2PAA - JenaLib

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Title :   CRYSTAL STRUCTURE OF PHOSPHOGLYCERATE KINASE-2 BOUND TO ATP AND 3PG

Authors :   G. M. Sawyer, A. F. Monzingo, E. C. Poteet, J. D. Robertus

Date :   27 Mar 07 (Deposition) - 27 Nov 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.70

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

Keywords :   Transferase, Phosphoglycerate Kinase, Enzyme-Ligand Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   G. M. Sawyer, A. F. Monzingo, E. C. Poteet, D. A. O'Brien, J. D. Robertus
X-Ray Analysis Of Phosphoglycerate Kinase 2, A Sperm-Specific Isoform From Mus Musculus.
Proteins V. 71 1134 2007
PubMed-ID: 18004764 | Reference-DOI: 10.1002/PROT.21801
(for further references see the PDB file header)

Molecule 1 - PHOSPHOGLYCERATE KINASE, TESTIS SPECIFIC
	Chains	:	A, B
	EC Number	:	2.7.2.3
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGK-2-PGEX4T3
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	PGK2, PGK-2
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Strain	:	C3H/HE

		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, 2)

No.	Name	Count	Type	Full Name
1	3PG	1	Ligand/Ion	3-PHOSPHOGLYCERIC ACID
2	ATP	1	Ligand/Ion	ADENOSINE-5'-TRIPHOSPHATE

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	3PG	-1	Ligand/Ion	3-PHOSPHOGLYCERIC ACID
2	ATP	1	Ligand/Ion	ADENOSINE-5'-TRIPHOSPHATE

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	3PG	1	Ligand/Ion	3-PHOSPHOGLYCERIC ACID
2	ATP	-1	Ligand/Ion	ADENOSINE-5'-TRIPHOSPHATE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:212 , GLY A:213 , ALA A:214 , LYS A:219 , GLY A:237 , GLY A:238 , LEU A:256 , GLY A:312 , LEU A:313 , ASN A:336 , GLY A:337 , PRO A:338 , GLY A:340 , VAL A:341 , GLU A:343 , GLY A:373 , ASP A:374 , THR A:375	BINDING SITE FOR RESIDUE ATP A 500
2	AC2	SOFTWARE	HIS B:62 , ARG B:122 , GLY B:166 , ARG B:170	BINDING SITE FOR RESIDUE 3PG B 501

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

Asymmetric Unit

No.	Residues
1	Arg A:205	-	Pro A:206
2	Arg B:205	-	Pro B:206

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

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PGLYCERATE_KINASE	PS00111	Phosphoglycerate kinase signature.	PGK2_MOUSE	18-28	2	A:17-27 B:17-27

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PGLYCERATE_KINASE	PS00111	Phosphoglycerate kinase signature.	PGK2_MOUSE	18-28	1	A:17-27 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PGLYCERATE_KINASE	PS00111	Phosphoglycerate kinase signature.	PGK2_MOUSE	18-28	1	- B:17-27

(no "Exon" information available for 2PAA)

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:413
 aligned with PGK2_MOUSE | P09041 from UniProtKB/Swiss-Prot  Length:417

    Alignment length:413
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414   
           PGK2_MOUSE     5 AKLTLDKVDLKGKRVIMRVDFNVPMKNNQITNNQRIKAAIPSIKHCLDNGAKSVVLMSHLGRPDGIPMPDKYSLEPVADELKSLLNKDVIFLKDCVGPEVEQACANPDNGSIILLENLRFHVEEEGKGKDSSGKKISADPAKVEAFQASLSKLGDVYVNDAFGTAHRAHSSTVGVNLPQKASGFLMKKELDYFSKALEKPERPFLAILGGAKVKDKIQLIKNMLDKVNFMIIGGGMAYTFLKELKNMQIGASLFDEEGATIVKEIMEKAEKNGVKIVFPVDFVTGDKFDENAKVGQATIESGIPSGWMGLDCGPESIKINAQIVAQAKLIVWNGPIGVFEWDAFAKGTKALMDEVVKATSNGCVTIIGGGDTATCCAKWGTEDKVSHVSTGGGASLELLEGKILPGVEALSNM 417
               SCOP domains d2paaa_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 2paaA01 A:4-188  [code=3.40.50.1260, no name defined]                                                                                                                                    ------2paaA02 A:195-403  [code=3.40.50.1270, no name defined]                                                                                                                                                          ------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhh.....eeeeee.............hhhhhhhhhhhhhhhhh...eeeee..........hhhhhhhhhhhhhhhhhhh...ee.....hhhhhhhh......eeee..hhhhhhhhhheee.....eee.hhhhhhhhhhhhhhh..eeeeehhhhh...hhhhhh.....eeehhhhhhhhhhhhhh.......eeeee.......hhhhhhhhhh...eeee..hhhhhhhhhhh...........hhhhhhhhhhhhhhhh..eee...eeeee........eeeee.........eeeeehhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhhhhhhhh..eeee..hhhhhhhhhh.......ee..hhhhhhhhhhh..hhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------PGLYCERATE_----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2paa A   4 AKLTLDKVDLKGKRVIMRVDFNVPMKNNQITNNQRIKAAIPSIKHCLDNGAKSVVLMSHLGRPDGIPMPDKYSLEPVADELKSLLNKDVIFLKDCVGPEVEQACANPDNGSIILLENLRFHVEEEGKGKDSSGKKISADPAKVEAFRASLSKLGDVYVNDAFGTAHRAHSSMVGVNLPQKASGFLMKKELDYFSKALEKPERPFLAILGGAKVKDKIQLIKNMLDKVNFMIIGGGMAYTFLKELKNMQIGASLFDEEGATIVKEIMEKAEKNGVKIVFPVDFVTGDKFDENAKVGQATIESGIPSGWMGLDCGPESIKINAQIVAQAKLIVWNGPIGVFEWDAFAKGTKALMDEVVKATSNGCVTIIGGGDTATCCAKWGTEDKVSHVSTGGGASLELLEGKILPGVEALSNM 416
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413

