A 1401
5	AC5	SOFTWARE	ARG A:60 , TYR A:68 , GLY A:227 , ARG A:281 , HOH A:1530	BINDING SITE FOR RESIDUE GOL A 1402
6	AC6	SOFTWARE	GLY A:92 , SER A:93 , GLU A:117 , ARG A:130 , GLU B:126 , ARG B:130 , HOH B:1472 , HOH B:1488	BINDING SITE FOR RESIDUE GOL B 1403
7	AC7	SOFTWARE	ARG B:60 , PRO B:61 , TYR B:68 , GLY B:227 , ARG B:281 , HOH B:1448 , HOH B:1486	BINDING SITE FOR RESIDUE GOL B 1404

(no "SS Bond" information available for 1V6S)

Asymmetric Unit

No.	Residues
1	Arg A:184	-	Pro A:185
2	Val A:285	-	Pro A:286
3	Pro A:322	-	Pro A:323
4	Arg B:184	-	Pro B:185
5	Val B:285	-	Pro B:286
6	Pro B:322	-	Pro B:323

(no "SAP(SNP)/Variant" information available for 1V6S)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PGLYCERATE_KINASE	PS00111	Phosphoglycerate kinase signature.	PGK_THET8	13-23	2	A:13-23 B:13-23

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PGLYCERATE_KINASE	PS00111	Phosphoglycerate kinase signature.	PGK_THET8	13-23	1	A:13-23 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PGLYCERATE_KINASE	PS00111	Phosphoglycerate kinase signature.	PGK_THET8	13-23	1	- B:13-23

(no "Exon" information available for 1V6S)

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:390
 aligned with PGK_THET8 | P09403 from UniProtKB/Swiss-Prot  Length:390

    Alignment length:390
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390
            PGK_THET8     1 MRTLLDLDPKGKRVLVRVDYNVPVQDGKVQDETRILESLPTLRHLLAGGASLVLLSHLGRPKGPDPKYSLAPVGEALRAHLPEARFAPFPPGSEEARREAEALRPGEVLLLENVRFEPGEEKNDPELSARYARLGEAFVLDAFGSAHRAHASVVGVARLLPAYAGFLMEKEVRALSRLLKDPERPYAVVLGGAKVSDKIGVIESLLPRIDRLLIGGAMAFTFLKALGGEVGRSLVEEDRLDLAKDLLGRAEALGVRVYLPEDVVAAERIEAGVETRVFPARAIPVPYMGLDIGPKTREAFARALEGARTVFWNGPMGVFEVPPFDEGTLAVGQAIAALEGAFTVVGGGDSVAAVNRLGLKERFGHVSTGGGASLEFLEKGTLPGLEVLEG 390
               SCOP domains d1v6sa_ A: Phosphoglycerate kinase                                                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 1v6sA01 A:1-177  [code=3.40.50.1260, no name defined]                                                                                                                            1v6sA02 A:178-390  [code=3.40.50.1270, no name defined]                                                                                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhh.....eeeee......ee..ee..hhhhhhhhhhhhhhhhh..eeeee.........hhhhhhhhhhhhhhhhh..eee......hhhhhhhhhh.....eee..hhhhh......hhhhhhhhhhhh.eeee.hhhhh........hhhhh..eeehhhhhhhhhhhhh........eeeee...hhhhhhhhhhhhhhhh.eeee...hhhhhhhhh.........hhhhhhhhhhhhhhhhhhh.eee...eeeee.........eeee........eeeeehhhhhhhhhhhh....eeeee...........hhhhhhhhhhhhh....eeeeehhhhhhhhhh..hhhhh.ee....hhhhhhhhhh.hhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------PGLYCERATE_------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1v6s A   1 MRTLLDLDPKGKRVLVRVDYNVPVQDGKVQDETRILESLPTLRHLLAGGASLVLLSHLGRPKGPDPKYSLAPVGEALRAHLPEARFAPFPPGSEEARREAEALRPGEVLLLENVRFEPGEEKNDPELSARYARLGEAFVLDAFGSAHRAHASVVGVARLLPAYAGFLMEKEVRALSRLLKDPERPYAVVLGGAKVSDKIGVIESLLPRIDRLLIGGAMAFTFLKALGGEVGRSLVEEDRLDLAKDLLGRAEALGVRVYLPEDVVAAERIEAGVETRVFPARAIPVPYMGLDIGPKTREAFARALEGARTVFWNGPMGVFEVPPFDEGTLAVGQAIAALEGAFTVVGGGDSVAAVNRLGLKERFGHVSTGGGASLEFLEKGTLPGLEVLEG 390
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390

Chain B from PDB  Type:PROTEIN  Length:390
 aligned with PGK_THET8 | P09403 from UniProtKB/Swiss-Prot  Length:390

