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(-) Description

Title :  CRYSTAL STRUCTURE OF THE C123S 2-METHYLISOCITRATE LYASE MUTANT FROM ESCHERICHIA COLI IN COMPLEX WITH THE REACTION PRODUCT, MG(II)-PYRUVATE AND SUCCINATE
 
Authors :  S. Liu, Z. Lu, Y. Han, E. Melamud, D. Dunaway-Mariano, O. Herzberg
Date :  16 Sep 04  (Deposition) - 01 Mar 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  2-Methylisocitrate Lyase/Product Complex, Succinate, Pyruvate, Isocitrate Lyase Superfamily (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Liu, Z. Lu, Y. Han, E. Melamud, D. Dunaway-Mariano, O. Herzberg
Crystal Structures Of 2-Methylisocitrate Lyase In Complex With Product And With Isocitrate Inhibitor Provide Insight Into Lyase Substrate Specificity, Catalysis And Evolution
Biochemistry V. 44 2949 2005
PubMed-ID: 15723538  |  Reference-DOI: 10.1021/BI0479712
(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 BL21(DE3)
    Expression System Plasmid: PET3C
    Expression System Strain: BL21 DE3
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: PRPB
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: 2-METHYLISOCITRATE LYASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 11)

Asymmetric/Biological Unit (3, 11)
No.NameCountTypeFull Name
1MG4Ligand/IonMAGNESIUM ION
2PYR4Ligand/IonPYRUVIC ACID
3SIN3Ligand/IonSUCCINIC ACID

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:85 , PYR A:2105 , HOH A:2354 , HOH A:2355 , HOH A:2356BINDING SITE FOR RESIDUE MG A 2101
02AC2SOFTWAREASP B:85 , PYR B:2205 , HOH B:2481 , HOH B:2482 , HOH B:2483BINDING SITE FOR RESIDUE MG B 2201
03AC3SOFTWAREASP C:85 , PYR C:2305 , HOH C:2570 , HOH C:2571 , HOH C:2572BINDING SITE FOR RESIDUE MG C 2301
04AC4SOFTWAREASP D:85 , PYR D:2405 , HOH D:2671 , HOH D:2672 , HOH D:2673BINDING SITE FOR RESIDUE MG D 2401
05AC5SOFTWARETYR A:43 , SER A:45 , GLY A:46 , GLY A:47 , ASP A:85 , ARG A:158 , PRO A:236 , MG A:2101 , SIN A:2106 , HOH A:2354 , HOH A:2355BINDING SITE FOR RESIDUE PYR A 2105
06AC6SOFTWARESER A:123 , GLY A:124 , HIS A:125 , ARG A:158 , GLU A:188 , ASN A:210 , THR A:212 , ARG A:241 , PYR A:2105 , HOH A:2210 , HOH A:2241 , HOH A:2355 , ARG B:270BINDING SITE FOR RESIDUE SIN A 2106
07AC7SOFTWARETYR B:43 , SER B:45 , GLY B:46 , GLY B:47 , ASP B:85 , ARG B:158 , PRO B:236 , MG B:2201 , SIN B:2206 , HOH B:2481BINDING SITE FOR RESIDUE PYR B 2205
08AC8SOFTWAREARG A:270 , SER B:123 , GLY B:124 , HIS B:125 , ARG B:158 , GLU B:188 , ASN B:210 , THR B:212 , ARG B:241 , PYR B:2205 , HOH B:2305 , HOH B:2482BINDING SITE FOR RESIDUE SIN B 2206
09AC9SOFTWARETYR C:43 , SER C:45 , GLY C:46 , GLY C:47 , ASP C:85 , ARG C:158 , ASN C:210 , PRO C:236 , MG C:2301 , HOH C:2525BINDING SITE FOR RESIDUE PYR C 2305
10BC1SOFTWARETYR D:43 , SER D:45 , GLY D:46 , GLY D:47 , ASP D:85 , ARG D:158 , PRO D:236 , MG D:2401 , SIN D:2406 , HOH D:2671 , HOH D:2672BINDING SITE FOR RESIDUE PYR D 2405
11BC2SOFTWAREARG C:270 , SER D:123 , GLY D:124 , HIS D:125 , ARG D:158 , GLU D:188 , ASN D:210 , THR D:212 , ARG D:241 , PYR D:2405 , HOH D:2458 , HOH D:2509 , HOH D:2672BINDING SITE FOR RESIDUE SIN D 2406

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1XG3)

(-) 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 1XG3)

(-) PROSITE Motifs  (1, 4)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1XG3)

