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(-) Description

Title :  THE CATALYTICALLY ACTIVE FULLY CLOSED CONFORMATION OF HUMAN PHOSPHOGLYCERATE KINASE K219A MUTANT IN COMPLEX WITH AMP-PCP AND 3PG
 
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 :  21 Dec 09  (Deposition) - 29 Dec 10  (Release) - 29 Dec 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Transition State Analogue, Hereditary Hemolytic Anemia, Atp-Binding, Kinase, Glycolysis, Transferase, Disease Mutation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  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
The Structure Of Human Phosphoglycerate Kinase In Its Fully Active Conformation In Complex With Ground State Analogues
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PHOSPHOGLYCERATE KINASE 1
    Chains: A
    EC Number: 2.7.2.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PRIMER 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  (3, 3)

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
13PG1Ligand/Ion3-PHOSPHOGLYCERIC ACID
2ACP1Ligand/IonPHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
3MG1Ligand/IonMAGNESIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:375 , ACP A:1420 , HOH A:2208 , HOH A:2217BINDING SITE FOR RESIDUE MG A1418
2AC2SOFTWAREASP A:24 , ASN A:26 , ARG A:39 , HIS A:63 , ARG A:66 , ARG A:123 , GLY A:167 , THR A:168 , ARG A:171 , LYS A:216 , ACP A:1420 , HOH A:2069 , HOH A:2207 , HOH A:2208 , HOH A:2209 , HOH A:2211BINDING SITE FOR RESIDUE 3PG A1419
3AC3SOFTWAREARG A:39 , GLY A:214 , ALA A:215 , LYS A:216 , GLY A:238 , GLY A:239 , LEU A:257 , GLY A:313 , LEU A:314 , ASN A:337 , PRO A:339 , GLY A:341 , VAL A:342 , GLU A:344 , GLY A:372 , GLY A:373 , GLY A:374 , ASP A:375 , THR A:376 , GLY A:396 , GLY A:397 , MG A:1418 , 3PG A:1419 , HOH A:2175 , HOH A:2208 , HOH A:2210 , HOH A:2211 , HOH A:2212 , HOH A:2213 , HOH A:2214 , HOH A:2215 , HOH A:2216 , HOH A:2217 , HOH A:2218BINDING SITE FOR RESIDUE ACP A1420

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2X14)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Val A:100 -Gly A:101
2Glu A:129 -Gly A:130
3Arg A:206 -Pro A:207

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (11, 11)

Asymmetric/Biological Unit (11, 11)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_006076L88PPGK1_HUMANDisease (PGK1D)137852531AL88P
02UniProtVAR_006077G158VPGK1_HUMANDisease (PGK1D)137852532AG158V
03UniProtVAR_006078D164VPGK1_HUMANDisease (PGK1D)137852538AD164V
04UniProtVAR_006080R206PPGK1_HUMANDisease (PGK1D)137852529AR206P
05UniProtVAR_006081E252APGK1_HUMANDisease (PGK1D)  ---AE252A
06UniProtVAR_006082V266MPGK1_HUMANDisease (PGK1D)431905501AV266M
07UniProtVAR_006083D268NPGK1_HUMANPolymorphism137852528AD268N
08UniProtVAR_006084D285VPGK1_HUMANDisease (PGK1D)137852535AD285V
09UniProtVAR_006085D315NPGK1_HUMANDisease (PGK1D)  ---AD315N
10UniProtVAR_006086C316RPGK1_HUMANDisease (PGK1D)137852533AC316R
11UniProtVAR_006087T352NPGK1_HUMANPolymorphism137852530AT352N
  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:18-28

(-) Exons   (0, 0)

(no "Exon" information available for 2X14)

(-) 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 d2x14a_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----PGK-2x14A01 A:8-406                                                                                                                                                                                                                                                                                                                                                                                            ----------- Pfam domains
         Sec.struct. author ......hhhh.....eeeee......ee..ee..hhhhhhhhhhhhhhhhh...eeeee..........hhhhhhhhhhhhhhhhhhh...ee.....hhhhhhhhhh....eeee..hhhhh.......----------hhhhhhhhhhhhhh...eeee.hhhhh...hhhhhh.....eeehhhhhhhhhhhhhhh......eeeee...hhhhhhhhhhhhh....eeee...hhhhhhhhhhh........hhhhhhhhhhhhhhhhhhh.eee...eeeee........eeeee.........eeeeehhhhhhhhhhhhhhh.eeeee.......hhhhhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhh......ee...hhhhhhhhh...hhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------P---------------------------------------------------------------------V-----V-----------------------------------------P---------------------------------------------A-------------M-N----------------V-----------------------------NR-----------------------------------N----------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------PGLYCERATE_----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2x14 A   3 LSNKLTLDKLDVKGKRVVMRVDFNVPMKNNQITNNQRIKAAVPSIKFCLDNGAKSVVLMSHLGRPDGVPMPDKYSLEPVAVELKSLLGKDVLFLKDCVGPEVEKACANPAAGSVILLENLRFHVEEEGKG----------EPAKIEAFRASLSKLGDVYVNDAFGTAHRAHSSMVGVNLPQKAGGFLMKKELNYFAKALESPERPFLAILGGAKVADAIQLINNMLDKVNEMIIGGGMAFTFLKVLNNMEIGTSLFDEEGAKIVKDLMSKAEKNGVKITLPVDFVTADKFDENAKTGQATVASGIPAGWMGLDCGPESSKKYAEAVTRAKQIVWNGPVGVFEWEAFARGTKALMDEVVKATSRGCITIIGGGDTATCCAKWNTEDKVSHVSTGGGASLELLEGKVLPGVDALSNI 417
                                    12        22        32        42        52        62        72        82        92       102       112       122       132         -|      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     
                                                                                                                                                           132        143
   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
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2X14)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: PGK] (23)

(-) 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 | P00558: 2wzb 2wzc 2wzd 2x13 2x15 2xe6 2xe7 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
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
2xe7 THE COMPLETE REACTION CYCLE OF HUMAN PHOSPHOGLYCERATE KINASE: THE OPEN TERNARY COMPLEX WITH 3PG AND ADP
2xe8 THE COMPLETE REACTION CYCLE OF HUMAN PHOSPHOGLYCERATE KINASE: THE OPEN TERNARY COMPLEX WITH 3PG AND AMP-PNP
2y3i THE STRUCTURE OF THE FULLY CLOSED CONFORMATION OF HUMAN PGK IN COMPLEX WITH L-ADP, 3PG AND THE TSA ALUMINIUM TETRAFLUORIDE