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(-) Description

Title :  CRYSTAL STRUCTURAL ANALYSIS OF PHOSPHOGLYCERATE MUTASE COCRYSTALLIZED WITH 3-PHOSPHOGLYCERATE
 
Authors :  M. J. Jedrzejas, M. Chander, P. Setlow, G. Krishnasamy
Date :  02 Mar 00  (Deposition) - 02 Mar 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Alpha/Beta-Type Structure, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. J. Jedrzejas, M. Chander, P. Setlow, G. Krishnasamy
Structure And Mechanism Of Action Of A Novel Phosphoglycerate Mutase From Bacillus Stearothermophilus.
Embo J. V. 19 1419 2000
PubMed-ID: 10747010  |  Reference-DOI: 10.1093/EMBOJ/19.7.1419
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PHOSPHOGLYCERATE MUTASE
    ChainsA
    EC Number5.4.2.1
    EngineeredYES
    Expression SystemBACILLUS SUBTILIS
    Expression System PlasmidPGS3
    Expression System Taxid1423
    Expression System Vector TypePLASMID
    Organism ScientificGEOBACILLUS STEAROTHERMOPHILUS
    Organism Taxid1422

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
13PG1Ligand/Ion3-PHOSPHOGLYCERIC ACID
2MN2Ligand/IonMANGANESE (II) ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:403 , HIS A:407 , HIS A:462 , 3PG A:601BINDING SITE FOR RESIDUE MN A 701
2AC2SOFTWAREASP A:12 , SER A:62 , LYS A:336 , ASP A:444 , HIS A:445 , 3PG A:601BINDING SITE FOR RESIDUE MN A 801
3AC3SOFTWAREASN A:61 , SER A:62 , HIS A:123 , ARG A:153 , ASP A:154 , ARG A:185 , ARG A:191 , ARG A:261 , ARG A:264 , LYS A:336 , ASP A:403 , HIS A:407 , HIS A:445 , HIS A:462 , MN A:701 , MN A:801 , HOH A:1017BINDING SITE FOR RESIDUE 3PG A 601

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1EJJ)

(-) Exons   (0, 0)

(no "Exon" information available for 1EJJ)

(-) 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:508
 aligned with GPMI_GEOSE | Q9X519 from UniProtKB/Swiss-Prot  Length:511

    Alignment length:508
                                    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       422       432       442       452       462       472       482       492       502        
           GPMI_GEOSE     3 KKPVALIILDGFALRDETYGNAVAQANKPNFDRYWNEYPHTTLKACGEAVGLPEGQMGNSEVGHLNIGAGRIVYQSLTRINIAIREGEFDRNETFLAAMNHVKQHGTSLHLFGLLSDGGVHSHIHHLYALLRLAAKEGVKRVYIHGFLDGRDVGPQTAPQYIKELQEKIKEYGVGEIATLSGRYYSMDRDKRWDRVEKAYRAMVYGEGPTYRDPLECIEDSYKHGIYDEFVLPSVIVREDGRPVATIQDNDAIIFYNFRPDRAIQISNTFTNEDFREFDRGPKHPKHLFFVCLTHFSETVKGYVAFKPTNLDNTIGEVLSQHGLRQLRIAETEKYPHVTFFMSGGREEKFPGEDRILINSPKVPTYDLKPEMSAYEVTDALLKEIEADKYDAIILNYANPDMVGHSGKLEPTIKAVEAVDECLGKVVDAILAKGGIAIITADHGNADEVLTPDGKPQTAHTTNPVPVIVTKKGIKLRDGGILGDLAPTMLDLLGLPQPKEMTGKSLIV 510
               SCOP domains d1ejja2 A:3-76,A:311-510                                                  d1ejja1 A:77-310 2,3-Bisphosphoglycerate-independent phosphoglycerate mutase, substrate-binding domain                                                                                                                                    d1ejja2 A:3-76,A:311-510 2,3-Bisphosphoglycerate-independent phosphoglycerate mutase, catalytic domain                                                                                                   SCOP domains
               CATH domains 1ejjA02 A:3-76,A:313-510 Alkaline Phosphatase, subunit A                  1ejjA01 A:77-312 2,3-Bisphosphoglycerate-independent phosphoglycerate mutase, substrate-binding domain                                                                                                                                      1ejjA02 A:3-76,A:313-510 Alkaline Phosphatase, subunit A                                                                                                                                               CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee...........hhhhhh.hhhhhhhhhhh.eeee..hhhhhh.......hhhhhhhhhhhh....hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh...eeeeeee.......hhhhhhhhhhhhhhh....eeeeeee........hhhhhhhhhhhhhhhhh...eeeeeehhhhh....hhhhhhhhhhhhhhh...ee.hhhhhhhhhhhh..hhhhh..eee...............eeee.......hhhhhhhhhh................eeeeee........eeee.......hhhhhhhhh...eeeeee..hhhhhh.............eeeeee......hhhhh...hhhhhhhhhhhhhhhh...eeeeeehhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee........................eeeee..............hhhhhhhhhh............... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ejj A   3 KKPVALIILDGFALRDETYGNAVAQANKPNFDRYWNEYPHTTLKACGEAVGLPEGQMGNSEVGHLNIGAGRIVYQSLTRINIAIREGEFDRNETFLAAMNHVKQHGTSLHLFGLLSDGGVHSHIHHLYALLRLAAKEGVKRVYIHGFLDGRDVGPQTAPQYIKELQEKIKEYGVGEIATLSGRYYSMDRDKRWDRVEKAYRAMVYGEGPTYRDPLECIEDSYKHGIYDEFVLPSVIVREDGRPVATIQDNDAIIFYNFRPDRAIQISNTFTNEDFREFDRGPKHPKHLFFVCLTHFSETVAGYVAFKPTNLDNTIGEVLSQHGLRQLRIAETEKYPHVTFFMSGGREEEFPGEDRILINSPKVPTYDLKPEMSAYEVTDALLKEIEADKYDAIILNYANPDMVGHSGKLEPTIKAVEAVDECLGKVVDAILAKGGIAIITADHGNADEVLTPDGKPQTAHTTNPVPVIVTKKGIKLRDGGILGDLAPTMLDLLGLPQPKEMTGKSLIV 510
                                    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       422       432       442       452       462       472       482       492       502        

   Legend:   → Mismatch (orange background)
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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  (2, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1EJJ)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (GPMI_GEOSE | Q9X519)
molecular function
    GO:0046537    2,3-bisphosphoglycerate-independent phosphoglycerate mutase activity    Catalysis of the reaction: 2-phospho-D-glycerate = 3-phospho-D glycerate; this reaction does not require 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: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:0030145    manganese ion binding    Interacting selectively and non-covalently with manganese (Mn) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004619    phosphoglycerate mutase activity    Catalysis of the reaction: 2-phospho-D-glycerate = 3-phospho-D-glycerate.
biological process
    GO:0006007    glucose catabolic process    The chemical reactions and pathways resulting in the breakdown of glucose, the aldohexose gluco-hexose.
    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:0043937    regulation of sporulation    Any process that modulates the frequency, rate or extent of sporulation, the process whose specific outcome is the progression of a spore over time, from its initiation to the mature structure.
    GO:0030435    sporulation resulting in formation of a cellular spore    The process in which a relatively unspecialized cell acquires the specialized features of a cellular spore, a cell form that can be used for dissemination, for survival of adverse conditions because of its heat and dessication resistance, and/or for reproduction.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

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

UniProtKB/Swiss-Prot
        GPMI_GEOSE | Q9X5191eqj 1o98 1o99

(-) Related Entries Specified in the PDB File

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