(-) 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:288
 aligned with PRPB_ECOLI | P77541 from UniProtKB/Swiss-Prot  Length:296

    Alignment length:288
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281        
           PRPB_ECOLI     2 SLHSPGKAFRAALTKENPLQIVGTINANHALLAQRAGYQAIYLSGGGVAAGSLGLPDLGISTLDDVLTDIRRITDVCSLPLLVDADIGFGSSAFNVARTVKSMIKAGAAGLHIEDQVGAKRCGHRPNKAIVSKEEMVDRIRAAVDAKTDPDFVIMARTDALAVEGLDAAIERAQAYVEAGAEMLFPEAITELAMYRQFADAVQVPILANITEFGATPLFTTDELRSAHVAMALYPLSAFRAMNRAAEHVYNVLRQEGTQKSVIDTMQTRNELYESINYYQYEEKLDNL 289
               SCOP domains d1xg3a_ A: 2-methylisocitrate lyase                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 1xg3A00 A:2-289 Phosphoenolpyruvate-binding domains                                                                                                                                                                                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhh..eeeee..hhhhhhhhhhh....eeehhhhhhhh..........hhhhhhhhhhhhhhhh...eeee.......hhhhhhhhhhhhhhhh..eeeee.................hhhhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhh...eee..........hhhhhhhh...eeee.hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh.hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------ISOCIT------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1xg3 A   2 SLHSPGKAFRAALTKENPLQIVGTINANHALLAQRAGYQAIYLSGGGVAAGSLGLPDLGISTLDDVLTDIRRITDVCSLPLLVDADIGFGSSAFNVARTVKSMIKAGAAGLHIEDQVGAKRSGHRPNKAIVSKEEMVDRIRAAVDAKTDPDFVIMARTDALAVEGLDAAIERAQAYVEAGAEMLFPEAITELAMYRQFADAVQVPILANITEFGATPLFTTDELRSAHVAMALYPLSAFRAMNRAAEHVYNVLRQEGTQKSVIDTMQTRNELYESINYYQYEEKLDNL 289
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281        


Chain B from PDB  Type:PROTEIN  Length:286
 aligned with PRPB_ECOLI | P77541 from UniProtKB/Swiss-Prot  Length:296

    Alignment length:286
                                    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 LHSPGKAFRAALTKENPLQIVGTINANHALLAQRAGYQAIYLSGGGVAAGSLGLPDLGISTLDDVLTDIRRITDVCSLPLLVDADIGFGSSAFNVARTVKSMIKAGAAGLHIEDQVGAKRCGHRPNKAIVSKEEMVDRIRAAVDAKTDPDFVIMARTDALAVEGLDAAIERAQAYVEAGAEMLFPEAITELAMYRQFADAVQVPILANITEFGATPLFTTDELRSAHVAMALYPLSAFRAMNRAAEHVYNVLRQEGTQKSVIDTMQTRNELYESINYYQYEEKLDN 288
               SCOP domains d1xg3b_ B: 2-methylisocitrate lyase                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 1xg3B00 B:3-288 Phosphoenolpyruvate-binding domains                                                                                                                                                                                                                                            CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh..eeeee..hhhhhhhhhhh...eeeehhhhhhhh..........hhhhhhhhhhhhhhhh...eeee.......hhhhhhhhhhhhhhhh..eeeee.................hhhhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhh...eee..........hhhhhhhh...eeee.hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh.hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------ISOCIT------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xg3 B   3 LHSPGKAFRAALTKENPLQIVGTINANHALLAQRAGYQAIYLSGGGVAAGSLGLPDLGISTLDDVLTDIRRITDVCSLPLLVDADIGFGSSAFNVARTVKSMIKAGAAGLHIEDQVGAKRSGHRPNKAIVSKEEMVDRIRAAVDAKTDPDFVIMARTDALAVEGLDAAIERAQAYVEAGAEMLFPEAITELAMYRQFADAVQVPILANITEFGATPLFTTDELRSAHVAMALYPLSAFRAMNRAAEHVYNVLRQEGTQKSVIDTMQTRNELYESINYYQYEEKLDN 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      


Chain C from PDB  Type:PROTEIN  Length:287
 aligned with PRPB_ECOLI | P77541 from UniProtKB/Swiss-Prot  Length:296

