2WZB - JenaLib

Title :   THE CATALYTICALLY ACTIVE FULLY CLOSED CONFORMATION OF HUMAN PHOSPHOGLYCERATE KINASE IN COMPLEX WITH ADP, 3PG AND MAGNESIUM TRIFLUORIDE

Authors :   M. W. Bowler, M. J. Cliff, J. P. M. Marston, N. J. Baxter, A. M. H. Hownslow A. V. Varga, J. Szabo, M. Vas, G. M. Blackburn, J. P. Waltho

Date :   27 Nov 09 (Deposition) - 14 Apr 10 (Release) - 07 Dec 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.47

Chains :   Asym./Biol. Unit : A

Keywords :   Hereditary Hemolytic Anemia, Transferase, Phosphoprotein, Kinase, Glycolysis, Nucleotide-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. J. Cliff, M. W. Bowler, J. Szabo, J. P. M. Marston, A. V. Varga, A. M. H. Hownslow, N. J. Baxter, G. M. Blackburn, M. Vas, J. P. Waltho
Transition State Analogue Structures Of Human Phosphoglycerate Kinase Establish The Importance Of Charge Balance In Catalysis.
J. Am. Chem. Soc. V. 132 6507 2010
PubMed-ID: 20397725 | Reference-DOI: 10.1021/JA100974T

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 5)

Sites (5, 5)

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:374 , ADP A:1419 , MGF A:1421 , HOH A:2608 , HOH A:2614	BINDING SITE FOR RESIDUE MG A1417
2	AC2	SOFTWARE	ARG A:65 , LYS A:215 , ASP A:218 , HOH A:2362	BINDING SITE FOR RESIDUE CL A1418
3	AC3	SOFTWARE	GLY A:213 , ALA A:214 , LYS A:215 , LYS A:219 , GLY A:237 , GLY A:238 , LEU A:256 , GLY A:312 , ASN A:336 , PRO A:338 , GLY A:340 , VAL A:341 , GLU A:343 , GLY A:371 , GLY A:372 , GLY A:373 , ASP A:374 , THR A:375 , MG A:1417 , MGF A:1421 , HOH A:2527 , HOH A:2557 , HOH A:2608 , HOH A:2609 , HOH A:2610 , HOH A:2611 , HOH A:2612 , HOH A:2613 , HOH A:2614	BINDING SITE FOR RESIDUE ADP A1419
4	AC4	SOFTWARE	ASP A:23 , ASN A:25 , ARG A:38 , HIS A:62 , ARG A:65 , ARG A:122 , GLY A:166 , ARG A:170 , LYS A:215 , MGF A:1421 , HOH A:2303 , HOH A:2614 , HOH A:2615 , HOH A:2616 , HOH A:2617	BINDING SITE FOR RESIDUE 3PG A1420
5	AC5	SOFTWARE	ARG A:38 , LYS A:215 , LYS A:219 , GLY A:372 , GLY A:373 , GLY A:395 , GLY A:396 , MG A:1417 , ADP A:1419 , 3PG A:1420 , HOH A:2608 , HOH A:2614 , HOH A:2617	BINDING SITE FOR RESIDUE MGF A1421

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (11, 11)

Asymmetric/Biological Unit (11, 11)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
01	UniProt	VAR_006076	L	88	P	PGK1_HUMAN	Disease (PGK1D)	137852531	A	L	87	P
02	UniProt	VAR_006077	G	158	V	PGK1_HUMAN	Disease (PGK1D)	137852532	A	G	157	V
03	UniProt	VAR_006078	D	164	V	PGK1_HUMAN	Disease (PGK1D)	137852538	A	D	163	V
04	UniProt	VAR_006080	R	206	P	PGK1_HUMAN	Disease (PGK1D)	137852529	A	R	205	P
05	UniProt	VAR_006081	E	252	A	PGK1_HUMAN	Disease (PGK1D)	---	A	E	251	A
06	UniProt	VAR_006082	V	266	M	PGK1_HUMAN	Disease (PGK1D)	431905501	A	V	265	M
07	UniProt	VAR_006083	D	268	N	PGK1_HUMAN	Polymorphism	137852528	A	D	267	N
08	UniProt	VAR_006084	D	285	V	PGK1_HUMAN	Disease (PGK1D)	137852535	A	D	284	V
09	UniProt	VAR_006085	D	315	N	PGK1_HUMAN	Disease (PGK1D)	---	A	D	314	N
10	UniProt	VAR_006086	C	316	R	PGK1_HUMAN	Disease (PGK1D)	137852533	A	C	315	R
11	UniProt	VAR_006087	T	352	N	PGK1_HUMAN	Polymorphism	137852530	A	T	351	N

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

PROSITE Motifs (1, 1)

Exons (0, 0)

