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(-) Description

Title :  CRYSTAL STRUCTURE OF PHOSPHOENOLPYRUVATE MUTASE COMPLEXED WITH MG(II)
 
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) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Phosphoenolpyruvate Mutase, Pep Mutase, Phosphonopyruvate, Phosphonate Biosynthesis Pathway, X-Ray Structure, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Liu, Z. Lu, Y. Han, Y. Jia, A. Howard, D. Dunaway-Mariano, O. Herzberg
Conformational Flexibility Of Pep Mutase
Biochemistry V. 43 4447 2004
PubMed-ID: 15078090  |  Reference-DOI: 10.1021/BI036255H
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PHOSPHOENOLPYRUVATE PHOSPHOMUTASE
    Chains: A, B, C, D
    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
    Organism Scientific: MYTILUS EDULIS
    Organism Taxid: 6550
    Synonym: PHOSPHOENOLPYRUVATE MUTASE, PEP MUTASE, PEP PHOSPHOMUTASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1MG4Ligand/IonMAGNESIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:85 , ARG A:159 , HOH A:1007 , HOH A:1114 , HOH A:1163 , HOH A:1211 , HOH A:1224BINDING SITE FOR RESIDUE MG A 1001
2AC2SOFTWAREASP B:58 , ASP B:85 , HOH B:1196 , HOH B:1234 , HOH B:1235 , HOH B:1236 , HOH B:1238BINDING SITE FOR RESIDUE MG B 1002
3AC3SOFTWAREASP C:58 , ASP C:85 , HOH C:1119 , HOH C:1193 , HOH C:1221 , HOH C:1242 , HOH C:1243BINDING SITE FOR RESIDUE MG C 1003
4AC4SOFTWAREASP D:85 , HOH D:1065 , HOH D:1187 , HOH D:1189 , HOH D:1196 , HOH D:1228BINDING SITE FOR RESIDUE MG D 1004

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1S2V)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Phe A:118 -Pro A:119
2Phe B:118 -Pro B:119
3Phe C:118 -Pro C:119
4Phe D:118 -Pro D:119

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1S2V)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1S2V)

(-) Exons   (0, 0)

(no "Exon" information available for 1S2V)

(-) 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:282
 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 d1s2va_ A: Phosphoenolpyruvate mutase                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 1s2vA00 A:5-293 Phosphoenolpyruvate-binding domains                                                                                                                                                                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh....eeeeee.hhhhhhhhhhhh...eeehhhhhhhhh........hhhhhhhhhhhhhhh....eeee......hhhhhhhhhhhhhhhh..eeeee........-------....hhhhhhhhhhhhhhhh.....eeeeeehhhhhh.hhhhhhhhhhhhhhhh..eeee......hhhhhhhhhhhh....eee........hhhhhhhhh..eeee.hhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1s2v A   5 VKKTTQLKQMLNSKDLEFIMEAHNGLSARIVQEAGFKGIWGSGLSVSAQLGVRDSNEASWTQVVEVLEFMSDASDVPILLDADTGYGNFNNARRLVRKLEDRGVAGACLEDKLFPKTN-------QPLADIEEFALKIKACKDSQTDPDFCIVARVEAFIAGWGLDEALKRAEAYRNAGADAILMHSKKADPSDIEAFMKAWNNQGPVVIVPTKYYKTPTDHFRDMGVSMVIWANHNLRASVSAIQQTTKQIYDDQSLVNVEDKIVSVKEIFRLQRDDELVQAEDKYLP 293
                                    14        24        34        44        54        64        74        84        94       104       114       | -     | 134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284         
                                                                                                                                               122     130                                                                                                                                                                   


Chain B from PDB  Type:PROTEIN  Length:287
 aligned with PEPM_MYTED | P56839 from UniProtKB/Swiss-Prot  Length:295

