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(-) Description

Title :  YEAST PHOSPHOGLYCERATE MUTASE-3PG COMPLEX STRUCTURE TO 1.7 A
 
Authors :  G. Crowhurst, J. Littlechild, H. C. Watson
Date :  13 May 99  (Deposition) - 10 Jun 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Transferase (Phosphoryl) (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. S. Crowhurst, A. R. Dalby, M. N. Isupov, J. W. Campbell, J. A. Littlechild
Structure Of A Phosphoglycerate Mutase:3-Phosphoglyceric Acid Complex At 1. 7 A.
Acta Crystallogr. , Sect. D V. 55 1822 1999
PubMed-ID: 10531478  |  Reference-DOI: 10.1107/S0907444999009944
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN (PHOSPHOGLYCERATE MUTASE)
    Chains: A, B
    EC Number: 5.4.2.1
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
13PG2Ligand/Ion3-PHOSPHOGLYCERIC ACID
2SO44Ligand/IonSULFATE ION
Biological Unit 1 (2, 12)
No.NameCountTypeFull Name
13PG4Ligand/Ion3-PHOSPHOGLYCERIC ACID
2SO48Ligand/IonSULFATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:8 , SER A:11 , ASN A:14 , THR A:20 , ARG A:59 , 3PG A:252 , HOH A:331BINDING SITE FOR RESIDUE SO4 A 248
2AC2SOFTWAREHIS B:8 , SER B:11 , ASN B:14 , THR B:20 , 3PG B:253 , HOH B:348 , HOH B:349 , HOH B:352BINDING SITE FOR RESIDUE SO4 B 249
3AC3SOFTWARETYR B:89 , ARG B:113 , HOH B:347 , HOH B:369BINDING SITE FOR RESIDUE SO4 B 250
4AC4SOFTWAREPHE A:19 , TYR A:89 , LYS A:97 , ARG A:113 , VAL A:240 , HOH A:286BINDING SITE FOR RESIDUE SO4 A 251
5AC5SOFTWAREARG A:7 , HIS A:8 , GLY A:9 , GLN A:10 , SER A:11 , ASN A:14 , THR A:20 , ARG A:59 , THR A:207 , SO4 A:248 , HOH A:331 , HOH A:345BINDING SITE FOR RESIDUE 3PG A 252
6AC6SOFTWAREARG B:7 , HIS B:8 , GLY B:9 , GLN B:10 , SER B:11 , ASN B:14 , THR B:20 , ARG B:59 , THR B:207 , SO4 B:249 , HOH B:348 , HOH B:349 , HOH B:352BINDING SITE FOR RESIDUE 3PG B 253
7PGAAUTHORHIS A:8 , HIS A:1813PG BINDING SITE
8PGBAUTHORHIS B:8 , HIS B:1813PG BINDING SITE

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PG_MUTASEPS00175 Phosphoglycerate mutase family phosphohistidine signature.PMG1_YEAST6-15
 		  2A:5-14
B:5-14
Biological Unit 1 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PG_MUTASEPS00175 Phosphoglycerate mutase family phosphohistidine signature.PMG1_YEAST6-15
 		  4A:5-14
B:5-14

(-) Exons   (1, 2)

Asymmetric Unit (1, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YKL152C1YKL152C.1XI:164390-163647744PMG1_YEAST1-2472472A:1-240
B:1-240		240
240

(-) 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:240
 aligned with PMG1_YEAST | P00950 from UniProtKB/Swiss-Prot  Length:247

    Alignment length:240
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241
           PMG1_YEAST     2 PKLVLVRHGQSEWNEKNLFTGWVDVKLSAKGQQEAARAGELLKEKKVYPDVLYTSKLSRAIQTANIALEKADRLWIPVNRSWRLNERHYGDLQGKDKAETLKKFGEEKFNTYRRSFDVPPPPIDASSPFSQKGDERYKYVDPNVLPETESLALVIDRLLPYWQDVIAKDLLSGKTVMIAAHGNSLRGLVKHLEGISDADIAKLNIPTGIPLVFELDENLKPSKPSYYLDPEAAAAGAAAV 241
               SCOP domains d1qhfa_ A: Phosphoglycerate mutase                                                                                                                                                                                                               SCOP domains
               CATH domains 1qhfA00 A:1-240 Phosphoglycerate mutase-like                                                                                                                                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeee....hhhh.............hhhhhhhhhhhhhhhh......eeee...hhhhhhhhhhhhh......eeee.hhh.....hhh....hhhhhhhhhhhhhhhhhh....................hhh....hhh......hhhhhhhhhhhhhh.hhhhhh....eeeee.hhhhhhhhhhhh......hhh........eeee.......................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----PG_MUTASE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:1-240 UniProt: 1-247 [INCOMPLETE]                                                                                                                                                                                               Transcript 1
                 1qhf A   1 PKLVLVRHGQSEWNEKNLFTGWVDVKLSAKGQQEAARAGELLKEKKVYPDVLYTSKLSRAIQTANIALEKADRLWIPVNRSWRLNERHYGDLQGKDKAETLKKFGEEKFNTYRRSFDVPPPPIDASSPFSQKGDERYKYVDPNVLPETESLALVIDRLLPYWQDVIAKDLLSGKTVMIAAHGNSLRGLVKHLEGISDADIAKLNIPTGIPLVFELDENLKPSKPSYYLDPEAAAAGAAAV 240
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240


