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(-) Description

Title :  3-PHOSPHOGLYCERATE KINASE, MUTATION R65Q
 
Authors :  T. M. Mcphillips, B. T. Hsu, M. A. Sherman, M. T. Mas, D. C. Rees
Date :  04 Jan 96  (Deposition) - 10 Jun 96  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A
Keywords :  Phosphotransferase (Carboxyl Acceptor), Kinase, Acetylation, Glycolysis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. M. Mcphillips, B. T. Hsu, M. A. Sherman, M. T. Mas, D. C. Rees
Structure Of The R65Q Mutant Of Yeast 3-Phosphoglycerate Kinase Complexed With Mg-Amp-Pnp And 3-Phospho-D-Glycerate.
Biochemistry V. 35 4118 1996
PubMed-ID: 8672447  |  Reference-DOI: 10.1021/BI952500O
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 3-PHOSPHOGLYCERATE KINASE
    Chains: A
    EC Number: 2.7.2.3
    Engineered: YES
    Expression System: SACCHAROMYCES CEREVISIAE
    Expression System Common: BAKER'S YEAST
    Expression System Plasmid: YEP9T-PGK
    Expression System Strain: PGK-XSB44-35D
    Expression System Taxid: 4932
    Mutation: YES
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: PGK

 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
2MAP1Ligand/IonMAGNESIUM-5'-ADENYLY-IMIDO-TRIPHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:211 , GLY A:235 , GLY A:236 , PHE A:239 , GLY A:310 , ASN A:334 , GLY A:335 , PRO A:336 , GLY A:338 , VAL A:339 , PHE A:340 , GLU A:341 , GLY A:370 , GLY A:371 , ASP A:372 , THR A:373 , HOH A:541 , HOH A:545BINDING SITE FOR RESIDUE MAP A 450
2AC2SOFTWAREASP A:23 , ASN A:25 , ARG A:38 , HIS A:62 , ARG A:121 , GLY A:164 , HOH A:537BINDING SITE FOR RESIDUE 3PG A 451

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Arg A:203 -Pro A:204

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) 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:1-415415

(-) 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:415
 aligned with PGK_YEAST | P00560 from UniProtKB/Swiss-Prot  Length:416

    Alignment length:415
                                    11        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     
            PGK_YEAST     2 SLSSKLSVQDLDLKDKRVFIRVDFNVPLDGKKITSNQRIVAALPTIKYVLEHHPRYVVLASHLGRPNGERNEKYSLAPVAKELQSLLGKDVTFLNDCVGPEVEAAVKASAPGSVILLENLRYHIEEEGSRKVDGQKVKASKEDVQKFRHELSSLADVYINDAFGTAHRAHSSMVGFDLPQRAAGFLLEKELKYFGKALENPTRPFLAILGGAKVADKIQLIDNLLDKVDSIIIGGGMAFTFKKVLENTEIGDSIFDKAGAEIVPKLMEKAKAKGVEVVLPVDFIIADAFSADANTKTVTDKEGIPAGWQGLDNGPESRKLFAATVAKAKTIVWNGPPGVFEFEKFAAGTKALLDEVVKSSAAGNTVIIGGGDTATVAKKYGVTDKISHVSTGGGASLELLEGKELPGVAFLSEKK 416
               SCOP domains d1qpga_ A: Phosphoglycerate kinase                                                                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 1qpgA01 A:1-186  [code=3.40.50.1260, no name defined]                                                                                                                                     ------1qpgA02 A:193-401  [code=3.40.50.1270, no name defined]                                                                                                                                                          -------------- CATH domains
               Pfam domains ------PGK-1qpgA01 A:7-403                                                                                                                                                                                                                                                                                                                                                                                          ------------ Pfam domains
         Sec.struct. author .......hhh......eeeee...............hhhhhhhhhhhhhhhh...eeeee...........hhh..hhhhhhhhhhh....eee.....hhhhhhhh.....eeeee..hhh.hhhh.eeee..eeee..hhhhhhhhhhhhhh..eeee..hhh.....hhhh......eee.hhhhhhhhhhhhhh......eeeee.....hhhhhhhhhhhhh..eeee....hhhhhhhh...........hhhhhhhhhhhhhhhhh..eeee..eeeee..........eee.........eeeee.hhhhhhhhhhhhh..eeeee........hhh.hhhhhhhhhhhhhhhh..eeee..hhhhhhhhh...hhh........hhhhhhh.....hhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------PGLYCERATE_---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:1-415 UniProt: 1-416 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                              Transcript 1
                 1qpg A   1 SLSSKLSVQDLDLKDKRVFIRVDFNVPLDGKKITSNQRIVAALPTIKYVLEHHPRYVVLASHLGQPNGERNEKYSLAPVAKELQSLLGKDVTFLNDCVGPEVEAAVKASAPGSVILLENLRYHIEEEGSRKVDGQKVKASKEDVQKFRHELSSLADVYINDAFGTAHRAHSSMVGFDLPQRAAGFLLEKELKYFGKALENPTRPFLAILGGAKVADKIQLIDNLLDKVDSIIIGGGMAFTFKKVLENTEIGDSIFDKAGAEIVPKLMEKAKAKGVEVVLPVDFIIADAFSADANTKTVTDKEGIPAGWQGLDNGPESRKLFAATVAKAKTIVWNGPPGVFEFEKFAAGTKALLDEVVKSSAAGNTVIIGGGDTATVAKKYGVTDKISHVSTGGGASLELLEGKELPGVAFLSEKK 415
                                    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
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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  (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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 Related Entries

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

UniProtKB/Swiss-Prot
        PGK_YEAST | P00560: 1fw8 3pgk

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