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(-) Description

Title :  THE STRUCTURE OF RV0554 FROM MYCOBACTERIUM TUBERCULOSIS
 
Authors :  J. M. Johnston, E. N. Baker
Date :  06 Aug 08  (Deposition) - 23 Jun 09  (Release) - 09 Mar 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.35
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Alpha/Beta Hydrolase, Oxidoreductase, Peroxidase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. M. Johnston, M. Jiang, Z. Guo, E. N. Baker
Structural And Functional Analysis Of Rv0554 From Mycobacterium Tuberculosis: Testing A Putative Role In Menaquinone Biosynthesis.
Acta Crystallogr. , Sect. D V. 66 909 2010
PubMed-ID: 20693690  |  Reference-DOI: 10.1107/S0907444910025771

(-) Compounds

Molecule 1 - POSSIBLE PEROXIDASE BPOC
    Chains: A, B
    EC Number: 1.11.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PPROEX
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: BPOC, MT0580, RV0554
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 1773
    Strain: H37 RV
    Synonym: NON-HAEM PEROXIDASE, PUTATIVE BROMOPEROXIDASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2MPD1Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:146 , LEU A:240 , PHE A:243BINDING SITE FOR RESIDUE MPD A 265
2AC2SOFTWAREMET B:-5BINDING SITE FOR RESIDUE ACT B 263

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3E3A)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ala A:79 -Pro A:80
2Ala B:79 -Pro B:80

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3E3A)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3E3A)

(-) Exons   (0, 0)

(no "Exon" information available for 3E3A)

(-) 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:274
 aligned with BPOC_MYCTO | P9WNH0 from UniProtKB/Swiss-Prot  Length:262

    Alignment length:274
                                        1                                                                                                                                                                                                                                                                     
                                     -  |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258    
           BPOC_MYCTO     - ------------MINLAYDDNGTGDPVVFIAGRGGAGRTWHPHQVPAFLAAGYRCITFDNRGIGATENAEGFTTQTMVADTAALIETLDIAPARVVGVSMGAFIAQELMVVAPELVSSAVLMATRGRLDRARQFFNKAEAELYDSGVQLPPTYDARARLLENFSRKTLNDDVAVGDWIAMFSMWPIKSTPGLRCQLDCAPQTNRLPAYRNIAAPVLVIGFADDVVTPPYLGREVADALPNGRYLQIPDAGHLGFFERPEAVNTAMLKFFASVKA 262
               SCOP domains d3e3aa_ A: automated matches                                                                                                                                                                                                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee..........eeeeeee...eeeeee.....hhhhhh..hhhhhhhh.eeeeee....hhhhh.....hhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhhhhh...eeeeeee......hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhh......hhhhhh.....eeeeee......hhhhhhhhhhhh..eeeeee.....hhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3e3a A -11 LYFQGAMDPEFRVINLAYDDNGTGDPVVFIAGRGGAGRTWHPHQVPAFLAAGYRCITFDNRGIGATENAEGFTTQTMVADTAALIETLDIAPARVVGVSMGAFIAQELMVVAPELVSSAVLMATRGRLDRARQFFNKAEAELYDSGVQLPPTYDARARLLENFSRKTLNDDVAVGDWIAMFSMWPIKSTPGLRCQLDCAPQTNRLPAYRNIAAPVLVIGFADDVVTPPYLGREVADALPNGRYLQIPDAGHLGFFERPEAVNTAMLKFFASVKA 262
                                    -2         8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258    


Chain A from PDB  Type:PROTEIN  Length:274
 aligned with BPOC_MYCTU | P9WNH1 from UniProtKB/Swiss-Prot  Length:262