    Alignment length:390
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390
            PGK_THET8     1 MRTLLDLDPKGKRVLVRVDYNVPVQDGKVQDETRILESLPTLRHLLAGGASLVLLSHLGRPKGPDPKYSLAPVGEALRAHLPEARFAPFPPGSEEARREAEALRPGEVLLLENVRFEPGEEKNDPELSARYARLGEAFVLDAFGSAHRAHASVVGVARLLPAYAGFLMEKEVRALSRLLKDPERPYAVVLGGAKVSDKIGVIESLLPRIDRLLIGGAMAFTFLKALGGEVGRSLVEEDRLDLAKDLLGRAEALGVRVYLPEDVVAAERIEAGVETRVFPARAIPVPYMGLDIGPKTREAFARALEGARTVFWNGPMGVFEVPPFDEGTLAVGQAIAALEGAFTVVGGGDSVAAVNRLGLKERFGHVSTGGGASLEFLEKGTLPGLEVLEG 390
               SCOP domains d1v6sb_ B: Phosphoglycerate kinase                                                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 1v6sB01 B:1-177  [code=3.40.50.1260, no name defined]                                                                                                                            1v6sB02 B:178-390  [code=3.40.50.1270, no name defined]                                                                                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhh.....eeeee......ee..ee..hhhhhhhhhhhhhhhhh..eeeee.........hhhhhhhhhhhhhhh....eee......hhhhhhhhhh.....eee..hhhhh......hhhhhhhhhhhh.eeee.hhhhh........hhhhh..eeehhhhhhhhhhhhhh.......eeeee...hhhhhhhhhhhhhhhh.eeee..hhhhhhhhhh.........hhhhhhhhhhhhhhhhhh..eee...eeeee.........eeee........eeeeehhhhhhhhhhhhh...eeeee...........hhhhhhhhhhhhhh...eeeeehhhhhhhhhhh.hhhhh.ee.....hhhhhhhhh.hhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------PGLYCERATE_------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1v6s B   1 MRTLLDLDPKGKRVLVRVDYNVPVQDGKVQDETRILESLPTLRHLLAGGASLVLLSHLGRPKGPDPKYSLAPVGEALRAHLPEARFAPFPPGSEEARREAEALRPGEVLLLENVRFEPGEEKNDPELSARYARLGEAFVLDAFGSAHRAHASVVGVARLLPAYAGFLMEKEVRALSRLLKDPERPYAVVLGGAKVSDKIGVIESLLPRIDRLLIGGAMAFTFLKALGGEVGRSLVEEDRLDLAKDLLGRAEALGVRVYLPEDVVAAERIEAGVETRVFPARAIPVPYMGLDIGPKTREAFARALEGARTVFWNGPMGVFEVPPFDEGTLAVGQAIAALEGAFTVVGGGDSVAAVNRLGLKERFGHVSTGGGASLEFLEKGTLPGLEVLEG 390
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390

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( (-)

)

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

Fold: Phosphoglycerate kinase (42)

Superfamily: Phosphoglycerate kinase (42)

Family: Phosphoglycerate kinase (39)

Protein domain: Phosphoglycerate kinase (16)

Thermus thermophilus [TaxId: 274] (1)

1a	d1v6sa_	A:
1b	d1v6sb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

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

Topology: Rossmann fold (7312)

Homologous Superfamily: [code=3.40.50.1260, no name defined] (25)

Thermus thermophilus. Organism_taxid: 274. (1)

1a	1v6sA01	A:1-177
1b	1v6sB01	B:1-177

Homologous Superfamily: [code=3.40.50.1270, no name defined] (25)

Thermus thermophilus. Organism_taxid: 274. (1)

2a	1v6sA02	A:178-390
2b	1v6sB02	B:178-390

(no "Pfam Domain" information available for 1V6S)

Asymmetric Unit(hide GO term definitions)

Chain A,B (PGK_THET8 | P09403)

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:0004618	phosphoglycerate kinase activity	Catalysis of the reaction: 3-phospho-D-glycerate + ATP = 3-phospho-D-glyceroyl phosphate + ADP + H(+).
	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:0006096	glycolytic process	The chemical reactions and pathways resulting in the breakdown of a carbohydrate into pyruvate, with the concomitant production of a small amount of ATP and the reduction of NAD(P) to NAD(P)H. Glycolysis begins with the metabolism of a carbohydrate to generate products that can enter the pathway and ends with the production of pyruvate. Pyruvate may be converted to acetyl-coenzyme A, ethanol, lactate, or other small molecules.
	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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	Cis Peptide Bonds
		Arg A:184 - Pro A:185	[ RasMol ]
		Arg B:184 - Pro B:185	[ RasMol ]
		Pro A:322 - Pro A:323	[ RasMol ]
		Pro B:322 - Pro B:323	[ RasMol ]
		Val A:285 - Pro A:286	[ RasMol ]
		Val B:285 - Pro B:286	[ RasMol ]

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