    Alignment length:290
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293
           PEPM_MYTED     4 KVKKTTQLKQMLNSKDLEFIMEAHNGLSARIVQEAGFKGIWGSGLSVSAQLGVRDSNEASWTQVVEVLEFMSDASDVPILLDADTGYGNFNNARRLVRKLEDRGVAGACLEDKLFPKTNSLHDGRAQPLADIEEFALKIKACKDSQTDPDFCIVARVEAFIAGWGLDEALKRAEAYRNAGADAILMHSKKADPSDIEAFMKAWNNQGPVVIVPTKYYKTPTDHFRDMGVSMVIWANHNLRASVSAIQQTTKQIYDDQSLVNVEDKIVSVKEIFRLQRDDELVQAEDKYLP 293
               SCOP domains d1s2vb_ B: Phosphoenolpyruvate mutase                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 1s2vB00 B:4-293 Phosphoenolpyruvate-binding domains                                                                                                                                                                                                                                                CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh...eeeeee.hhhhhhhhhhhh...eeehhhhhhhhh........hhhhhhhhhhhhhhh....eeee......hhhhhhhhhhhhhhhh..eeeee.........---.......hhhhhhhhhhhhhhhh.....eeeeeehhhhhh.hhhhhhhhhhhhhh....eeee......hhhhhhhhhhhh....eee........hhhhhhhhh..eeee.hhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1s2v B   4 KVKKTTQLKQMLNSKDLEFIMEAHNGLSARIVQEAGFKGIWGSGLSVSAQLGVRDSNEASWTQVVEVLEFMSDASDVPILLDADTGYGNFNNARRLVRKLEDRGVAGACLEDKLFPKTNS---GRAQPLADIEEFALKIKACKDSQTDPDFCIVARVEAFIAGWGLDEALKRAEAYRNAGADAILMHSKKADPSDIEAFMKAWNNQGPVVIVPTKYYKTPTDHFRDMGVSMVIWANHNLRASVSAIQQTTKQIYDDQSLVNVEDKIVSVKEIFRLQRDDELVQAEDKYLP 293
                                    13        23        33        43        53        63        73        83        93       103       113       123   |   133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293
                                                                                                                                                 123 127                                                                                                                                                                      


Chain C from PDB  Type:PROTEIN  Length:282
 aligned with PEPM_MYTED | P56839 from UniProtKB/Swiss-Prot  Length:295

    Alignment length:291
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293 
           PEPM_MYTED     4 KVKKTTQLKQMLNSKDLEFIMEAHNGLSARIVQEAGFKGIWGSGLSVSAQLGVRDSNEASWTQVVEVLEFMSDASDVPILLDADTGYGNFNNARRLVRKLEDRGVAGACLEDKLFPKTNSLHDGRAQPLADIEEFALKIKACKDSQTDPDFCIVARVEAFIAGWGLDEALKRAEAYRNAGADAILMHSKKADPSDIEAFMKAWNNQGPVVIVPTKYYKTPTDHFRDMGVSMVIWANHNLRASVSAIQQTTKQIYDDQSLVNVEDKIVSVKEIFRLQRDDELVQAEDKYLPK 294
               SCOP domains d1s2vc_ C: Phosphoenolpyruvate mutase                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 1s2vC00 C:4-294 Phosphoenolpyruvate-binding domains                                                                                                                                                                                                                                                 CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh...eeeeee.hhhhhhhhhhhh...eeehhhhhhhhh........hhhhhhhhhhhhhhh....eeee......hhhhhhhhhhhhhhhh..eeeee......---------....hhhhhhhhhhhhhhhh.....eeeeee.......hhhhhhhhhhhhhhh...eeee......hhhhhhhhhhhh....eee.........hhhhhhh...eeee.hhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1s2v C   4 KVKKTTQLKQMLNSKDLEFIMEAHNGLSARIVQEAGFKGIWGSGLSVSAQLGVRDSNEASWTQVVEVLEFMSDASDVPILLDADTGYGNFNNARRLVRKLEDRGVAGACLEDKLFPK---------QPLADIEEFALKIKACKDSQTDPDFCIVARVEAFIAGWGLDEALKRAEAYRNAGADAILMHSKKADPSDIEAFMKAWNNQGPVVIVPTKYYKTPTDHFRDMGVSMVIWANHNLRASVSAIQQTTKQIYDDQSLVNVEDKIVSVKEIFRLQRDDELVQAEDKYLPK 294
                                    13        23        33        43        53        63        73        83        93       103       113      |  -      |133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293 
                                                                                                                                              120       130                                                                                                                                                                    


