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(-) Description

Title :  CRYSTAL STRUCTURE OF 4-METHYLMUCONOLACTONE METHYLISOMERASE (H52A) IN COMPLEX WITH 4-METHYLMUCONOLACTONE
 
Authors :  M. Marin, D. W. Heinz, D. H. Pieper, B. U. Klink
Date :  12 May 09  (Deposition) - 29 Sep 09  (Release) - 22 Jan 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,D  (1x)
Biol. Unit 2:  B,C  (1x)
Keywords :  Ferredoxin, Ferredoxin-Like Fold, Beta-Barrel, Isomerase, 4- Methylmuconolactone Methylisomerase, H52A, Biodegradation, Ortho- Cleavage (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Marin, D. W. Heinz, D. H. Pieper, B. U. Klink
Crystal Structure And Catalytic Mechanism Of 4-Methylmuconolactone Methylisomerase
J. Biol. Chem. V. 284 32709 2009
PubMed-ID: 19801657  |  Reference-DOI: 10.1074/JBC.M109.024604

(-) Compounds

Molecule 1 - 4-METHYLMUCONOLACTONE METHYLISOMERASE
    Chains: A, B, C, D
    EC Number: 5.4.99.14
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PASKIBAMMLI
    Expression System Strain: JM109
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: MMLI
    Mutation: YES
    Organism Scientific: PSEUDOMONAS REINEKEI
    Organism Taxid: 395598
    Strain: MT1

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A  D
Biological Unit 2 (1x):  BC 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 7)

Asymmetric Unit (1, 7)
No.NameCountTypeFull Name
14ML7Ligand/Ion[(2S)-2-METHYL-5-OXO-2,5-DIHYDROFURAN-2-YL]ACETIC ACID
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
14ML3Ligand/Ion[(2S)-2-METHYL-5-OXO-2,5-DIHYDROFURAN-2-YL]ACETIC ACID
Biological Unit 2 (1, 4)
No.NameCountTypeFull Name
14ML4Ligand/Ion[(2S)-2-METHYL-5-OXO-2,5-DIHYDROFURAN-2-YL]ACETIC ACID

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:6 , HIS A:26 , TYR A:39 , TYR A:78 , TRP A:87 , PHE A:88 , GLY A:91 , ILE A:95 , 4ML A:202BINDING SITE FOR RESIDUE 4ML A 201
2AC2SOFTWAREILE A:4 , TYR A:6 , TYR A:78 , MET A:79 , ARG A:84 , PHE A:88 , 4ML A:201 , PRO D:48 , THR D:51 , ALA D:52BINDING SITE FOR RESIDUE 4ML A 202
3AC3SOFTWARETYR B:6 , HIS B:26 , TYR B:39 , TYR B:78 , TRP B:87 , PHE B:88 , GLY B:91 , ILE B:95 , 4ML B:202BINDING SITE FOR RESIDUE 4ML B 201
4AC4SOFTWARETYR B:6 , TYR B:78 , MET B:79 , ARG B:84 , PHE B:88 , LEU B:98 , 4ML B:201 , PRO C:48 , THR C:51 , ALA C:52BINDING SITE FOR RESIDUE 4ML B 202
5AC5SOFTWARETYR C:6 , LEU C:8 , HIS C:26 , TYR C:39 , CYS C:67 , PHE C:88 , GLY C:91BINDING SITE FOR RESIDUE 4ML C 201
6AC6SOFTWARETHR B:51 , ALA B:52 , HOH B:482 , ILE C:4 , TYR C:6 , TYR C:75 , PHE C:88 , HOH C:123BINDING SITE FOR RESIDUE 4ML C 202
7AC7SOFTWARETYR D:6 , LEU D:8 , HIS D:26 , TYR D:39 , CYS D:67 , PHE D:88 , GLY D:91BINDING SITE FOR RESIDUE 4ML D 201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3HFK)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3HFK)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3HFK)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3HFK)

(-) Exons   (0, 0)

(no "Exon" information available for 3HFK)

(-) 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:115
 aligned with C5MR76_9PSED | C5MR76 from UniProtKB/TrEMBL  Length:107

