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(-) Description

Title :  CRYSTAL STRUCTURE OF SE-MET METHYLMALONYL-COA EPIMERASE
 
Authors :  A. A. Mc Carthy, H. M. Baker, S. C. Shewry, M. L. Patchett, E. N. Baker
Date :  07 Jun 01  (Deposition) - 11 Jul 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Vicinal Oxygen Chelate Superfamily, Methylmalonyl-Coa, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. A. Mccarthy, H. M. Baker, S. C. Shewry, M. L. Patchett, E. N. Baker
Crystal Structure Of Methylmalonyl-Coenzyme A Epimerase From P. Shermanii: A Novel Enzymatic Function On An Ancient Metal Binding Scaffold.
Structure V. 9 637 2001
PubMed-ID: 11470438  |  Reference-DOI: 10.1016/S0969-2126(01)00622-0
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - METHYLMALONYL-COA EPIMERASE
    Chains: A, B, C, D
    EC Number: 5.1.99.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PPROEXHTA
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Organism Scientific: PROPIONIBACTERIUM FREUDENREICHII SUBSP. SHERMANII
    Organism Taxid: 1752
    Strain: SUBSP. SHERMANII

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 30)

Asymmetric Unit (2, 30)
No.NameCountTypeFull Name
1MSE24Mod. Amino AcidSELENOMETHIONINE
2SO46Ligand/IonSULFATE ION
Biological Unit 1 (2, 15)
No.NameCountTypeFull Name
1MSE12Mod. Amino AcidSELENOMETHIONINE
2SO43Ligand/IonSULFATE ION
Biological Unit 2 (2, 15)
No.NameCountTypeFull Name
1MSE12Mod. Amino AcidSELENOMETHIONINE
2SO43Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:58 , GLU A:59 , HIS A:60 , MSE A:61 , THR B:58 , HIS B:60 , MSE B:61BINDING SITE FOR RESIDUE SO4 A 201
2AC2SOFTWARETHR C:58 , GLU C:59 , HIS C:60 , MSE C:61 , THR D:58 , GLU D:59 , HIS D:60 , MSE D:61BINDING SITE FOR RESIDUE SO4 D 202
3AC3SOFTWAREGLU A:48 , GLN A:65 , GLY A:121 , THR A:122 , ILE A:127 , GLU A:141 , HOH A:205 , HOH A:209BINDING SITE FOR RESIDUE SO4 A 203
4AC4SOFTWAREHIS B:12 , GLU B:48 , GLN B:65 , THR B:122 , ILE B:127 , GLU B:141 , HOH B:205BINDING SITE FOR RESIDUE SO4 B 204
5AC5SOFTWAREHIS C:12 , GLU C:48 , GLN C:65 , GLY C:121 , THR C:122 , ILE C:127 , GLU C:141 , HOH C:206BINDING SITE FOR RESIDUE SO4 C 205
6AC6SOFTWAREGLU D:48 , GLN D:65 , GLY D:121 , THR D:122 , GLU D:141 , HOH D:207 , HOH D:222BINDING SITE FOR RESIDUE SO4 D 206

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1JC4)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1JC4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1JC4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1JC4)

(-) Exons   (0, 0)

(no "Exon" information available for 1JC4)

(-) 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:145
 aligned with Q8VQN0_PROFR | Q8VQN0 from UniProtKB/TrEMBL  Length:148

    Alignment length:145
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142     
         Q8VQN0_PROFR     3 NEDLFICIDHVAYACPDADEASKYYQETFGWHELHREENPEQGVVEIMMAPAAKLTEHMTQVQVMAPLNDESTVAKWLAKHNGRAGLHHMAWRVDDIDAVSATLRERGVQLLYDEPKLGTGGNRINFMHPKSGKGVLIELTQYPK 147
               SCOP domains d1jc4a_ A: Methylmalonyl-CoA epimerase                                                                                                            SCOP domains
               CATH domains 1jc4A00 A:3-147 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1                                                                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeee..hhhhhhhhhhhhhh.eeeeeeee....eeeeeee..........eeeeeee....hhhhhhhhhh....eeeeeeee..hhhhhhhhhhhhh........ee.....eeee.hhhhhh...eeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jc4 A   3 NEDLFICIDHVAYACPDADEASKYYQETFGWHELHREENPEQGVVEImmAPAAKLTEHmTQVQVmAPLNDESTVAKWLAKHNGRAGLHHmAWRVDDIDAVSATLRERGVQLLYDEPKLGTGGNRINFmHPKSGKGVLIELTQYPK 147
                                    12        22        32        42       |52        62    |   72        82        92       102       112       122       132       142     
                                                                          50-MSE     61-MSE |                       92-MSE                               130-MSE             
                                                                           51-MSE          67-MSE                                                                            


Chain B from PDB  Type:PROTEIN  Length:144
 aligned with Q8VQN0_PROFR | Q8VQN0 from UniProtKB/TrEMBL  Length:148