Chain D from PDB  Type:PROTEIN  Length:281
 aligned with PEPM_MYTED | P56839 from UniProtKB/Swiss-Prot  Length:295

    Alignment length:291
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293 
           PEPM_MYTED     4 KVKKTTQLKQMLNSKDLEFIMEAHNGLSARIVQEAGFKGIWGSGLSVSAQLGVRDSNEASWTQVVEVLEFMSDASDVPILLDADTGYGNFNNARRLVRKLEDRGVAGACLEDKLFPKTNSLHDGRAQPLADIEEFALKIKACKDSQTDPDFCIVARVEAFIAGWGLDEALKRAEAYRNAGADAILMHSKKADPSDIEAFMKAWNNQGPVVIVPTKYYKTPTDHFRDMGVSMVIWANHNLRASVSAIQQTTKQIYDDQSLVNVEDKIVSVKEIFRLQRDDELVQAEDKYLPK 294
               SCOP domains d1s2vd_ D: Phosphoenolpyruvate mutase                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 1s2vD00 D:4-294 Phosphoenolpyruvate-binding domains                                                                                                                                                                                                                                                 CATH domains
           Pfam domains (1) -------PEP_mutase-1s2vD01 D:11-257                                                                                                                                                                                                                            ------------------------------------- Pfam domains (1)
           Pfam domains (2) -------PEP_mutase-1s2vD02 D:11-257                                                                                                                                                                                                                            ------------------------------------- Pfam domains (2)
           Pfam domains (3) -------PEP_mutase-1s2vD03 D:11-257                                                                                                                                                                                                                            ------------------------------------- Pfam domains (3)
           Pfam domains (4) -------PEP_mutase-1s2vD04 D:11-257                                                                                                                                                                                                                            ------------------------------------- Pfam domains (4)
         Sec.struct. author ..hhhhhhhhhhhh...eeeeee.hhhhhhhhhhhh...eeehhhhhhhhh........hhhhhhhhhhhhhhh....eeee......hhhhhhhhhhhhhhhh..eeeee.....----------....hhhhhhhhhhhhhhhh.....eeeeee.......hhhhhhhhhhhhhhh...eeee......hhhhhhhhhhhh....eee........hhhhhhhhh..eeee.hhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1s2v D   4 KVKKTTQLKQMLNSKDLEFIMEAHNGLSARIVQEAGFKGIWGSGLSVSAQLGVRDSNEASWTQVVEVLEFMSDASDVPILLDADTGYGNFNNARRLVRKLEDRGVAGACLEDKLFP----------QPLADIEEFALKIKACKDSQTDPDFCIVARVEAFIAGWGLDEALKRAEAYRNAGADAILMHSKKADPSDIEAFMKAWNNQGPVVIVPTKYYKTPTDHFRDMGVSMVIWANHNLRASVSAIQQTTKQIYDDQSLVNVEDKIVSVKEIFRLQRDDELVQAEDKYLPK 294
                                    13        23        33        43        53        63        73        83        93       103       113     |   -      |133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293 
                                                                                                                                             119        130
   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, 4)

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

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Clan: PK_TIM (63)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (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

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

UniProtKB/Swiss-Prot
        PEPM_MYTED | P56839: 1m1b 1pym 1s2t 1s2u 1s2w

(-) Related Entries Specified in the PDB File

1m1b 1pym 1s2t 1s2u 1s2w