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(-) Description

Title :  THE COMPLETE REACTION CYCLE OF HUMAN PHOSPHOGLYCERATE KINASE: THE OPEN TERNARY COMPLEX WITH 3PG AND ADP
 
Authors :  M. J. Cliff, N. J. Baxter, G. M. Blackburn, A. Merli, M. Vas, J. P. Waltho, M. W. Bowler
Date :  11 May 10  (Deposition) - 19 Jan 11  (Release) - 26 Oct 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A
Keywords :  Transition State Analogue, Hereditary Hemolytic Anemia, Phosphoprotein, Glycolysis, Transferase, Phosphoryl Transfer, Nucleotide-Binding, Domain Motions (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  L. Zerrad, A. Merli, G. F. Schroder, A. Varga, E. Graczer, P. Pernot, A. Round, M. Vas, M. W. Bowler
A Spring Loaded Release Mechanism Regulates Domain Movement And Catalysis In Phosphoglycerate Kinase.
J. Biol. Chem. V. 286 14040 2011
PubMed-ID: 21349853  |  Reference-DOI: 10.1074/JBC.M110.206813

(-) Compounds

Molecule 1 - PHOSPHOGLYCERATE KINASE 1
    ChainsA
    EC Number2.7.2.3
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET22A
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System VectorPET
    Expression System Vector TypePLASMID
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPRIMER RECOGNITION PROTEIN 2, PRP 2, CELL MIGRATION-INDUCING GENE 10 PROTEIN

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
13PG1Ligand/Ion3-PHOSPHOGLYCERIC ACID
2ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:23 , ASN A:25 , ARG A:38 , HIS A:62 , ARG A:65 , ARG A:122 , GLY A:166 , THR A:167 , ARG A:170 , HOH A:2024 , HOH A:2063BINDING SITE FOR RESIDUE 3PG A1417
2AC2SOFTWAREGLY A:213 , ALA A:214 , LYS A:215 , 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:372 , GLY A:373 , ASP A:374 , THR A:375 , HOH A:2064BINDING SITE FOR RESIDUE ADP A1418

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2XE7)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Arg A:205 -Pro A:206
2Ala A:308 -Gly A:309

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (11, 11)

Asymmetric/Biological Unit (11, 11)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_006076L88PPGK1_HUMANDisease (PGK1D)137852531AL87P
02UniProtVAR_006077G158VPGK1_HUMANDisease (PGK1D)137852532AG157V
03UniProtVAR_006078D164VPGK1_HUMANDisease (PGK1D)137852538AD163V
04UniProtVAR_006080R206PPGK1_HUMANDisease (PGK1D)137852529AR205P
05UniProtVAR_006081E252APGK1_HUMANDisease (PGK1D)  ---AE251A
06UniProtVAR_006082V266MPGK1_HUMANDisease (PGK1D)431905501AV265M
07UniProtVAR_006083D268NPGK1_HUMANPolymorphism137852528AD267N
08UniProtVAR_006084D285VPGK1_HUMANDisease (PGK1D)137852535AD284V
09UniProtVAR_006085D315NPGK1_HUMANDisease (PGK1D)  ---AD314N
10UniProtVAR_006086C316RPGK1_HUMANDisease (PGK1D)137852533AC315R
11UniProtVAR_006087T352NPGK1_HUMANPolymorphism137852530AT351N

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PGLYCERATE_KINASEPS00111 Phosphoglycerate kinase signature.PGK1_HUMAN18-28  1A:17-27

(-) Exons   (0, 0)

(no "Exon" information available for 2XE7)