    Alignment length:287
                                    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 LHSPGKAFRAALTKENPLQIVGTINANHALLAQRAGYQAIYLSGGGVAAGSLGLPDLGISTLDDVLTDIRRITDVCSLPLLVDADIGFGSSAFNVARTVKSMIKAGAAGLHIEDQVGAKRCGHRPNKAIVSKEEMVDRIRAAVDAKTDPDFVIMARTDALAVEGLDAAIERAQAYVEAGAEMLFPEAITELAMYRQFADAVQVPILANITEFGATPLFTTDELRSAHVAMALYPLSAFRAMNRAAEHVYNVLRQEGTQKSVIDTMQTRNELYESINYYQYEEKLDNL 289
               SCOP domains d1xg3c_ C: 2-methylisocitrate lyase                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 1xg3C00 C:3-289 Phosphoenolpyruvate-binding domains                                                                                                                                                                                                                                             CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh..eeeee..hhhhhhhhhhh....eeehhhhhhhh..........hhhhhhhhhhhhhhhh...eeee.......hhhhhhhhhhhhhhhh..eeeee.................hhhhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhh...eee..........hhhhhhhh...eeee.hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh.hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------ISOCIT------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xg3 C   3 LHSPGKAFRAALTKENPLQIVGTINANHALLAQRAGYQAIYLSGGGVAAGSLGLPDLGISTLDDVLTDIRRITDVCSLPLLVDADIGFGSSAFNVARTVKSMIKAGAAGLHIEDQVGAKRSGHRPNKAIVSKEEMVDRIRAAVDAKTDPDFVIMARTDALAVEGLDAAIERAQAYVEAGAEMLFPEAITELAMYRQFADAVQVPILANITEFGATPLFTTDELRSAHVAMALYPLSAFRAMNRAAEHVYNVLRQEGTQKSVIDTMQTRNELYESINYYQYEEKLDNL 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       


Chain D from PDB  Type:PROTEIN  Length:283
 aligned with PRPB_ECOLI | P77541 from UniProtKB/Swiss-Prot  Length:296

    Alignment length:283
                                    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 LHSPGKAFRAALTKENPLQIVGTINANHALLAQRAGYQAIYLSGGGVAAGSLGLPDLGISTLDDVLTDIRRITDVCSLPLLVDADIGFGSSAFNVARTVKSMIKAGAAGLHIEDQVGAKRCGHRPNKAIVSKEEMVDRIRAAVDAKTDPDFVIMARTDALAVEGLDAAIERAQAYVEAGAEMLFPEAITELAMYRQFADAVQVPILANITEFGATPLFTTDELRSAHVAMALYPLSAFRAMNRAAEHVYNVLRQEGTQKSVIDTMQTRNELYESINYYQYEEK 285
               SCOP domains d1xg3d_ D: 2-methylisocitrate lyase                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 1xg3D00 D:3-285 Phosphoenolpyruvate-binding domains                                                                                                                                                                                                                                         CATH domains
           Pfam domains (1) -------PEP_mutase-1xg3D01 D:10-255                                                                                                                                                                                                                           ------------------------------ Pfam domains (1)
           Pfam domains (2) -------PEP_mutase-1xg3D02 D:10-255                                                                                                                                                                                                                           ------------------------------ Pfam domains (2)
           Pfam domains (3) -------PEP_mutase-1xg3D03 D:10-255                                                                                                                                                                                                                           ------------------------------ Pfam domains (3)
           Pfam domains (4) -------PEP_mutase-1xg3D04 D:10-255                                                                                                                                                                                                                           ------------------------------ Pfam domains (4)
         Sec.struct. author ..hhhhhhhhhhhhh..eeeee..hhhhhhhhhhh....eeehhhhhhhh..........hhhhhhhhhhhhhhhh...eeee.......hhhhhhhhhhhhhhhh..eeeee.................hhhhhhhhhhhhhhhh.....eeeeeehhhhhhhhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhh...eee..........hhhhhhhh...eeee.hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh.hhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------ISOCIT--------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xg3 D   3 LHSPGKAFRAALTKENPLQIVGTINANHALLAQRAGYQAIYLSGGGVAAGSLGLPDLGISTLDDVLTDIRRITDVCSLPLLVDADIGFGSSAFNVARTVKSMIKAGAAGLHIEDQVGAKRSGHRPNKAIVSKEEMVDRIRAAVDAKTDPDFVIMARTDALAVEGLDAAIERAQAYVEAGAEMLFPEAITELAMYRQFADAVQVPILANITEFGATPLFTTDELRSAHVAMALYPLSAFRAMNRAAEHVYNVLRQEGTQKSVIDTMQTRNELYESINYYQYEEK 285
                                    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, 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  (10, 10)

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

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

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

(-) Related Entries Specified in the PDB File

1oqf THE WILD-TYPE ENZYME IN THE UNBOUND STATE