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(-) Description

Title :  CRYSTAL STRUCTURE OF THE GAMMA-CARBOXYMUCONOLACTONE DECARBOXYLASE FROM METHANOBACTERIUM THERMOAUTOTROPHICUM. NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET TT747.
 
Authors :  S. M. Vorobiev, A. Kuzin, T. Skarina, A. Savchenko, A. Semesi, C. Arrowsmith, A. Edwards, G. T. Montelione, L. Tong, Northeast Structural Genomics Consortium (Nesg)
Date :  25 Jul 05  (Deposition) - 09 Aug 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.81
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H,I
Biol. Unit 1:  A,C,D,E,F,I  (1x)
Biol. Unit 2:  B,G,H  (2x)
Keywords :  Gamma-Carboxymuconolactone Decarboxylase, O26336_metth, Nesg, Tt747, Structural Genomics, Psi, Protein Structure Initiative, Northeast Structural Genomics Consortium, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. M. Vorobiev, A. Kuzin, T. Skarina, A. Savchenko, A. Semesi, C. Arrowsmith, A. Edwards, G. T. Montelione, L. Tong
Crystal Structure Of The Gamma-Carboxymuconolactone Decarboxylase From Methanobacterium Thermoautotrophicum.
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GAMMA-CARBOXYMUCONOLACTONE DECARBOXYLASE
    Chains: A, B, C, D, E, F, G, H, I
    EC Number: 4.1.1.44
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: BL21(DE3)+MAGIC
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: MTH234
    Organism Scientific: METHANOTHERMOBACTER THERMAUTOTROPHICUS
    Organism Taxid: 145262

 Structural Features

(-) Chains, Units

  123456789
Asymmetric Unit : ABCDEFGHI
Biological Unit 1 (1x): A CDEF  I
Biological Unit 2 (2x):  B    GH 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 39)

Asymmetric Unit (1, 39)
No.NameCountTypeFull Name
1MSE39Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 27)
No.NameCountTypeFull Name
1MSE27Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 24)
No.NameCountTypeFull Name
1MSE24Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 2AF7)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2AF7)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2AF7)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2AF7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2AF7)

(-) Exons   (0, 0)

(no "Exon" information available for 2AF7)

(-) 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:119
 aligned with O26336_METTH | O26336 from UniProtKB/TrEMBL  Length:125

    Alignment length:119
                                    10        20        30        40        50        60        70        80        90       100       110         
         O26336_METTH     1 MERYRRGMEILNRMNRKSYTAIRDELEDVAPDLARFVAEFAYGDVYSRGVLDLKTRELLTLAALTVLRADDQLKSHVRGALNAGCSKDEIIEVMIQMAVYAGFPAAINAVLAAKEVFTE 119
               SCOP domains d2af7a1 A:1-119 Gamma-carboxymuconolactone decarboxylase, CMD                                                           SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh.hhhhhhhh.....hhhhhhhhhhh............hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 2af7 A   1 mERYRRGmEILNRmNRKSYTAIRDELEDVAPDLARFVAEFAYGDVYSRGVLDLKTRELLTLAALTVLRADDQLKSHVRGALNAGCSKDEIIEVmIQmAVYAGFPAAINAVLAAKEVFTE 119
                            |      |10   |    20        30        40        50        60        70        80        90   |  |100       110         
                            |      8-MSE |                                                                              94-MSE                     
                            1-MSE       14-MSE                                                                             97-MSE                  


Chain B from PDB  Type:PROTEIN  Length:118
 aligned with O26336_METTH | O26336 from UniProtKB/TrEMBL  Length:125

    Alignment length:118
                                    11        21        31        41        51        61        71        81        91       101       111        
         O26336_METTH     2 ERYRRGMEILNRMNRKSYTAIRDELEDVAPDLARFVAEFAYGDVYSRGVLDLKTRELLTLAALTVLRADDQLKSHVRGALNAGCSKDEIIEVMIQMAVYAGFPAAINAVLAAKEVFTE 119
               SCOP domains d2af7b_ B: Gamma-carboxymuconolactone decarboxylase, CMD                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhh....hhhhh.....hhhhh.hhhhhhhhhh.......hhhhhhhhhhhhh...hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 2af7 B   2 ERYRRGmEILNRmNRKSYTAIRDELEDVAPDLARFVAEFAYGDVYSRGVLDLKTRELLTLAALTVLRADDQLKSHVRGALNAGCSKDEIIEVmIQmAVYAGFPAAINAVLAAKEVFTE 119
                                  | 11  |     21        31        41        51        61        71        81        91  |  | 101       111        
                                  8-MSE |                                                                              94-MSE                     
                                       14-MSE                                                                             97-MSE                  