    Alignment length:144
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143    
         Q8VQN0_PROFR     4 EDLFICIDHVAYACPDADEASKYYQETFGWHELHREENPEQGVVEIMMAPAAKLTEHMTQVQVMAPLNDESTVAKWLAKHNGRAGLHHMAWRVDDIDAVSATLRERGVQLLYDEPKLGTGGNRINFMHPKSGKGVLIELTQYPK 147
               SCOP domains d1jc4b_ B: Methylmalonyl-CoA epimerase                                                                                                           SCOP domains
               CATH domains 1jc4B00 B:4-147 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeeeeeee..hhhhhhhhhhhhhh.eeeeeeee....eeeeeee..........eeeeeee....hhhhhhhhhh....eeeeeeeee.hhhhhhhhhhhh.........ee.hhh.eeeee.........eeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1jc4 B   4 EDLFICIDHVAYACPDADEASKYYQETFGWHELHREENPEQGVVEImmAPAAKLTEHmTQVQVmAPLNDESTVAKWLAKHNGRAGLHHmAWRVDDIDAVSATLRERGVQLLYDEPKLGTGGNRINFmHPKSGKGVLIELTQYPK 147
                                    13        23        33        43      ||53       |63   |    73        83        93       103       113       123      |133       143    
                                                                         50-MSE     61-MSE |                       92-MSE                               130-MSE             
                                                                          51-MSE          67-MSE                                                                            


Chain C from PDB  Type:PROTEIN  Length:145
 aligned with Q8VQN0_PROFR | Q8VQN0 from UniProtKB/TrEMBL  Length:148

    Alignment length:145
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142     
         Q8VQN0_PROFR     3 NEDLFICIDHVAYACPDADEASKYYQETFGWHELHREENPEQGVVEIMMAPAAKLTEHMTQVQVMAPLNDESTVAKWLAKHNGRAGLHHMAWRVDDIDAVSATLRERGVQLLYDEPKLGTGGNRINFMHPKSGKGVLIELTQYPK 147
               SCOP domains d1jc4c_ C: Methylmalonyl-CoA epimerase                                                                                                            SCOP domains
               CATH domains 1jc4C00 C:3-147 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1                                                                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeee..hhhhhhhhhhhh...eeeeeeee....eeeeeee..........eeeeeee....hhhhhhhhhh....eeeeeeee..hhhhhhhhhhhh.........ee.hhh.eeeee.........eeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jc4 C   3 NEDLFICIDHVAYACPDADEASKYYQETFGWHELHREENPEQGVVEImmAPAAKLTEHmTQVQVmAPLNDESTVAKWLAKHNGRAGLHHmAWRVDDIDAVSATLRERGVQLLYDEPKLGTGGNRINFmHPKSGKGVLIELTQYPK 147
                                    12        22        32        42       |52        62    |   72        82        92       102       112       122       132       142     
                                                                          50-MSE     61-MSE |                       92-MSE                               130-MSE             
                                                                           51-MSE          67-MSE                                                                            


Chain D from PDB  Type:PROTEIN  Length:145
 aligned with Q8VQN0_PROFR | Q8VQN0 from UniProtKB/TrEMBL  Length:148

    Alignment length:145
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142     
         Q8VQN0_PROFR     3 NEDLFICIDHVAYACPDADEASKYYQETFGWHELHREENPEQGVVEIMMAPAAKLTEHMTQVQVMAPLNDESTVAKWLAKHNGRAGLHHMAWRVDDIDAVSATLRERGVQLLYDEPKLGTGGNRINFMHPKSGKGVLIELTQYPK 147
               SCOP domains d1jc4d_ D: Methylmalonyl-CoA epimerase                                                                                                            SCOP domains
               CATH domains 1jc4D00 D:3-147 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1                                                                                   CATH domains
           Pfam domains (1) --------Glyoxalase_4-1jc4D01 D:11-129                                                                                          ------------------ Pfam domains (1)
           Pfam domains (2) --------Glyoxalase_4-1jc4D02 D:11-129                                                                                          ------------------ Pfam domains (2)
           Pfam domains (3) --------Glyoxalase_4-1jc4D03 D:11-129                                                                                          ------------------ Pfam domains (3)
           Pfam domains (4) --------Glyoxalase_4-1jc4D04 D:11-129                                                                                          ------------------ Pfam domains (4)
         Sec.struct. author ......eeeeeeee..hhhhhhhhhhhhhh.eeeeeeee....eeeeeee..........eeeeeee....hhhhhhhhhh....eeeeeeee..hhhhhhhhhhhh.........ee.....eeee.hhhhhh...eeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jc4 D   3 NEDLFICIDHVAYACPDADEASKYYQETFGWHELHREENPEQGVVEImmAPAAKLTEHmTQVQVmAPLNDESTVAKWLAKHNGRAGLHHmAWRVDDIDAVSATLRERGVQLLYDEPKLGTGGNRINFmHPKSGKGVLIELTQYPK 147
                                    12        22        32        42       |52        62    |   72        82        92       102       112       122       132       142     
                                                                          50-MSE     61-MSE |                       92-MSE                               130-MSE             
                                                                           51-MSE          67-MSE
   Legend:   → Mismatch (orange background)
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  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  (1, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: Glyoxalase (58)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q8VQN0_PROFR | Q8VQN0)
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.
    GO:0004493    methylmalonyl-CoA epimerase activity    Catalysis of the reaction: (R)-methylmalonyl-CoA = (S)-methylmalonyl-CoA.

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 Related Entries

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        Q8VQN0_PROFR | Q8VQN0: 1jc5

(-) Related Entries Specified in the PDB File

1jc5 1JC5 CONTAINS THE NATIVE PROTEIN