Chain B from PDB  Type:PROTEIN  Length:398
 aligned with PGK2_MOUSE | P09041 from UniProtKB/Swiss-Prot  Length:417

    Alignment length:413
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414   
           PGK2_MOUSE     5 AKLTLDKVDLKGKRVIMRVDFNVPMKNNQITNNQRIKAAIPSIKHCLDNGAKSVVLMSHLGRPDGIPMPDKYSLEPVADELKSLLNKDVIFLKDCVGPEVEQACANPDNGSIILLENLRFHVEEEGKGKDSSGKKISADPAKVEAFQASLSKLGDVYVNDAFGTAHRAHSSTVGVNLPQKASGFLMKKELDYFSKALEKPERPFLAILGGAKVKDKIQLIKNMLDKVNFMIIGGGMAYTFLKELKNMQIGASLFDEEGATIVKEIMEKAEKNGVKIVFPVDFVTGDKFDENAKVGQATIESGIPSGWMGLDCGPESIKINAQIVAQAKLIVWNGPIGVFEWDAFAKGTKALMDEVVKATSNGCVTIIGGGDTATCCAKWGTEDKVSHVSTGGGASLELLEGKILPGVEALSNM 417
               SCOP domains d2paab_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 2paaB01 B:4-188  [code=3.40.50.1260, no name defined]                                                                                                                                    ------2paaB02 B:195-403  [code=3.40.50.1270, no name defined]                                                                                                                                                          ------------- CATH domains
           Pfam domains (1) ---PGK-2paaB01 B:7-405                                                                                                                                                                                                                                                                                                                                                                                            ----------- Pfam domains (1)
           Pfam domains (2) ---PGK-2paaB02 B:7-405                                                                                                                                                                                                                                                                                                                                                                                            ----------- Pfam domains (2)
         Sec.struct. author ...hhhhh.....eeeee..............hhhhhhhhhhhhhhhhh...eeeee................hhhhhhhhhhhhh...ee.....hhhhhhhhhh....eeee..hhhhh.....eee.....eee.hhhhhhhhhhhhhh...eeee.hhhhh...hhhhhh.....eeehhhhhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhh.eeee...hhhhhhhhh............hhhhhhhhhhhhhhhh........eeeee........eeeee.........eeeeehhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhhhhhhhh..eeee.---------------...ee..hhhhhhhhhhh..hhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------PGLYCERATE_----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2paa B   4 AKLTLDKVDLKGKRVIMRVDFNVPMKNNQITNNQRIKAAIPSIKHCLDNGAKSVVLMSHLGRPDGIPMPDKYSLEPVADELKSLLNKDVIFLKDCVGPEVEQACANPDNGSIILLENLRFHVEEEGKGKDSSGKKISADPAKVEAFRASLSKLGDVYVNDAFGTAHRAHSSMVGVNLPQKASGFLMKKELDYFSKALEKPERPFLAILGGAKVKDKIQLIKNMLDKVNFMIIGGGMAYTFLKELKNMQIGASLFDEEGATIVKEIMEKAEKNGVKIVFPVDFVTGDKFDENAKVGQATIESGIPSGWMGLDCGPESIKINAQIVAQAKLIVWNGPIGVFEWDAFAKGTKALMDEVVKATSNGCVTIIG---------------KVSHVSTGGGASLELLEGKILPGVEALSNM 416
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       | -         -   |   393       403       413   
                                                                                                                                                                                                                                                                                                                                                                                                         371             387

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: automated matches (23)

Mouse (Mus musculus) [TaxId: 10090] (3)

1a	d2paaa_	A:
1b	d2paab_	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)

House mouse (Mus musculus) (3)

1a	2paaA01	A:4-188
1b	2paaB01	B:4-188

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

House mouse (Mus musculus) (3)

2a	2paaA02	A:195-403
2b	2paaB02	B:195-403

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: PGK] (23)

Family: PGK (23)

Mus musculus (Mouse) (2)

1a	PGK-2paaB01	B:7-405
1b	PGK-2paaB02	B:7-405

Asymmetric Unit(hide GO term definitions)

Chain A,B (PGK2_MOUSE | P09041)

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:0030317	flagellated sperm motility	Any process involved in the controlled movement of a flagellated sperm cell.
	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.
	GO:0098779	positive regulation of macromitophagy in response to mitochondrial depolarization	The macromitophagy process that is triggered by a detection of the loss of mitochondrial membrane potential.
cellular component
	GO:0005929	cilium	A specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface and of some cytoplasmic parts. Each cilium is largely bounded by an extrusion of the cytoplasmic (plasma) membrane, and contains a regular longitudinal array of microtubules, anchored to a basal body.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
	GO:0035686	sperm fibrous sheath	A cytoskeletal structure surrounding the axoneme and outer dense fibers of the sperm flagellum. Consists of two longitudinal columns connected by closely arrayed semicircular ribs that assemble from distal to proximal throughout spermiogenesis. The fibrous sheath probably influences the degree of flexibility, plane of flagellar motion, and the shape of the flagellar beat.

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	2paa
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	2.7.2.3
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	PGK2_MOUSE \| P09041	:	2p9q 2p9t

2p9q	APO PHOSPHOGLYCERATE KINASE-2
2p9t	PHOSPHOGLYCERATE KINASE-2 BOUND TO 3PG

Description

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Ligands, Modified Residues, Ions (2, 2)

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