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(-) Description

Title :  THE STRUCTURE OF YEAST PHOSPHOGLYCERATE KINASE AT 0.25 NM RESOLUTION
 
Authors :  P. J. Shaw, N. P. Walker, H. C. Watson
Date :  15 Jul 82  (Deposition) - 24 Sep 82  (Release) - 06 Oct 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Phosphotransferase(Carboxyl As Acceptor), Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. C. Watson, N. P. Walker, P. J. Shaw, T. N. Bryant, P. L. Wendell, L. A. Fothergill, R. E. Perkins, S. C. Conroy, M. J. Dobson, M. F. Tuite
Sequence And Structure Of Yeast Phosphoglycerate Kinase.
Embo J. V. 1 1635 1982
PubMed-ID: 6765200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PHOSPHOGLYCERATE KINASE
    Chains: A
    EC Number: 2.7.2.3
    Engineered: YES
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 4)

Asymmetric/Biological Unit (4, 4)
No.NameCountTypeFull Name
13PG1Ligand/Ion3-PHOSPHOGLYCERIC ACID
2ACE1Mod. Amino AcidACETYL GROUP
3ATP1Ligand/IonADENOSINE-5'-TRIPHOSPHATE
4MG1Ligand/IonMAGNESIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:372 , ATP A:417BINDING SITE FOR RESIDUE MG A 416
2AC2SOFTWAREGLY A:211 , ALA A:212 , LYS A:213 , LYS A:217 , ILE A:250 , ILE A:285 , LYS A:301 , GLU A:302 , GLY A:303 , PRO A:305 , ALA A:306 , GLN A:309 , LEU A:311 , ASP A:312 , ASN A:334 , GLY A:335 , PRO A:336 , GLY A:338 , VAL A:339 , GLU A:341 , ASP A:372 , MG A:416 , 3PG A:418BINDING SITE FOR RESIDUE ATP A 417
3AC3SOFTWARELYS A:5 , GLY A:370 , GLY A:392 , GLY A:393 , GLY A:394 , ATP A:417BINDING SITE FOR RESIDUE 3PG A 418

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3PGK)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3PGK)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3PGK)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PGLYCERATE_KINASEPS00111 Phosphoglycerate kinase signature.PGK_YEAST18-28  1A:17-27

(-) Exons   (1, 1)

Asymmetric/Biological Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YCR012W1YCR012W.1III:137744-1389941251PGK_YEAST1-4164161A:0-415416

(-) 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:416
 aligned with PGK_YEAST | P00560 from UniProtKB/Swiss-Prot  Length:416

    Alignment length: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       380       390       400       410      
            PGK_YEAST     1 MSLSSKLSVQDLDLKDKRVFIRVDFNVPLDGKKITSNQRIVAALPTIKYVLEHHPRYVVLASHLGRPNGERNEKYSLAPVAKELQSLLGKDVTFLNDCVGPEVEAAVKASAPGSVILLENLRYHIEEEGSRKVDGQKVKASKEDVQKFRHELSSLADVYINDAFGTAHRAHSSMVGFDLPQRAAGFLLEKELKYFGKALENPTRPFLAILGGAKVADKIQLIDNLLDKVDSIIIGGGMAFTFKKVLENTEIGDSIFDKAGAEIVPKLMEKAKAKGVEVVLPVDFIIADAFSADANTKTVTDKEGIPAGWQGLDNGPESRKLFAATVAKAKTIVWNGPPGVFEFEKFAAGTKALLDEVVKSSAAGNTVIIGGGDTATVAKKYGVTDKISHVSTGGGASLELLEGKELPGVAFLSEKK 416
               SCOP domains d3pgka_ A: Phosphoglycerate kinase                                                                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains -3pgkA01 A:1-186  [code=3.40.50.1260, no name defined]                                                                                                                                     ------3pgkA02 A:193-401  [code=3.40.50.1270, no name defined]                                                                                                                                                          -------------- CATH domains
               Pfam domains -------PGK-3pgkA01 A:7-403                                                                                                                                                                                                                                                                                                                                                                                          ------------ Pfam domains
         Sec.struct. author .................eeeee...............hhhhhhhhhhhhhhh......ee.................hhhhhhhhhhh...eee......hhhhhhhhh....eeee.........................hhhhhhhhhhh....eee.....................eee.hhhhhhhhhhhhhhh.....eeeee.......hhhhhhhhhh....eeeee.hhhhhhh..hhhhhh.....hhhhhhhhhhhhhhhhh..eeee..eeeee.......eeeee................hhhhhhhhhhh.....eee..............hhhhhhhhhhhh......eee...hhhhhhhhh......eee...hhhhhhhhh....hhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------PGLYCERATE_---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:0-415 UniProt: 1-416                                                                                                                                                                                                                                                                                                                                                                                            Transcript 1
                 3pgk A   0 xSLSSKLSVQDLDLKDKRVFIRVDFNVPLDGKKITSNQRIVAALPTIKYVLEHHPRYVVLASHLGRPNGERNEKYSLAPVAKELQSLLGKDVTFLNDCVGPEVEAAVKASAPGSVILLENLRYHIEEEGSRKVDGQKVKASKEDVQKFRHELSSLADVYINDAFGTAHRAHSSMVGFDLPQRAAGFLLEKELKYFGKALENPTRPFLAILGGAKVADKIQLIDNLLDKVDSIIIGGGMAFTFKKVLENTEIGDSIFDKAVGPEIAKLMEKAKAKGVEVVLPVDFIIADAFSASANTKTVTDKEGIPAGWQGLDNGPESRKLFAATVAKATVILWNGPPGVFEFEKFAAGTKALLDEVVKSSAAGNTVIIGGGDTATVAKKYGVTDKISHVSTGGGASLELLEGKELPGVAFLSEKK 415
                            |        9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409      
                            |                                                                                                                                                                                                                                                                                                                                                                                                                               
                            0-ACE
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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  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

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

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PGK_YEAST | P00560)
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: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:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

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        PGK_YEAST | P00560: 1fw8 1qpg

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