Sequences/Alignments

Asymmetric/Biological 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:405
 aligned with PGK1_HUMAN | P00558 from UniProtKB/Swiss-Prot  Length:417

    Alignment length:415
                                    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       312       322       332       342       352       362       372       382       392       402       412     
           PGK1_HUMAN     3 LSNKLTLDKLDVKGKRVVMRVDFNVPMKNNQITNNQRIKAAVPSIKFCLDNGAKSVVLMSHLGRPDGVPMPDKYSLEPVAVELKSLLGKDVLFLKDCVGPEVEKACANPAAGSVILLENLRFHVEEEGKGKDASGNKVKAEPAKIEAFRASLSKLGDVYVNDAFGTAHRAHSSMVGVNLPQKAGGFLMKKELNYFAKALESPERPFLAILGGAKVADKIQLINNMLDKVNEMIIGGGMAFTFLKVLNNMEIGTSLFDEEGAKIVKDLMSKAEKNGVKITLPVDFVTADKFDENAKTGQATVASGIPAGWMGLDCGPESSKKYAEAVTRAKQIVWNGPVGVFEWEAFARGTKALMDEVVKATSRGCITIIGGGDTATCCAKWNTEDKVSHVSTGGGASLELLEGKVLPGVDALSNI 417
               SCOP domains d2wzba_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains -2wzbA01 A:3-188  [code=3.40.50.1260, no name defined]                                                                                                                                     ------2wzbA02 A:195-403  [code=3.40.50.1270, no name defined]                                                                                                                                                          ------------- CATH domains
               Pfam domains -----PGK-2wzbA01 A:7-405                                                                                                                                                                                                                                                                                                                                                                                            ----------- Pfam domains
         Sec.struct. author ......hhhh.....eeeee......ee..ee..hhhhhhhhhhhhhhhhh...eeeee..........hhhhhhhhhhhhhhhhhhh...ee.....hhhhhhhhhh....eeee..hhhhh.......----------hhhhhhhhhhhhhhh..eeee.hhhhh...hhhhhh.....eeehhhhhhhhhhhhhhhhh....eeeee...hhhhhh.hhhhhh....eeee...hhhhhhhhhhh........hhhhhhhhhhhhhhhhhh..eee...eeeee........eeeee.........eeeeehhhhhhhhhhhhhhh.eeeee.......hhhhhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhh.......eee..hhhhhhhhhh..hhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------P---------------------------------------------------------------------V-----V-----------------------------------------P---------------------------------------------A-------------M-N----------------V-----------------------------NR-----------------------------------N----------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------PGLYCERATE_----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wzb A   2 LSNKLTLDKLDVKGKRVVMRVDFNVPMKNNQITNNQRIKAAVPSIKFCLDNGAKSVVLMSHLGRPDGVPMPDKYSLEPVAVELKSLLGKDVLFLKDCVGPEVEKACANPAAGSVILLENLRFHVEEEGKG----------EPAKIEAFRASLSKLGDVYVNDAFGTAHRAHSSMVGVNLPQKAGGFLMKKELNYFAKALESPERPFLAILGGAKVADKIQLINNMLDKVNEMIIGGGMAFTFLKVLNNMEIGTSLFDEEGAKIVKDLMSKAEKNGVKITLPVDFVTADKFDENAKTGQATVASGIPAGWMGLDCGPESSKKYAEAVTRAKQIVWNGPVGVFEWEAFARGTKALMDEVVKATSRGCITIIGGGDTATCCAKWNTEDKVSHVSTGGGASLELLEGKVLPGVDALSNI 416
                                    11        21        31        41        51        61        71        81        91       101       111       121       131         -|      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     
                                                                                                                                                           131        142

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 '\|'

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (2, 2)

Pfam Domains (1, 1)

Gene Ontology (16, 16)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (PGK1_HUMAN | P00558)

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:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	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:0061621	canonical glycolysis	The glycolytic process that begins with the conversion of glucose to glucose-6-phosphate by glucokinase activity. Glycolytic processes are the chemical reactions and pathways resulting in the breakdown of a carbohydrate into pyruvate, with the concomitant production of a small amount of ATP.
	GO:0030855	epithelial cell differentiation	The process in which a relatively unspecialized cell acquires specialized features of an epithelial cell, any of the cells making up an epithelium.
	GO:0006094	gluconeogenesis	The formation of glucose from noncarbohydrate precursors, such as pyruvate, amino acids and glycerol.
	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.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	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:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0045121	membrane raft	Any of the small (10-200 nm), heterogeneous, highly dynamic, sterol- and sphingolipid-enriched membrane domains that compartmentalize cellular processes. Small rafts can sometimes be stabilized to form larger platforms through protein-protein and protein-lipid interactions.

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