2P9Q - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF PHOSPHOGLYCERATE KINASE-2

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

Date :   26 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 (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)

(no "Ligand,Modified Residues,Ions" information available for 2P9Q)

(no "Site" information available for 2P9Q)

(no "SS Bond" information available for 2P9Q)

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 2P9Q)

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 2P9Q)

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:404
 aligned with PGK2_MOUSE | P09041 from UniProtKB/Swiss-Prot  Length:417

    Alignment length:416
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411      
           PGK2_MOUSE     2 ALSAKLTLDKVDLKGKRVIMRVDFNVPMKNNQITNNQRIKAAIPSIKHCLDNGAKSVVLMSHLGRPDGIPMPDKYSLEPVADELKSLLNKDVIFLKDCVGPEVEQACANPDNGSIILLENLRFHVEEEGKGKDSSGKKISADPAKVEAFQASLSKLGDVYVNDAFGTAHRAHSSTVGVNLPQKASGFLMKKELDYFSKALEKPERPFLAILGGAKVKDKIQLIKNMLDKVNFMIIGGGMAYTFLKELKNMQIGASLFDEEGATIVKEIMEKAEKNGVKIVFPVDFVTGDKFDENAKVGQATIESGIPSGWMGLDCGPESIKINAQIVAQAKLIVWNGPIGVFEWDAFAKGTKALMDEVVKATSNGCVTIIGGGDTATCCAKWGTEDKVSHVSTGGGASLELLEGKILPGVEALSNM 417
               SCOP domains d2p9qa_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains --2p9qA01 A:3-188  [code=3.40.50.1260, no name defined]                                                                                                                                     ------2p9qA02 A:195-403  [code=3.40.50.1270, no name defined]                                                                                                                                                          ------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhh......eeee..............hhhhhhhhhhhhhhhhh...eeeee................hhhhhhhhhhhhh..eee....hhhhhhhhh......eeee..hhhhhhhhhheee.....eee...hhhhhhhhhhhhh..eeee.hhhhh...hhhhhh.....eeehhhhhhhhhhhhhhh......eeeee.......hhhhhhhhh....eeee..hhhhhhhhhhh...........hhhhhhhhhhhhhhhhh.eee...eeeee........eeeee.........eeeeehhhhhhhhhhhhhh..eeeee...........hhhhhhhhhhhhhhhhh..eeee..------------.....ee..hhhhhhhhhh...hhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------PGLYCERATE_----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2p9q A   1 ALSAKLTLDKVDLKGKRVIMRVDFNVPMKNNQITNNQRIKAAIPSIKHCLDNGAKSVVLMSHLGRPDGIPMPDKYSLEPVADELKSLLNKDVIFLKDCVGPEVEQACANPDNGSIILLENLRFHVEEEGKGKDSSGKKISADPAKVEAFRASLSKLGDVYVNDAFGTAHRAHSSMVGVNLPQKASGFLMKKELDYFSKALEKPERPFLAILGGAKVKDKIQLIKNMLDKVNFMIIGGGMAYTFLKELKNMQIGASLFDEEGATIVKEIMEKAEKNGVKIVFPVDFVTGDKFDENAKVGQATIESGIPSGWMGLDCGPESIKINAQIVAQAKLIVWNGPIGVFEWDAFAKGTKALMDEVVKATSNGCVTIIGG------------EDKVSHVSTGGGASLELLEGKILPGVEALSNM 416
                                    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 |       -    |  390       400       410      
                                                                                                                                                                                                                                                                                                                                                                                                             372          385

Chain B from PDB  Type:PROTEIN  Length:403
 aligned with PGK2_MOUSE | P09041 from UniProtKB/Swiss-Prot  Length:417

