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(-) Description

Title :  PHOSPHOENOLPYRUVATE MUTASE FROM MOLLUSK IN WITH BOUND MG2-OXALATE
 
Authors :  K. Huang, Z. Li, O. Herzberg
Date :  25 Feb 99  (Deposition) - 21 Jul 99  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Phosphotransferase, Phosphomutase, P-C Bond Formation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Huang, Z. Li, Y. Jia, D. Dunaway-Mariano, O. Herzberg
Helix Swapping Between Two Alpha/Beta Barrels: Crystal Structure Of Phosphoenolpyruvate Mutase With Bound Mg(2+)-Oxalate.
Structure Fold. Des. V. 7 539 1999
PubMed-ID: 10378273  |  Reference-DOI: 10.1016/S0969-2126(99)80070-7

(-) Compounds

Molecule 1 - PROTEIN (PHOSPHOENOLPYRUVATE MUTASE)
    Chains: A, B
    EC Number: 5.4.2.9
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: B834(DE3)
    Expression System Taxid: 562
    Expression System Vector: PET24A(+)
    Organism Scientific: MYTILUS EDULIS
    Organism Taxid: 6550
    Other Details: WITH BOUND MG2+-OXALATE INHIBITOR
    Synonym: PHOSPHOENOLPYRUVATE 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  (3, 18)

Asymmetric Unit (3, 18)
No.NameCountTypeFull Name
1MG2Ligand/IonMAGNESIUM ION
2MSE14Mod. Amino AcidSELENOMETHIONINE
3OXL2Ligand/IonOXALATE ION
Biological Unit 1 (2, 32)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2MSE28Mod. Amino AcidSELENOMETHIONINE
3OXL4Ligand/IonOXALATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:44 , SER A:46 , GLY A:47 , LEU A:48 , ASP A:85 , ARG A:159 , ALA A:238 , MG A:1003 , HOH A:1073 , HOH A:1086 , HOH A:1109 , HOH A:1245BINDING SITE FOR RESIDUE OXL A 1001
2AC2SOFTWARETRP B:44 , SER B:46 , GLY B:47 , LEU B:48 , ASP B:85 , ARG B:159 , ALA B:238 , MG B:1004 , HOH B:1010 , HOH B:1144BINDING SITE FOR RESIDUE OXL B 1002
3AC3SOFTWAREASP A:85 , OXL A:1001 , HOH A:1073 , HOH A:1086 , HOH A:1158BINDING SITE FOR RESIDUE MG A 1003
4AC4SOFTWAREASP B:85 , OXL B:1002 , HOH B:1089 , HOH B:1094 , HOH B:1115BINDING SITE FOR RESIDUE MG B 1004
5PEPAUTHORASP A:58 , ASP A:85 , ASP A:87 , GLU A:114 , ARG A:159 , LYS A:120 , GLY A:47 , LEU A:48 , ASP B:58 , ASP B:85 , ASP B:87 , GLU B:114 , ARG B:159 , LYS B:120 , GLY B:47 , LEU B:48CATALYTIC SITE

(-) SS Bonds  (0, 0)

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

(-) 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 1PYM)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1PYM)

(-) 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:291
 aligned with PEPM_MYTED | P56839 from UniProtKB/Swiss-Prot  Length:295

    Alignment length:291
                                    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 VKKTTQLKQMLNSKDLEFIMEAHNGLSARIVQEAGFKGIWGSGLSVSAQLGVRDSNEASWTQVVEVLEFMSDASDVPILLDADTGYGNFNNARRLVRKLEDRGVAGACLEDKLFPKTNSLHDGRAQPLADIEEFALKIKACKDSQTDPDFCIVARVEAFIAGWGLDEALKRAEAYRNAGADAILMHSKKADPSDIEAFMKAWNNQGPVVIVPTKYYKTPTDHFRDMGVSMVIWANHNLRASVSAIQQTTKQIYDDQSLVNVEDKIVSVKEIFRLQRDDELVQAEDKYLPKN 295
               SCOP domains d1pyma_ A: Phosphoenolpyruvate mutase                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 1pymA00 A:5-295 Phosphoenolpyruvate-binding domains                                                                                                                                                                                                                                                 CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhh............hhhhhhhhh....eeee.hhhhhhhh.........hhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhh...eeeee....................hhhhhhhhhhhhh.......eeeee.........hhhhhhhhhhhhh....eee........hhhhhhhhh..................hhhhh...........hhhhhhhhhhhhhhhhhhhh...hhhh.....hhhhhhh..hhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pym A   5 VKKTTQLKQmLNSKDLEFImEAHNGLSARIVQEAGFKGIWGSGLSVSAQLGVRDSNEASWTQVVEVLEFmSDASDVPILLDADTGYGNFNNARRLVRKLEDRGVAGACLEDKLFPKTNSLHDGRAQPLADIEEFALKIKACKDSQTDPDFCIVARVEAFIAGWGLDEALKRAEAYRNAGADAILmHSKKADPSDIEAFmKAWNNQGPVVIVPTKYYKTPTDHFRDmGVSmVIWANHNLRASVSAIQQTTKQIYDDQSLVNVEDKIVSVKEIFRLQRDDELVQAEDKYLPKN 295
                                    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 
                                    14-MSE    24-MSE                                            74-MSE                                                                                                            189-MSE       203-MSE                    230-MSE                                                             
                                                                                                                                                                                                                                                               234-MSE                                                         


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 d1pymb_ B: Phosphoenolpyruvate mutase                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 1pymB00 B:5-293 Phosphoenolpyruvate-binding domains                                                                                                                                                                                                                                               CATH domains
           Pfam domains (1) ------PEP_mutase-1pymB01 B:11-257                                                                                                                                                                                                                            ------------------------------------ Pfam domains (1)
           Pfam domains (2) ------PEP_mutase-1pymB02 B:11-257                                                                                                                                                                                                                            ------------------------------------ Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhh............hhhhhhhhhh...eeee.hhhhhhhh.........hhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhh...eeeee....................hhhhhhhhhhhhhh......eeeee.........hhhhhhhhhhhhh....eee........hhhhhhhhh..................hhhhh...........hhhhhhhhhhhhhhhhhhhh...hhhh.....hhhhhhh..hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pym B   5 VKKTTQLKQmLNSKDLEFImEAHNGLSARIVQEAGFKGIWGSGLSVSAQLGVRDSNEASWTQVVEVLEFmSDASDVPILLDADTGYGNFNNARRLVRKLEDRGVAGACLEDKLFPKTNSLHDGRAQPLADIEEFALKIKACKDSQTDPDFCIVARVEAFIAGWGLDEALKRAEAYRNAGADAILmHSKKADPSDIEAFmKAWNNQGPVVIVPTKYYKTPTDHFRDmGVSmVIWANHNLRASVSAIQQTTKQIYDDQSLVNVEDKIVSVKEIFRLQRDDELVQAEDKYLP 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         
                                    14-MSE    24-MSE                                            74-MSE                                                                                                            189-MSE       203-MSE                    230-MSE                                                           
                                                                                                                                                                                                                                                               234-MSE
   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: 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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        PEPM_MYTED | P56839: 1m1b 1s2t 1s2u 1s2v 1s2w

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