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Theoretical Model  (Jmol Viewer)

(-) Description

Title :  THEORETICAL MODEL OF THE CLOSED CONFORMATION OF ESCHERICHIA COLI 2-METHYL-ISOCITRATE LYASE (PRPB) BOUND TO ITS SUBSTRATES
 
Authors :  A. Evers, C. Grimm, K. Reuter
Date :  10 Oct 02  (Deposition) - 29 Apr 03  (Release) - 29 Apr 03  (Revision)
Method :  THEORETICAL MODEL
Resolution :  NOT APPLICABLE
Chains :  Theor. Model :  A,_#
#:   chains that contain no standard or modified protein/DNA/RNA residue)
 
Keywords :  Tim-Barrel, Isocitrate, Pyruvate, Succinate, Isocitrate Lyase, Homology Modelling, Prpb (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: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROBABLE METHYLISOCITRATE LYASE
    ChainsA
    EC Number4.1.3.30
    Organism CommonBACTERIA
    Organism ScientificESCHERICHIA COLI
    Synonym2-METHYLISOCITRATE LYASE

 Structural Features

(-) Chains, Units

  
Theoretical Model 
#:   chains that contain no standard or modified protein/DNA/RNA residue)
 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 3)

Theoretical Model (3, 3)
No.NameCountTypeFull Name
1MG1Ligand/IonMAGNESIUM ION
2PYR1Ligand/IonPYRUVIC ACID
3SIN1Ligand/IonSUCCINIC ACID

(-) Sites  (0, 0)

(no "Site" information available for 1MZX)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Theoretical Model
No.Residues
1Asn A:18 -Pro A:19

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Theoretical Model (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ISOCITRATE_LYASEPS00161 Isocitrate lyase signature.PRPB_ECOLI121-126  1A:121-126

(-) Exons   (0, 0)

(no "Exon" information available for 1MZX)

(-) Sequences/Alignments

Theoretical Model
   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:288
 aligned with PRPB_ECOLI | P77541 from UniProtKB/Swiss-Prot  Length:296

    Alignment length:288
                                    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 LHSPGKAFRAALTKENPLQIVGTINANHALLAQRAGYQAIYLSGGGVAAGSLGLPDLGISTLDDVLTDIRRITDVCSLPLLVDADIGFGSSAFNVARTVKSMIKAGAAGLHIEDQVGAKRCGHRPNKAIVSKEEMVDRIRAAVDAKTDPDFVIMARTDALAVEGLDAAIERAQAYVEAGAEMLFPEAITELAMYRQFADAVQVPILANITEFGATPLFTTDELRSAHVAMALYPLSAFRAMNRAAEHVYNVLRQEGTQKSVIDTMQTRNELYESINYYQYEEKLDNLF 290
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh..eeeee..hhhhhhhhhhhh...eeehhhhhhhh..........hhhhhhhhhhhhhhhh...eeee.......hhhhhhhhhhhhhhhh..eeeee.................hhhhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhh...eee..........hhhhhhhh...eeee.hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh.hhhhhhhhh.hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------ISOCIT-------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1mzx A   3 LHSPGKAFRAALTKENPLQIVGTINANHALLAQRAGYQAIYLSGGGVAAGSLGLPDLGISTLDDVLTDIRRITDVCSLPLLVDADIGFGSSAFNVARTVKSMIKAGAAGLHIEDQVGAKRCGHRPNKAIVSKEEMVDRIRAAVDAKTDPDFVIMARTDALAVEGLDAAIERAQAYVEAGAEMLFPEAITELAMYRQFADAVQVPILANITEFGATPLFTTDELRSAHVAMALYPLSAFRAMNRAAEHVYNVLRQEGTQKSVIDTMQTRNELYESINYYQYEEKLDNLF 290
                                    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  (0, 0)

(no "SCOP Domain" information available for 1MZX)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1MZX)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (10, 10)

Theoretical Model(hide GO term definitions)
Chain A   (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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    Asn A:18 - Pro A:19   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        PRPB_ECOLI | P775411mum 1oqf 1xg3 1xg4

(-) Related Entries Specified in the PDB File

1mum CRYSTAL STRUCTURE OF THE OPEN FORM OF PRPB