    Alignment length:416
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411      
           PGK2_MOUSE     2 ALSAKLTLDKVDLKGKRVIMRVDFNVPMKNNQITNNQRIKAAIPSIKHCLDNGAKSVVLMSHLGRPDGIPMPDKYSLEPVADELKSLLNKDVIFLKDCVGPEVEQACANPDNGSIILLENLRFHVEEEGKGKDSSGKKISADPAKVEAFQASLSKLGDVYVNDAFGTAHRAHSSTVGVNLPQKASGFLMKKELDYFSKALEKPERPFLAILGGAKVKDKIQLIKNMLDKVNFMIIGGGMAYTFLKELKNMQIGASLFDEEGATIVKEIMEKAEKNGVKIVFPVDFVTGDKFDENAKVGQATIESGIPSGWMGLDCGPESIKINAQIVAQAKLIVWNGPIGVFEWDAFAKGTKALMDEVVKATSNGCVTIIGGGDTATCCAKWGTEDKVSHVSTGGGASLELLEGKILPGVEALSNM 417
               SCOP domains d2p9qb_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains --2p9qB01 B:3-188  [code=3.40.50.1260, no name defined]                                                                                                                                     ------2p9qB02 B:195-403  [code=3.40.50.1270, no name defined]                                                                                                                                                          ------------- CATH domains
           Pfam domains (1) ------PGK-2p9qB01 B:7-405                                                                                                                                                                                                                                                                                                                                                                                            ----------- Pfam domains (1)
           Pfam domains (2) ------PGK-2p9qB02 B:7-405                                                                                                                                                                                                                                                                                                                                                                                            ----------- Pfam domains (2)
         Sec.struct. author hhhhh.hhhhh....eeeeee..............hhhhhhhhhhhhhhhh..eeeeeee................hhhhhhhhhhh.....eee....hhhhhhhhhh......eee.hhhhh...................hhhhhhhhhhhh...eeee.hhhhh...hhhhhh.....eeehhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhh....eeee..hhhhhhhhhhh...........hhhhhhhhhhhhhhhh..eee...eeeee........eeeee.........eeeeehhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhhhhhhhh..eeee.-------------.....ee..hhhhhhhhhh...hhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------PGLYCERATE_----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2p9q B   1 ALSAKLTLDKVDLKGKRVIMRVDFNVPMKNNQITNNQRIKAAIPSIKHCLDNGAKSVVLMSHLGRPDGIPMPDKYSLEPVADELKSLLNKDVIFLKDCVGPEVEQACANPDNGSIILLENLRFHVEEEGKGKDSSGKKISADPAKVEAFRASLSKLGDVYVNDAFGTAHRAHSSMVGVNLPQKASGFLMKKELDYFSKALEKPERPFLAILGGAKVKDKIQLIKNMLDKVNFMIIGGGMAYTFLKELKNMQIGASLFDEEGATIVKEIMEKAEKNGVKIVFPVDFVTGDKFDENAKVGQATIESGIPSGWMGLDCGPESIKINAQIVAQAKLIVWNGPIGVFEWDAFAKGTKALMDEVVKATSNGCVTIIG-------------EDKVSHVSTGGGASLELLEGKILPGVEALSNM 416
                                    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|        -    |  390       400       410      
                                                                                                                                                                                                                                                                                                                                                                                                            371           385

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: Phosphoglycerate kinase (42)

Superfamily: Phosphoglycerate kinase (42)

Family: Phosphoglycerate kinase (39)

Protein domain: automated matches (23)

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

1a	d2p9qa_	A:
1b	d2p9qb_	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	2p9qA01	A:3-188
1b	2p9qB01	B:3-188

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

House mouse (Mus musculus) (3)

2a	2p9qA02	A:195-403
2b	2p9qB02	B:195-403

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

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

Family: PGK (23)

Mus musculus (Mouse) (2)

1a	PGK-2p9qB01	B:7-405
1b	PGK-2p9qB02	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.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 2p9q)

	Sites
(no "Sites" information available for 2p9q)

	Cis Peptide Bonds
		Arg A:205 - Pro A:206	[ RasMol ]
		Arg B:205 - Pro B:206	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

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

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

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SCOP Domains (1, 2)

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