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(-) Description

Title :  CRYSTAL STRUCTURE OF PYRUVATE AND MG2+ BOUND 2-METHYLISOCITRATE LYASE (PRPB) FROM SALMONELLA TYPHIMURIUM
 
Authors :  D. K. Simanshu, M. R. N. Murthy
Date :  04 Oct 03  (Deposition) - 25 Nov 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Prpb, Lyase, Methylisocitrate, Methylcitrate Cycle, Propionate Metabolism, Helix Swapping (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. K. Simanshu, P. S. Satheshkumar, H. S. Savithri, M. R. N. Murthy
Crystal Structure Of Salmonella Typhimurium 2-Methylisocitrate Lyase (Prpb) And Its Complex With Pyruvate And Mg(2+)
Biochem. Biophys. Res. Commun. V. 311 193 2003
PubMed-ID: 14575713  |  Reference-DOI: 10.1016/J.BBRC.2003.09.193
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROBABLE METHYLISOCITRATE LYASE
    Chains: A, B, C, D
    EC Number: 4.1.3.30
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-BLUE VECTOR
    Expression System Strain: BL21(DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PRPB
    Organism Scientific: SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM
    Organism Taxid: 90371
    Strain: IFO 12529
    Synonym: 2-METHYLISOCITRATE LYASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric/Biological Unit (2, 8)
No.NameCountTypeFull Name
1MG4Ligand/IonMAGNESIUM ION
2PYR4Ligand/IonPYRUVIC ACID

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:85 , PYR A:1302 , HOH A:1452 , HOH A:1455BINDING SITE FOR RESIDUE MG A 1301
2AC2SOFTWAREASP B:85 , ARG B:158 , PYR B:2302 , HOH B:2400 , HOH B:2454 , HOH B:2456BINDING SITE FOR RESIDUE MG B 2301
3AC3SOFTWAREASP C:85 , PYR C:3302 , HOH C:3379 , HOH C:3403BINDING SITE FOR RESIDUE MG C 3301
4AC4SOFTWAREASP D:85 , PYR D:4302 , HOH D:4376 , HOH D:4377 , HOH D:4380BINDING SITE FOR RESIDUE MG D 4301
5AC5SOFTWARETYR A:43 , SER A:45 , GLY A:46 , GLY A:47 , ASP A:85 , ARG A:158 , PRO A:236 , MG A:1301BINDING SITE FOR RESIDUE PYR A 1302
6AC6SOFTWARETYR B:43 , SER B:45 , GLY B:46 , GLY B:47 , ASP B:85 , ARG B:158 , PRO B:236 , MG B:2301BINDING SITE FOR RESIDUE PYR B 2302
7AC7SOFTWARETYR C:43 , SER C:45 , GLY C:46 , GLY C:47 , ASP C:85 , ARG C:158 , PRO C:236 , MG C:3301BINDING SITE FOR RESIDUE PYR C 3302
8AC8SOFTWARETYR D:43 , SER D:45 , GLY D:47 , ASP D:85 , ARG D:158 , PRO D:236 , MG D:4301 , HOH D:4385BINDING SITE FOR RESIDUE PYR D 4302

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1O5Q)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Asn A:18 -Pro A:19
2Asn B:18 -Pro B:19
3Asn C:18 -Pro C:19
4Asn D:18 -Pro D:19

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1O5Q)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1O5Q)

(-) Exons   (0, 0)

(no "Exon" information available for 1O5Q)

(-) 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:271
 aligned with PRPB_SALTY | Q56062 from UniProtKB/Swiss-Prot  Length:295

