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(-) Description

Title :  CRYSTAL STRUCTURE OF THE D58A PHOSPHOENOLPYRUVATE MUTASE MUTANT PROTEIN
 
Authors :  S. Liu, Z. Lu, Y. Han, Y. Jia, A. Howard, D. Dunaway-Mariano, O. Herzberg
Date :  11 Jan 04  (Deposition) - 04 May 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Phosphoenolpyruvate Mutase, Pep Mutase, Phosphonopyruvate, Phosphonate Biosynthesis Pathway, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Liu, Z. Lu, Y. Han, Y. Jia, A. Howard, D. Dunaway-Mariano, O. Herzber
Conformational Flexibility Of Pep Mutase
Biochemistry V. 43 4447 2004
PubMed-ID: 15078090  |  Reference-DOI: 10.1021/BI036255H

(-) Compounds

Molecule 1 - PHOSPHOENOLPYRUVATE PHOSPHOMUTASE
    Chains: A, B
    EC Number: 5.4.2.9
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET3C
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: MYTILUS EDULIS
    Organism Taxid: 6550
    Synonym: PHOSPHOENOLPYRUVATE MUTASE, PEP MUTASE, PEP PHOSPHOMUTASE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1PEG4Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:44 , SER A:46 , ASP A:85 , ARG A:159 , ALA A:238 , HOH A:843 , HOH A:858BINDING SITE FOR RESIDUE PEG A 600
2AC2SOFTWAREARG B:159 , HIS B:190 , VAL B:215 , THR B:217 , ASN B:239 , HOH B:735 , HOH B:744 , HOH B:873 , HOH B:936BINDING SITE FOR RESIDUE PEG B 700

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1S2U)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Phe A:118 -Pro A:119
2Phe B:118 -Pro B:119

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1S2U)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1S2U)

(-) Exons   (0, 0)

(no "Exon" information available for 1S2U)

(-) 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:290
 aligned with PEPM_MYTED | P56839 from UniProtKB/Swiss-Prot  Length:295

    Alignment length:290
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294
           PEPM_MYTED     5 VKKTTQLKQMLNSKDLEFIMEAHNGLSARIVQEAGFKGIWGSGLSVSAQLGVRDSNEASWTQVVEVLEFMSDASDVPILLDADTGYGNFNNARRLVRKLEDRGVAGACLEDKLFPKTNSLHDGRAQPLADIEEFALKIKACKDSQTDPDFCIVARVEAFIAGWGLDEALKRAEAYRNAGADAILMHSKKADPSDIEAFMKAWNNQGPVVIVPTKYYKTPTDHFRDMGVSMVIWANHNLRASVSAIQQTTKQIYDDQSLVNVEDKIVSVKEIFRLQRDDELVQAEDKYLPK 294
               SCOP domains d1s2ua_ A: Phosphoenolpyruvate mutase                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 1s2uA00 A:5-294 Phosphoenolpyruvate-binding domains                                                                                                                                                                                                                                                CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh...eeeeee.hhhhhhhhhhh....eeehhhhhhhhhh.......hhhhhhhhhhhhhhh....eeee......hhhhhhhhhhhhhhh...eeeee...................hhhhhhhhhhhhhhhh.....eeeeee.......hhhhhhhhhhhhhhh...eeee......hhhhhhhhhhhh....eee........hhhhhhhh...eeee.hhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1s2u A   5 VKKTTQLKQMLNSKDLEFIMEAHNGLSARIVQEAGFKGIWGSGLSVSAQLGVRASNEASWTQVVEVLEFMSDASDVPILLDADTGYGNFNNARRLVRKLEDRGVAGACLEDKLFPKTNSLHDGRAQPLADIEEFALKIKACKDSQTDPDFCIVARVEAFIAGWGLDEALKRAEAYRNAGADAILMHSKKADPSDIEAFMKAWNNQGPVVIVPTKYYKTPTDHFRDMGVSMVIWANHNLRASVSAIQQTTKQIYDDQSLVNVEDKIVSVKEIFRLQRDDELVQAEDKYLPK 294
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294


Chain B from PDB  Type:PROTEIN  Length:289
 aligned with PEPM_MYTED | P56839 from UniProtKB/Swiss-Prot  Length:295

    Alignment length:289
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284         
           PEPM_MYTED     5 VKKTTQLKQMLNSKDLEFIMEAHNGLSARIVQEAGFKGIWGSGLSVSAQLGVRDSNEASWTQVVEVLEFMSDASDVPILLDADTGYGNFNNARRLVRKLEDRGVAGACLEDKLFPKTNSLHDGRAQPLADIEEFALKIKACKDSQTDPDFCIVARVEAFIAGWGLDEALKRAEAYRNAGADAILMHSKKADPSDIEAFMKAWNNQGPVVIVPTKYYKTPTDHFRDMGVSMVIWANHNLRASVSAIQQTTKQIYDDQSLVNVEDKIVSVKEIFRLQRDDELVQAEDKYLP 293
               SCOP domains d1s2ub_ B: Phosphoenolpyruvate mutase                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 1s2uB00 B:5-293 Phosphoenolpyruvate-binding domains                                                                                                                                                                                                                                               CATH domains
           Pfam domains (1) ------PEP_mutase-1s2uB01 B:11-257                                                                                                                                                                                                                            ------------------------------------ Pfam domains (1)
           Pfam domains (2) ------PEP_mutase-1s2uB02 B:11-257                                                                                                                                                                                                                            ------------------------------------ Pfam domains (2)
         Sec.struct. author .hhhhhhhhhhhh...eeeeee.hhhhhhhhhhh....eeehhhhhhhhh........hhhhhhhhhhhhhhh....eeee......hhhhhhhhhhhhhhhh..eeeee...................hhhhhhhhhhhhhhhh.....eeeeee.......hhhhhhhhhhhhhhh...eeee......hhhhhhhhhhhh....eee........hhhhhhhh...eeee.hhhhhhhhhhhhhhhhhhhhhh....hhhhh.hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1s2u B   5 VKKTTQLKQMLNSKDLEFIMEAHNGLSARIVQEAGFKGIWGSGLSVSAQLGVRASNEASWTQVVEVLEFMSDASDVPILLDADTGYGNFNNARRLVRKLEDRGVAGACLEDKLFPKTNSLHDGRAQPLADIEEFALKIKACKDSQTDPDFCIVARVEAFIAGWGLDEALKRAEAYRNAGADAILMHSKKADPSDIEAFMKAWNNQGPVVIVPTKYYKTPTDHFRDMGVSMVIWANHNLRASVSAIQQTTKQIYDDQSLVNVEDKIVSVKEIFRLQRDDELVQAEDKYLP 293
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284
   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  (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: PK_TIM (63)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (PEPM_MYTED | P56839)
molecular function
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0050188    phosphoenolpyruvate mutase activity    Catalysis of the reaction: phosphoenolpyruvate = 3-phosphonopyruvate.
biological process
    GO:0032923    organic phosphonate biosynthetic process    The chemical reactions and pathways resulting in the formation of phosphonates, any organic compound containing one or more C-PO(OH)2 or C-PO(OR)2 (with R=alkyl, aryl) groups. Synthesis of phosphonic acid itself, an inorganic compound without the biochemically relevant C-P bond, is not included.

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 Related Entries

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UniProtKB/Swiss-Prot
        PEPM_MYTED | P56839: 1m1b 1pym 1s2t 1s2v 1s2w

(-) Related Entries Specified in the PDB File

1m1b 1pym 1s2t 1s2v 1s2w