Chain B from PDB  Type:PROTEIN  Length:240
 aligned with PMG1_YEAST | P00950 from UniProtKB/Swiss-Prot  Length:247

    Alignment length:240
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241
           PMG1_YEAST     2 PKLVLVRHGQSEWNEKNLFTGWVDVKLSAKGQQEAARAGELLKEKKVYPDVLYTSKLSRAIQTANIALEKADRLWIPVNRSWRLNERHYGDLQGKDKAETLKKFGEEKFNTYRRSFDVPPPPIDASSPFSQKGDERYKYVDPNVLPETESLALVIDRLLPYWQDVIAKDLLSGKTVMIAAHGNSLRGLVKHLEGISDADIAKLNIPTGIPLVFELDENLKPSKPSYYLDPEAAAAGAAAV 241
               SCOP domains d1qhfb_ B: Phosphoglycerate mutase                                                                                                                                                                                                               SCOP domains
               CATH domains 1qhfB00 B:1-240 Phosphoglycerate mutase-like                                                                                                                                                                                                     CATH domains
           Pfam domains (1) -His_Phos_1-1qhfB01 B:2-188                                                                                                                                                                 ---------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -His_Phos_1-1qhfB02 B:2-188                                                                                                                                                                 ---------------------------------------------------- Pfam domains (2)
         Sec.struct. author .eeeeee....hhhh.............hhhhhhhhhhhhhhhh......eeee...hhhhhhhhhhhhh......eeee.hhh.....hhh....hhhhhhhhhhhhhhhhhh....................hhh....hhh......hhhhhhhhhhhhhh.hhhhhh....eeeee.hhhhhhhhhhhh.....hhhh........eeee.......................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----PG_MUTASE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:1-240 UniProt: 1-247 [INCOMPLETE]                                                                                                                                                                                               Transcript 1
                 1qhf B   1 PKLVLVRHGQSEWNEKNLFTGWVDVKLSAKGQQEAARAGELLKEKKVYPDVLYTSKLSRAIQTANIALEKADRLWIPVNRSWRLNERHYGDLQGKDKAETLKKFGEEKFNTYRRSFDVPPPPIDASSPFSQKGDERYKYVDPNVLPETESLALVIDRLLPYWQDVIAKDLLSGKTVMIAAHGNSLRGLVKHLEGISDADIAKLNIPTGIPLVFELDENLKPSKPSYYLDPEAAAAGAAAV 240
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240
   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, 2)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: PGM (50)

(-) Gene Ontology  (15, 15)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (PMG1_YEAST | P00950)
molecular function
    GO:0046538    2,3-bisphosphoglycerate-dependent phosphoglycerate mutase activity    Catalysis of the reaction: 2-phospho-D-glycerate = 3-phospho-D-glycerate; this reaction requires the cofactor 2,3-bisphosphoglycerate.
    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:0016868    intramolecular transferase activity, phosphotransferases    Catalysis of the transfer of a phosphate group from one position to another within a single molecule.
    GO:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
    GO:0004619    phosphoglycerate mutase activity    Catalysis of the reaction: 2-phospho-D-glycerate = 3-phospho-D-glycerate.
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: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:0043456    regulation of pentose-phosphate shunt    Any process that modulates the frequency, rate or extent of the pentose-phosphate shunt, the process in which glucose is oxidized, coupled to NADPH synthesis.
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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005758    mitochondrial intermembrane space    The region between the inner and outer lipid bilayers of the mitochondrial envelope.
    GO:0005741    mitochondrial outer membrane    The outer, i.e. cytoplasm-facing, lipid bilayer of the mitochondrial envelope.
    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
        PMG1_YEAST | P00950: 1bq3 1bq4 3pgm 4pgm 5pgm

(-) Related Entries Specified in the PDB File

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