    Alignment length:282
                                    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  
           PRPB_SALTY     5 SPGQAFRAALAKENPLQIVGAINANHALLAQRAGYQAIYLSGGGVAAGSLGLPDLGISTLDDVLTDIRRITDVCPLPLLVDADIGFGSSAFNVARTVKSIAKAGAAALHIEDQVGAKRCGHRPNKAIVSKEEMVDRIRAAVDARTDPNFVIMARTDALAVEGLEAALDRAQAYVDAGADMLFPEAITELSMYRRFADVAQVPILANITEFGATPLFTTDELRSAHVAMALYPLSAFRAMNRAAEKVYTVLRQEGTQKNVIDIMQTRNELYESINYYQFEEKL 286
               SCOP domains d1o5qa_ A: 2-methylisocitrate lyase                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 1o5qA00 A:5-286 Phosphoenolpyruvate-binding domains                                                                                                                                                                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhh..eeeee..hhhhhhhhhhh...eeeehhhhhhhh..........hhhhhhhhhhhhhh.....eeee.......hhhhhhhhhhhhhhh...eeeee...-----------...hhhhhhhhhhhhhhhh.....eeeeeehhhhhhhhhhhhhhhhhhhhhh..eeee....hhhhhhhhhhhhh...eee..........hhhhhhh....eeee.hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh.hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1o5q A   5 SPGQAFRAALAKENPLQIVGAINANHALLAQRAGYQAIYLSGGGVAAGSLGLPDLGISTLDDVLTDIRRITDVCPLPLLVDADIGFGSSAFNVARTVKSIAKAGAAALHIEDQV-----------AIVSKEEMVDRIRAAVDARTDPNFVIMARTDALAVEGLEAALDRAQAYVDAGADMLFPEAITELSMYRRFADVAQVPILANITEFGATPLFTTDELRSAHVAMALYPLSAFRAMNRAAEKVYTVLRQEGTQKNVIDIMQTRNELYESINYYQFEEKL 286
                                    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  
                                                                                                                                           118         130                                                                                                                                                            


Chain B from PDB  Type:PROTEIN  Length:268
 aligned with PRPB_SALTY | Q56062 from UniProtKB/Swiss-Prot  Length:295

    Alignment length:279
                                    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         
           PRPB_SALTY     5 SPGQAFRAALAKENPLQIVGAINANHALLAQRAGYQAIYLSGGGVAAGSLGLPDLGISTLDDVLTDIRRITDVCPLPLLVDADIGFGSSAFNVARTVKSIAKAGAAALHIEDQVGAKRCGHRPNKAIVSKEEMVDRIRAAVDARTDPNFVIMARTDALAVEGLEAALDRAQAYVDAGADMLFPEAITELSMYRRFADVAQVPILANITEFGATPLFTTDELRSAHVAMALYPLSAFRAMNRAAEKVYTVLRQEGTQKNVIDIMQTRNELYESINYYQFE 283
               SCOP domains d1o5qb_ B: 2-methylisocitrate lyase                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 1o5qB00 B:5-283 Phosphoenolpyruvate-binding domains                                                                                                                                                                                                                                     CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh..eeeee..hhhhhhhhhhh....eeehhhhhhhh..........hhhhhhhhhhhhhhhh...eeee.......hhhhhhhhhhhhhhh...eeeee...-----------...hhhhhhhhhhhhhhhh.....eeeeeehhhhhhhhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhh...eee..........hhhhhhhh...eeee.hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh.hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1o5q B   5 SPGQAFRAALAKENPLQIVGAINANHALLAQRAGYQAIYLSGGGVAAGSLGLPDLGISTLDDVLTDIRRITDVCPLPLLVDADIGFGSSAFNVARTVKSIAKAGAAALHIEDQV-----------AIVSKEEMVDRIRAAVDARTDPNFVIMARTDALAVEGLEAALDRAQAYVDAGADMLFPEAITELSMYRRFADVAQVPILANITEFGATPLFTTDELRSAHVAMALYPLSAFRAMNRAAEKVYTVLRQEGTQKNVIDIMQTRNELYESINYYQFE 283
                                    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         
                                                                                                                                           118         130                                                                                                                                                         


Chain C from PDB  Type:PROTEIN  Length:275
 aligned with PRPB_SALTY | Q56062 from UniProtKB/Swiss-Prot  Length:295

