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(-) Description

Title :  THE REFINED THREE-DIMENSIONAL STRUCTURE OF CAT MUSCLE (M1) PYRUVATE KINASE, AT A RESOLUTION OF 2.6 ANGSTROMS
 
Authors :  S. C. Allen, H. Muirhead
Date :  13 Jul 95  (Deposition) - 15 Oct 95  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Pyruvate Kinase, Kinase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. C. Allen, H. Muirhead
Refined Three-Dimensional Structure Of Cat-Muscle (M1) Pyruvate Kinase At A Resolution Of 2. 6 A.
Acta Crystallogr. , Sect. D V. 52 499 1996
PubMed-ID: 15299671  |  Reference-DOI: 10.1107/S0907444995016040
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - M1 PYRUVATE KINASE
    ChainsA
    EC Number2.7.1.40
    Organism CommonDOMESTIC CAT
    Organism ScientificFELIS CATUS
    Organism Taxid9685
    SynonymPK
    TissueMUSCLE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (4x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1PKM)

(-) Sites  (0, 0)

(no "Site" information available for 1PKM)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1PKM)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1PKM)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1PKM)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PYRUVATE_KINASEPS00110 Pyruvate kinase active site signature.KPYM_FELCA265-277  1A:264-276
Biological Unit 1 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PYRUVATE_KINASEPS00110 Pyruvate kinase active site signature.KPYM_FELCA265-277  4A:264-276

(-) Exons   (0, 0)

(no "Exon" information available for 1PKM)

(-) Sequences/Alignments

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:519
 aligned with KPYM_FELCA | P11979 from UniProtKB/Swiss-Prot  Length:531

    Alignment length:519
                                    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       422       432       442       452       462       472       482       492       502       512       522         
           KPYM_FELCA    13 IQTQQLHAAMADTFLEHMCRLDIDSPPITARNTGIICTIGPASRSVEILKEMIKSGMNVARLNFSHGTHEYHAETIKNVRAATESFASDPIRYRPVAVALDTKGPEIRTGLIKGSGTAEVELKKGATLKITLDNAYMEKCDENVLWLDYKNICKVVEVGSKVYVDDGLISLLVKEKGADFLVTEVENGGSLGSKKGVNLPGAAVDLPAVSEKDIQDLKFGVEQDVDMVFASFIRKASDVHEVRKVLGEKGKNIKIISKIENHEGVRRFDEILEASDGIMVARGDLGIEIPAEKVFLAQKMMIGRCNRAGKPVICATQMLESMIKKPRPTRAEGSDVANAVLDGADCIMLSGETAKGDYPLEAVRMQHLIAREAEAAMFHRKLFEELVRGSSHSTDLMEAMAMGSVEASYKCLAAALIVLTESGRSAHQVARYRPRAPIIAVTRNHQTARQAHLYRGIFPVVCKDPVQEAWAEDVDLRVNLAMNVGKARGFFKHGDVVIVLTGWRPGSGFTNTMRVVPVP 531
               SCOP domains d1pkma2 A:12-115,A:218-395 Pyruvate kinase, N-terminal domain                                           d1pkma1 A:116-217 Pyruvate kinase (PK)                                                                d1pkma2 A:12-115,A:218-395 Pyruvate kinase, N-terminal domain                                                                                                                     d1pkma3 A:396-530 Pyruvate kinase, C-terminal domain                                                                                    SCOP domains
               CATH domains 1pkmA01 A:12-41,A:385-530     1pkmA02 A:42-115,A:219-384 Phosphoenolpyruvate-binding domains            1pkmA03 A:116-218 M1 Pyruvate Kinase; Domain 3                                                         1pkmA02 A:42-115,A:219-384 Phosphoenolpyruvate-binding domains                                                                                                        1pkmA01 A:12-41,A:385-530  [code=3.40.1380.20, no name defined]                                                                                    CATH domains
               Pfam domains -----------------------------PK-1pkmA01 A:41-394                                                                                                                                                                                                                                                                                                                                               -------------PK_C-1pkmA02 A:408-528                                                                                                   -- Pfam domains
         Sec.struct. author .....hhhhh...hhhhhh..............eeeee.......hhhhhhhhh..eeeeeee.....hhhhhhhhhhhhhhhhhh..........eeeee.....eee...........ee....eeeee............eee.....hhhh.....eeee....eeeeeeee...eeeeee...ee.....eee............hhhhhhhhhhhh....eeee.....hhhhhhhhhhh.......eeeeee...hhhh.hhhhhhh..eeeeehhhhhhh.....hhhhhhhhhhhhhhh..eeeee....hhhh......hhhhhhhhhhhhh...eeee.hhhh....hhhhhhhhhhhhhhhhh...hhhhhhhhhhhh.....hhhhhhhhhhhhhhhh...eeeee....hhhhhhhhh....eeeeee..hhhhhhhhh...eeeee........hhhhhhhhhhhhhhhhhh........eeeeee..........eeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PYRUVATE_KINA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pkm A  12 IQTQQLHAAMADTFLEHMCRLDIDSPPITARNTGIICTIGPASRSVEILKEMIKSGMNVARLNFSHGTHEYHAETIKNVRAATESFASDPIRYRPVAVALDTKGPEIRTGLIKGSGTAEVELKKGATLKITLDNAYMEKCDENVLWLDYKNICKVVEVGSKVYVDDGLISLLVKEKGADFLVTEVENGGSLGSKKGVNLPGAAVDLPAVSEKDIQDLKFGVEQDVDMVFASFIRKASDVHEVRKVLGEKGKNIKIISKIENHEGVRRFDEILEASDGIMVARGDLGIEIPAEKVFLAQKMMIGRCNRAGKPVICATQMLESMIKKPRPTRAEGSDVANAVLDGADCIMLSGETAKGDYPLEAVRMQHLIAREAEAAMFHRKLFEELVRGSSHSTDLMEAMAMGSVEASYKCLAAALIVLTESGRSAHQVARYRPRAPIIAVTRNHQTARQAHLYRGIFPVVCKDPVQEAWAEDVDLRVNLAMNVGKARGFFKHGDVVIVLTGWRPGSGFTNTMRVVPVP 530
                                    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       421       431       441       451       461       471       481       491       501       511       521         

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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (3, 3)

Asymmetric Unit

(-) CATH Domains  (3, 3)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (2, 2)

Asymmetric Unit
(-)
Clan: PK_TIM (63)

(-) Gene Ontology  (14, 14)

Asymmetric Unit(hide GO term definitions)
Chain A   (KPYM_FELCA | P11979)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0030955    potassium ion binding    Interacting selectively and non-covalently with potassium (K+) ions.
    GO:0004743    pyruvate kinase activity    Catalysis of the reaction: ATP + pyruvate = ADP + phosphoenolpyruvate.
    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: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:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    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: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.

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