(-) 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:413
 aligned with PGK1_HUMAN | P00558 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   
           PGK1_HUMAN     5 NKLTLDKLDVKGKRVVMRVDFNVPMKNNQITNNQRIKAAVPSIKFCLDNGAKSVVLMSHLGRPDGVPMPDKYSLEPVAVELKSLLGKDVLFLKDCVGPEVEKACANPAAGSVILLENLRFHVEEEGKGKDASGNKVKAEPAKIEAFRASLSKLGDVYVNDAFGTAHRAHSSMVGVNLPQKAGGFLMKKELNYFAKALESPERPFLAILGGAKVADKIQLINNMLDKVNEMIIGGGMAFTFLKVLNNMEIGTSLFDEEGAKIVKDLMSKAEKNGVKITLPVDFVTADKFDENAKTGQATVASGIPAGWMGLDCGPESSKKYAEAVTRAKQIVWNGPVGVFEWEAFARGTKALMDEVVKATSRGCITIIGGGDTATCCAKWNTEDKVSHVSTGGGASLELLEGKVLPGVDALSNI 417
               SCOP domains d2xe7a_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---PGK-2xe7A01 A:7-405                                                                                                                                                                                                                                                                                                                                                                                            ----------- Pfam domains
         Sec.struct. author ....hhhh.....eeeee......ee..ee..hhhhhhhhhhhhhhhhh...eeeee................hhhhhhhhhhhhh..eee.....hhhhhhhhh.....eeee..hhhhh.....eee.....eee.hhhhhhhhhhhhhh...eeee.hhhhh...hhhhhh.....eeehhhhhhhhhhhhhhhhh....eeeee........hhhhhhhh....eeee...hhhhhhhhhhh........hhhhhhhhhhhhhhhhhh..eee...eeeee........eeeee.........eeeeehhhhhhhhhhhhhhh.eeeee.......hhhhhhhhhhhhhhhhhhhhh..eeee.hhhhhhhhhhh.......ee..hhhhhhhhhh...hhhhhh.... Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------P---------------------------------------------------------------------V-----V-----------------------------------------P---------------------------------------------A-------------M-N----------------V-----------------------------NR-----------------------------------N----------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------PGLYCERATE_----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xe7 A   4 NKLTLDKLDVKGKRVVMRVDFNVPMKNNQITNNQRIKAAVPSIKFCLDNGAKSVVLMSHLGRPDGVPMPDKYSLEPVAVELKSLLGKDVLFLKDCVGPEVEKACANPAAGSVILLENLRFHVEEEGKGKDASGNKVKAEPAKIEAFRASLSKLGDVYVNDAFGTAHRAHSSMVGVNLPQKAGGFLMKKELNYFAKALESPERPFLAILGGAKVADKIQLINNMLDKVNEMIIGGGMAFTFLKVLNNMEIGTSLFDEEGAKIVKDLMSKAEKNGVKITLPVDFVTADKFDENAKTGQATVASGIPAGWMGLDCGPESSKKYAEAVTRAKQIVWNGPVGVFEWEAFARGTKALMDEVVKATSRGCITIIGGGDTATCCAKWNTEDKVSHVSTGGGASLELLEGKVLPGVDALSNI 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   

   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)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2XE7)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit

(-) 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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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        PGK1_HUMAN | P005582wzb 2wzc 2wzd 2x13 2x14 2x15 2xe6 2xe8 2y3i 2ybe 2zgv 3c39 3c3a 3c3b 3c3c 3zoz 4axx 4o33

(-) Related Entries Specified in the PDB File

2wzb THE CATALYTICALLY ACTIVE FULLY CLOSED CONFORMATION OF HUMAN PHOSPHOGLYCERATE KINASE IN COMPLEX WITH ADP, 3PG AND MAGNESIUM TRIFLUORIDE
2wzc THE CATALYTICALLY ACTIVE FULLY CLOSED CONFORMATION OF HUMAN PHOSPHOGLYCERATE KINASE IN COMPLEX WITH ADP, 3PG AND ALUMINIUM TETRAFLUORIDE
2wzd THE CATALYTICALLY ACTIVE FULLY CLOSED CONFORMATION OF HUMAN PHOSPHOGLYCERATE KINASE K219A MUTANT IN COMPLEX WITH ADP, 3PG AND ALUMINIUM TRIFLUORIDE
2x13 THE CATALYTICALLY ACTIVE FULLY CLOSED CONFORMATION OF HUMAN PHOSPHOGLYCERATE KINASE IN COMPLEX WITH ADP AND 3PHOSPHOGLYCERATE
2x14 THE CATALYTICALLY ACTIVE FULLY CLOSED CONFORMATION OF HUMAN PHOSPHOGLYCERATE KINASE K219A MUTANT IN COMPLEX WITH AMP-PCP AND 3PG
2x15 THE CATALYTICALLY ACTIVE FULLY CLOSED CONFORMATION OF HUMAN PHOSPHOGLYCERATE KINASE IN COMPLEX WITH ADP AND 1,3-BISPHOSPHOGLYCERATE
2xe6 THE COMPLETE REACTION CYCLE OF HUMAN PHOSPHOGLYCERATE KINASE: THE OPEN BINARY COMPLEX WITH 3PG
2xe8 THE COMPLETE REACTION CYCLE OF HUMAN PHOSPHOGLYCERATE KINASE: THE OPEN TERNARY COMPLEX WITH 3PG AND AMP-PNP