    Alignment length:286
                                    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      
           PRPB_SALTY     4 HSPGQAFRAALAKENPLQIVGAINANHALLAQRAGYQAIYLSGGGVAAGSLGLPDLGISTLDDVLTDIRRITDVCPLPLLVDADIGFGSSAFNVARTVKSIAKAGAAALHIEDQVGAKRCGHRPNKAIVSKEEMVDRIRAAVDARTDPNFVIMARTDALAVEGLEAALDRAQAYVDAGADMLFPEAITELSMYRRFADVAQVPILANITEFGATPLFTTDELRSAHVAMALYPLSAFRAMNRAAEKVYTVLRQEGTQKNVIDIMQTRNELYESINYYQFEEKLDAL 289
               SCOP domains d1o5qc_ C: 2-methylisocitrate lyase                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 1o5qC00 C:4-289 Phosphoenolpyruvate-binding domains                                                                                                                                                                                                                                            CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh..eeeee..hhhhhhhhhhh...eeeehhhhhhhh..........hhhhhhhhhhhhhhhh...eeee.......hhhhhhhhhhhhhhh...eeeee...-----------...hhhhhhhhhhhhhhhh.....eeeeeehhhhh.hhhhhhhhhhhhhhhh..eeee....hhhhhhhhhhhhh...eee..........hhhhhhhh...eeee.hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh.hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1o5q C   4 HSPGQAFRAALAKENPLQIVGAINANHALLAQRAGYQAIYLSGGGVAAGSLGLPDLGISTLDDVLTDIRRITDVCPLPLLVDADIGFGSSAFNVARTVKSIAKAGAAALHIEDQV-----------AIVSKEEMVDRIRAAVDARTDPNFVIMARTDALAVEGLEAALDRAQAYVDAGADMLFPEAITELSMYRRFADVAQVPILANITEFGATPLFTTDELRSAHVAMALYPLSAFRAMNRAAEKVYTVLRQEGTQKNVIDIMQTRNELYESINYYQFEEKLDAL 289
                                    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      
                                                                                                                                            118         130                                                                                                                                                               


Chain D from PDB  Type:PROTEIN  Length:268
 aligned with PRPB_SALTY | Q56062 from UniProtKB/Swiss-Prot  Length:295

    Alignment length:279
                                    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         
           PRPB_SALTY     4 HSPGQAFRAALAKENPLQIVGAINANHALLAQRAGYQAIYLSGGGVAAGSLGLPDLGISTLDDVLTDIRRITDVCPLPLLVDADIGFGSSAFNVARTVKSIAKAGAAALHIEDQVGAKRCGHRPNKAIVSKEEMVDRIRAAVDARTDPNFVIMARTDALAVEGLEAALDRAQAYVDAGADMLFPEAITELSMYRRFADVAQVPILANITEFGATPLFTTDELRSAHVAMALYPLSAFRAMNRAAEKVYTVLRQEGTQKNVIDIMQTRNELYESINYYQF 282
               SCOP domains d1o5qd_ D: 2-methylisocitrate lyase                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 1o5qD00 D:4-282 Phosphoenolpyruvate-binding domains                                                                                                                                                                                                                                     CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh..eeeee..hhhhhhhhhhh...eeeehhhhhhhh..........hhhhhhhhhhhhhhhh...eeee.......hhhhhhhhhhhhhhhh..eeeee...-----------...hhhhhhhhhhhhhhhh.....eeeeeehhhhhhhhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhh...eee..........hhhhhhhh...eeee.hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh.hhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1o5q D   4 HSPGQAFRAALAKENPLQIVGAINANHALLAQRAGYQAIYLSGGGVAAGSLGLPDLGISTLDDVLTDIRRITDVCPLPLLVDADIGFGSSAFNVARTVKSIAKAGAAALHIEDQV-----------AIVSKEEMVDRIRAAVDARTDPNFVIMARTDALAVEGLEAALDRAQAYVDAGADMLFPEAITELSMYRRFADVAQVPILANITEFGATPLFTTDELRSAHVAMALYPLSAFRAMNRAAEKVYTVLRQEGTQKNVIDIMQTRNELYESINYYQF 282
                                    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         
                                                                                                                                            118         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  (0, 0)

(no "Pfam Domain" information available for 1O5Q)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (PRPB_SALTY | Q56062)
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:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0046421    methylisocitrate lyase activity    Catalysis of the reaction: (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate = pyruvate + succinate.
    GO:0046912    transferase activity, transferring acyl groups, acyl groups converted into alkyl on transfer    Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor), with the acyl group being converted into alkyl on transfer.
biological process
    GO:0006097    glyoxylate cycle    A modification of the TCA cycle occurring in some plants and microorganisms, in which isocitrate is cleaved to glyoxylate and succinate. Glyoxylate can then react with acetyl-CoA to form malate.
    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:0019629    propionate catabolic process, 2-methylcitrate cycle    The chemical reactions and pathways resulting in the breakdown of propionate that occurs in the 2-methylcitrate cycle.
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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  1o5q
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  PRPB_SALTY | Q56062
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 Related Entries

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

UniProtKB/Swiss-Prot
        PRPB_SALTY | Q56062: 1ujq

(-) Related Entries Specified in the PDB File

1ujq THE SAME PROTEIN WITHOUT LIGAND.