Chain C from PDB  Type:PROTEIN  Length:118
 aligned with O26336_METTH | O26336 from UniProtKB/TrEMBL  Length:125

    Alignment length:118
                                    11        21        31        41        51        61        71        81        91       101       111        
         O26336_METTH     2 ERYRRGMEILNRMNRKSYTAIRDELEDVAPDLARFVAEFAYGDVYSRGVLDLKTRELLTLAALTVLRADDQLKSHVRGALNAGCSKDEIIEVMIQMAVYAGFPAAINAVLAAKEVFTE 119
               SCOP domains d2af7c_ C: Gamma-carboxymuconolactone decarboxylase, CMD                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh.hhhhhh.....hhhhhhh..hhhhhhhhhhh............hhhhhhhhhhhhhhh.hhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 2af7 C   2 ERYRRGmEILNRmNRKSYTAIRDELEDVAPDLARFVAEFAYGDVYSRGVLDLKTRELLTLAALTVLRADDQLKSHVRGALNAGCSKDEIIEVmIQmAVYAGFPAAINAVLAAKEVFTE 119
                                  | 11  |     21        31        41        51        61        71        81        91  |  | 101       111        
                                  8-MSE |                                                                              94-MSE                     
                                       14-MSE                                                                             97-MSE                  


Chain D from PDB  Type:PROTEIN  Length:122
 aligned with O26336_METTH | O26336 from UniProtKB/TrEMBL  Length:125

    Alignment length:122
                                    10        20        30        40        50        60        70        80        90       100       110       120  
         O26336_METTH     1 MERYRRGMEILNRMNRKSYTAIRDELEDVAPDLARFVAEFAYGDVYSRGVLDLKTRELLTLAALTVLRADDQLKSHVRGALNAGCSKDEIIEVMIQMAVYAGFPAAINAVLAAKEVFTENDP 122
               SCOP domains d2af7d_ D: Gamma-carboxymuconolactone decarboxylase, CMD                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh.hhhhhhhh.....hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 2af7 D   1 mERYRRGmEILNRmNRKSYTAIRDELEDVAPDLARFVAEFAYGDVYSRGVLDLKTRELLTLAALTVLRADDQLKSHVRGALNAGCSKDEIIEVmIQmAVYAGFPAAINAVLAAKEVFTENDP 122
                            |      |10   |    20        30        40        50        60        70        80        90   |  |100       110       120  
                            1-MSE  8-MSE |                                                                              94-MSE                        
                                        14-MSE                                                                             97-MSE                     


Chain E from PDB  Type:PROTEIN  Length:120
 aligned with O26336_METTH | O26336 from UniProtKB/TrEMBL  Length:125

    Alignment length:120
                                    10        20        30        40        50        60        70        80        90       100       110       120
         O26336_METTH     1 MERYRRGMEILNRMNRKSYTAIRDELEDVAPDLARFVAEFAYGDVYSRGVLDLKTRELLTLAALTVLRADDQLKSHVRGALNAGCSKDEIIEVMIQMAVYAGFPAAINAVLAAKEVFTEN 120
               SCOP domains d2af7e_ E: Gamma-carboxymuconolactone decarboxylase, CMD                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........hhhhhh...hhhhh......hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 2af7 E   1 mERYRRGmEILNRmNRKSYTAIRDELEDVAPDLARFVAEFAYGDVYSRGVLDLKTRELLTLAALTVLRADDQLKSHVRGALNAGCSKDEIIEVmIQmAVYAGFPAAINAVLAAKEVFTEN 120
                            |      |10   |    20        30        40        50        60        70        80        90   |  |100       110       120
                            1-MSE  8-MSE |                                                                              94-MSE                      
                                        14-MSE                                                                             97-MSE                   


Chain F from PDB  Type:PROTEIN  Length:120
 aligned with O26336_METTH | O26336 from UniProtKB/TrEMBL  Length:125

    Alignment length:120
                                    11        21        31        41        51        61        71        81        91       101       111       121
         O26336_METTH     2 ERYRRGMEILNRMNRKSYTAIRDELEDVAPDLARFVAEFAYGDVYSRGVLDLKTRELLTLAALTVLRADDQLKSHVRGALNAGCSKDEIIEVMIQMAVYAGFPAAINAVLAAKEVFTEND 121
               SCOP domains d2af7f_ F: Gamma-carboxymuconolactone decarboxylase, CMD                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhhh....................hhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 2af7 F   2 ERYRRGmEILNRmNRKSYTAIRDELEDVAPDLARFVAEFAYGDVYSRGVLDLKTRELLTLAALTVLRADDQLKSHVRGALNAGCSKDEIIEVmIQmAVYAGFPAAINAVLAAKEVFTEND 121
                                  | 11  |     21        31        41        51        61        71        81        91  |  | 101       111       121
                                  8-MSE |                                                                              94-MSE                       
                                       14-MSE                                                                             97-MSE                    