    Alignment length:115
                                    1                                                                                                          
                                    |2        12        22        32        42        52        62        72        82        92       102     
         C5MR76_9PSED     - --------MIRILYLLVKPESMSHEQFRKECVVHFQMSAGMPGLHKYEVRLVAGNPTDTHVPYLDVGRIDAIGECWFASEEQYQVYMESDIRKAWFEHGKYFIGQLKPFVTEELV 107
               SCOP domains d3hfka_ A: automated matches                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhh.eeeeeeee.....hhhhhhhhhhhhhhh........eeeeeeeee................eeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 3hfk A  -7 QFEKIEGRMIRILYLLVKPESMSHEQFRKECVVHFQMSAGMPGLHKYEVRLVAGNPTDTAVPYLDVGRIDAIGECWFASEEQYQVYMESDIRKAWFEHGKYFIGQLKPFVTEELV 107
                                     2        12        22        32        42        52        62        72        82        92       102     


Chain B from PDB  Type:PROTEIN  Length:116
 aligned with C5MR76_9PSED | C5MR76 from UniProtKB/TrEMBL  Length:107

    Alignment length:116
                                     1                                                                                                          
                                     1        11        21        31        41        51        61        71        81        91       101      
         C5MR76_9PSED     - ---------MIRILYLLVKPESMSHEQFRKECVVHFQMSAGMPGLHKYEVRLVAGNPTDTHVPYLDVGRIDAIGECWFASEEQYQVYMESDIRKAWFEHGKYFIGQLKPFVTEELV 107
               SCOP domains d3hfkb_ B: automated matches                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhh.eeeeeeee.....hhhhhhhhhhhhhhhhh......eeeeeeeee................eeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 3hfk B  -8 PQFEKIEGRMIRILYLLVKPESMSHEQFRKECVVHFQMSAGMPGLHKYEVRLVAGNPTDTAVPYLDVGRIDAIGECWFASEEQYQVYMESDIRKAWFEHGKYFIGQLKPFVTEELV 107
                                     1        11        21        31        41        51        61        71        81        91       101      


Chain C from PDB  Type:PROTEIN  Length:109
 aligned with C5MR76_9PSED | C5MR76 from UniProtKB/TrEMBL  Length:107

    Alignment length:109
                              1                                                                                                          
                              |      8        18        28        38        48        58        68        78        88        98         
         C5MR76_9PSED     - --MIRILYLLVKPESMSHEQFRKECVVHFQMSAGMPGLHKYEVRLVAGNPTDTHVPYLDVGRIDAIGECWFASEEQYQVYMESDIRKAWFEHGKYFIGQLKPFVTEELV 107
               SCOP domains d3hfkc_ C: automated matches                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee.....hhhhhhhhhhhhhhhh.......eeeeeeeee................eeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------- Transcript
                 3hfk C  -1 GRMIRILYLLVKPESMSHEQFRKECVVHFQMSAGMPGLHKYEVRLVAGNPTDTAVPYLDVGRIDAIGECWFASEEQYQVYMESDIRKAWFEHGKYFIGQLKPFVTEELV 107
                                     8        18        28        38        48        58        68        78        88        98         


Chain D from PDB  Type:PROTEIN  Length:108
 aligned with C5MR76_9PSED | C5MR76 from UniProtKB/TrEMBL  Length:107

    Alignment length:108
                             1                                                                                                          
                             |       9        19        29        39        49        59        69        79        89        99        
         C5MR76_9PSED     - -MIRILYLLVKPESMSHEQFRKECVVHFQMSAGMPGLHKYEVRLVAGNPTDTHVPYLDVGRIDAIGECWFASEEQYQVYMESDIRKAWFEHGKYFIGQLKPFVTEELV 107
               SCOP domains d3hfkd_ D: automated matches                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeeee.....hhhhhhhhhhhhhhhh.......eeeeeeeee................eeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 3hfk D   0 RMIRILYLLVKPESMSHEQFRKECVVHFQMSAGMPGLHKYEVRLVAGNPTDTAVPYLDVGRIDAIGECWFASEEQYQVYMESDIRKAWFEHGKYFIGQLKPFVTEELV 107
                                     9        19        29        39        49        59        69        79        89        99
   Legend:   → Mismatch (orange background)
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  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 Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3HFK)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3HFK)

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (C5MR76_9PSED | C5MR76)
molecular function
    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.

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 Related Entries

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

UniProtKB/TrEMBL
        C5MR76_9PSED | C5MR76: 3hds 3hf5

(-) Related Entries Specified in the PDB File

3hds THE WILDTYPE PROTEIN COMPLEXED WITH A MES BUFFER MOLECULE
3hf5 THE WILDTYPE PROTEIN COMPLEXED WITH 3-METHYLMUCONOLACTONE