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(-) Description

Title :  STRUCTURE OF THE 2-METHYLISOCITRATE LYASE (PRPB) FROM ESCHERICHIA COLI
 
Authors :  C. Grimm, K. Reuter
Date :  24 Sep 02  (Deposition) - 29 Apr 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Prpb, Lyase, Methylisocitrate, Methylcitrate Cycle, Tim-Barrel (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Grimm, A. Evers, M. Brock, C. Maerker, G. Klebe, W. Buckel, K. Reuter
Crystal Structure Of 2-Methylisocitrate Lyase (Prpb) From Escherichia Coli And Modelling Of Its Ligand Bound Active Centre.
J. Mol. Biol. V. 328 609 2003
PubMed-ID: 12706720  |  Reference-DOI: 10.1016/S0022-2836(03)00358-9

(-) Compounds

Molecule 1 - 2-METHYLISOCITRATE LYASE
    Chains: A, B
    EC Number: 4.1.3.30
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQUE30-PRPB
    Expression System Strain: TOP10
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Strain: W3350
    Synonym: PRPB

 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
1MG2Ligand/IonMAGNESIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:58 , ASP A:87 , HOH A:1006 , HOH A:1031 , HOH A:1044 , HOH A:1076 , HOH A:1093BINDING SITE FOR RESIDUE MG A 1001
2AC2SOFTWAREASP B:58 , ASP B:87 , HOH B:1047 , HOH B:1058 , HOH B:1125 , HOH B:1173BINDING SITE FOR RESIDUE MG B 1002

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ISOCITRATE_LYASEPS00161 Isocitrate lyase signature.PRPB_ECOLI121-126
 		  2A:121-126
B:121-126
Biological Unit 1 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ISOCITRATE_LYASEPS00161 Isocitrate lyase signature.PRPB_ECOLI121-126
 		  4A:121-126
B:121-126

(-) Exons   (0, 0)

(no "Exon" information available for 1MUM)

(-) 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:289
 aligned with PRPB_ECOLI | P77541 from UniProtKB/Swiss-Prot  Length:296

    Alignment length:289
                                    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         
           PRPB_ECOLI     3 LHSPGKAFRAALTKENPLQIVGTINANHALLAQRAGYQAIYLSGGGVAAGSLGLPDLGISTLDDVLTDIRRITDVCSLPLLVDADIGFGSSAFNVARTVKSMIKAGAAGLHIEDQVGAKRCGHRPNKAIVSKEEMVDRIRAAVDAKTDPDFVIMARTDALAVEGLDAAIERAQAYVEAGAEMLFPEAITELAMYRQFADAVQVPILANITEFGATPLFTTDELRSAHVAMALYPLSAFRAMNRAAEHVYNVLRQEGTQKSVIDTMQTRNELYESINYYQYEEKLDNLFA 291
               SCOP domains d1muma_ A: 2-methylisocitrate lyase                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 1mumA00 A:3-291 Phosphoenolpyruvate-binding domains                                                                                                                                                                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh..eeeee..hhhhhhhhhhh....eeehhhhhhhh..........hhhhhhhhhhhhhhhh...eeee.......hhhhhhhhhhhhhhh...eeeee.................hhhhhhhhhhhhhhh......eeeeee.hhhhhhhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhh...eee..........hhhhhhhh...eeee.hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh.hhhhhhhhh.hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------ISOCIT--------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1mum A   3 LHSPGKAFRAALTKENPLQIVGTINANHALLAQRAGYQAIYLSGGGVAAGSLGLPDLGISTLDDVLTDIRRITDVCSLPLLVDADIGFGSSAFNVARTVKSMIKAGAAGLHIEDQVGAKRCGHRPNKAIVSKEEMVDRIRAAVDAKTDPDFVIMARTDALAVEGLDAAIERAQAYVEAGAEMLFPEAITELAMYRQFADAVQVPILANITEFGATPLFTTDELRSAHVAMALYPLSAFRAMNRAAEHVYNVLRQEGTQKSVIDTMQTRNELYESINYYQYEEKLDNLFA 291
                                    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         


Chain B from PDB  Type:PROTEIN  Length:289
 aligned with PRPB_ECOLI | P77541 from UniProtKB/Swiss-Prot  Length:296

    Alignment length:289
                                    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         
           PRPB_ECOLI     3 LHSPGKAFRAALTKENPLQIVGTINANHALLAQRAGYQAIYLSGGGVAAGSLGLPDLGISTLDDVLTDIRRITDVCSLPLLVDADIGFGSSAFNVARTVKSMIKAGAAGLHIEDQVGAKRCGHRPNKAIVSKEEMVDRIRAAVDAKTDPDFVIMARTDALAVEGLDAAIERAQAYVEAGAEMLFPEAITELAMYRQFADAVQVPILANITEFGATPLFTTDELRSAHVAMALYPLSAFRAMNRAAEHVYNVLRQEGTQKSVIDTMQTRNELYESINYYQYEEKLDNLFA 291
               SCOP domains d1mumb_ B: 2-methylisocitrate lyase                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 1mumB00 B:3-291 Phosphoenolpyruvate-binding domains                                                                                                                                                                                                                                               CATH domains
           Pfam domains (1) -------PEP_mutase-1mumB01 B:10-255                                                                                                                                                                                                                           ------------------------------------ Pfam domains (1)
           Pfam domains (2) -------PEP_mutase-1mumB02 B:10-255                                                                                                                                                                                                                           ------------------------------------ Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhhhhh..eeeee..hhhhhhhhhhh....eeehhhhhhhh..........hhhhhhhhhhhhhhhh...eeee.......hhhhhhhhhhhhhhhh..eeeee.................hhhhhhhhhhhhhhhh.....eeeeeehhhhhhhhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhh...eee..........hhhhhhhh...eeee.hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh.hhhhhhhhh.hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------ISOCIT--------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1mum B   3 LHSPGKAFRAALTKENPLQIVGTINANHALLAQRAGYQAIYLSGGGVAAGSLGLPDLGISTLDDVLTDIRRITDVCSLPLLVDADIGFGSSAFNVARTVKSMIKAGAAGLHIEDQVGAKRCGHRPNKAIVSKEEMVDRIRAAVDAKTDPDFVIMARTDALAVEGLDAAIERAQAYVEAGAEMLFPEAITELAMYRQFADAVQVPILANITEFGATPLFTTDELRSAHVAMALYPLSAFRAMNRAAEHVYNVLRQEGTQKSVIDTMQTRNELYESINYYQYEEKLDNLFA 291
                                    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
   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  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (PRPB_ECOLI | P77541)
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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 Related Entries

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UniProtKB/Swiss-Prot
        PRPB_ECOLI | P77541: 1mzx 1oqf 1xg3 1xg4

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