Chain G from PDB  Type:PROTEIN  Length:118
 aligned with O26336_METTH | O26336 from UniProtKB/TrEMBL  Length:125

    Alignment length:118
                                    11        21        31        41        51        61        71        81        91       101       111        
         O26336_METTH     2 ERYRRGMEILNRMNRKSYTAIRDELEDVAPDLARFVAEFAYGDVYSRGVLDLKTRELLTLAALTVLRADDQLKSHVRGALNAGCSKDEIIEVMIQMAVYAGFPAAINAVLAAKEVFTE 119
               SCOP domains d2af7g_ G: Gamma-carboxymuconolactone decarboxylase, CMD                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhh...................hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 2af7 G   2 ERYRRGmEILNRmNRKSYTAIRDELEDVAPDLARFVAEFAYGDVYSRGVLDLKTRELLTLAALTVLRADDQLKSHVRGALNAGCSKDEIIEVmIQmAVYAGFPAAINAVLAAKEVFTE 119
                                  | 11  |     21        31        41        51        61        71        81        91  |  | 101       111        
                                  8-MSE |                                                                              94-MSE                     
                                       14-MSE                                                                             97-MSE                  


Chain H from PDB  Type:PROTEIN  Length:119
 aligned with O26336_METTH | O26336 from UniProtKB/TrEMBL  Length:125

    Alignment length:119
                                    11        21        31        41        51        61        71        81        91       101       111         
         O26336_METTH     2 ERYRRGMEILNRMNRKSYTAIRDELEDVAPDLARFVAEFAYGDVYSRGVLDLKTRELLTLAALTVLRADDQLKSHVRGALNAGCSKDEIIEVMIQMAVYAGFPAAINAVLAAKEVFTEN 120
               SCOP domains d2af7h_ H: Gamma-carboxymuconolactone decarboxylase, CMD                                                                SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh.hhhhhhh......hhhhhhhhhhhh...........hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 2af7 H   2 ERYRRGmEILNRmNRKSYTAIRDELEDVAPDLARFVAEFAYGDVYSRGVLDLKTRELLTLAALTVLRADDQLKSHVRGALNAGCSKDEIIEVmIQmAVYAGFPAAINAVLAAKEVFTEN 120
                                  | 11  |     21        31        41        51        61        71        81        91  |  | 101       111         
                                  8-MSE |                                                                              94-MSE                      
                                       14-MSE                                                                             97-MSE                   


Chain I from PDB  Type:PROTEIN  Length:120
 aligned with O26336_METTH | O26336 from UniProtKB/TrEMBL  Length:125

    Alignment length:120
                                    11        21        31        41        51        61        71        81        91       101       111       121
         O26336_METTH     2 ERYRRGMEILNRMNRKSYTAIRDELEDVAPDLARFVAEFAYGDVYSRGVLDLKTRELLTLAALTVLRADDQLKSHVRGALNAGCSKDEIIEVMIQMAVYAGFPAAINAVLAAKEVFTEND 121
               SCOP domains d2af7i_ I: Gamma-carboxymuconolactone decarboxylase, CMD                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hh.hhhhh..hhhhhhhhhh...hhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 2af7 I   2 ERYRRGmEILNRmNRKSYTAIRDELEDVAPDLARFVAEFAYGDVYSRGVLDLKTRELLTLAALTVLRADDQLKSHVRGALNAGCSKDEIIEVmIQmAVYAGFPAAINAVLAAKEVFTEND 121
                                  | 11  |     21        31        41        51        61        71        81        91  |  | 101       111       121
                                  8-MSE |                                                                              94-MSE                       
                                       14-MSE                                                                             97-MSE
   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, 9)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2AF7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2AF7)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F,G,H,I   (O26336_METTH | O26336)
molecular function
    GO:0051920    peroxiredoxin activity    Catalysis of the reaction: 2 R'-SH + ROOH = R'-S-S-R' + H2O + ROH.
biological process
    GO:0098869    cellular oxidant detoxification    Any process carried out at the cellular level that reduces or removes the toxicity superoxide radicals or hydrogen peroxide.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.

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 Related Entries

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(-) Related Entries Specified in the PDB File

1p8c
1vke RELATED ID: TT747 RELATED DB: TARGETDB