    Alignment length:274
                                        1                                                                                                                                                                                                                                                                     
                                     -  |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258    
           BPOC_MYCTU     - ------------MINLAYDDNGTGDPVVFIAGRGGAGRTWHPHQVPAFLAAGYRCITFDNRGIGATENAEGFTTQTMVADTAALIETLDIAPARVVGVSMGAFIAQELMVVAPELVSSAVLMATRGRLDRARQFFNKAEAELYDSGVQLPPTYDARARLLENFSRKTLNDDVAVGDWIAMFSMWPIKSTPGLRCQLDCAPQTNRLPAYRNIAAPVLVIGFADDVVTPPYLGREVADALPNGRYLQIPDAGHLGFFERPEAVNTAMLKFFASVKA 262
               SCOP domains d3e3aa_ A: automated matches                                                                                                                                                                                                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee..........eeeeeee...eeeeee.....hhhhhh..hhhhhhhh.eeeeee....hhhhh.....hhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhhhhh...eeeeeee......hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhh......hhhhhh.....eeeeee......hhhhhhhhhhhh..eeeeee.....hhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3e3a A -11 LYFQGAMDPEFRVINLAYDDNGTGDPVVFIAGRGGAGRTWHPHQVPAFLAAGYRCITFDNRGIGATENAEGFTTQTMVADTAALIETLDIAPARVVGVSMGAFIAQELMVVAPELVSSAVLMATRGRLDRARQFFNKAEAELYDSGVQLPPTYDARARLLENFSRKTLNDDVAVGDWIAMFSMWPIKSTPGLRCQLDCAPQTNRLPAYRNIAAPVLVIGFADDVVTPPYLGREVADALPNGRYLQIPDAGHLGFFERPEAVNTAMLKFFASVKA 262
                                    -2         8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258    


Chain B from PDB  Type:PROTEIN  Length:275
 aligned with BPOC_MYCTO | P9WNH0 from UniProtKB/Swiss-Prot  Length:262

    Alignment length:275
                                          1                                                                                                                                                                                                                                                                    
                                     -    |    6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256     
           BPOC_MYCTO     - --------------MINLAYDDNGTGDPVVFIAGRGGAGRTWHPHQVPAFLAAGYRCITFDNRGIGATENAEGFTTQTMVADTAALIETLDIAPARVVGVSMGAFIAQELMVVAPELVSSAVLMATRGRLDRARQFFNKAEAELYDSGVQLPPTYDARARLLENFSRKTLNDDVAVGDWIAMFSMWPIKSTPGLRCQLDCAPQTNRLPAYRNIAAPVLVIGFADDVVTPPYLGREVADALPNGRYLQIPDAGHLGFFERPEAVNTAMLKFFASVK 261
               SCOP domains d3e3ab_ B: automated matches                                                                                                                                                                                                                                                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..........eeeeeee...eeeeee.....hhhhhh.hhhhhhhhh.eeeeee....hhhhh.....hhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhhhhh...eeeeeee......hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhh.......hhhhhhhh...eeeeee......hhhhhhhhhhhh..eeeeee.....hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3e3a B -13 ENLYFQGAMDPEFRVINLAYDDNGTGDPVVFIAGRGGAGRTWHPHQVPAFLAAGYRCITFDNRGIGATENAEGFTTQTMVADTAALIETLDIAPARVVGVSMGAFIAQELMVVAPELVSSAVLMATRGRLDRARQFFNKAEAELYDSGVQLPPTYDARARLLENFSRKTLNDDVAVGDWIAMFSMWPIKSTPGLRCQLDCAPQTNRLPAYRNIAAPVLVIGFADDVVTPPYLGREVADALPNGRYLQIPDAGHLGFFERPEAVNTAMLKFFASVK 261
                                    -4         6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256     


Chain B from PDB  Type:PROTEIN  Length:275
 aligned with BPOC_MYCTU | P9WNH1 from UniProtKB/Swiss-Prot  Length:262

    Alignment length:275
                                          1                                                                                                                                                                                                                                                                    
                                     -    |    6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256     
           BPOC_MYCTU     - --------------MINLAYDDNGTGDPVVFIAGRGGAGRTWHPHQVPAFLAAGYRCITFDNRGIGATENAEGFTTQTMVADTAALIETLDIAPARVVGVSMGAFIAQELMVVAPELVSSAVLMATRGRLDRARQFFNKAEAELYDSGVQLPPTYDARARLLENFSRKTLNDDVAVGDWIAMFSMWPIKSTPGLRCQLDCAPQTNRLPAYRNIAAPVLVIGFADDVVTPPYLGREVADALPNGRYLQIPDAGHLGFFERPEAVNTAMLKFFASVK 261
               SCOP domains d3e3ab_ B: automated matches                                                                                                                                                                                                                                                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..........eeeeeee...eeeeee.....hhhhhh.hhhhhhhhh.eeeeee....hhhhh.....hhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhhhhh...eeeeeee......hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhh.......hhhhhhhh...eeeeee......hhhhhhhhhhhh..eeeeee.....hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3e3a B -13 ENLYFQGAMDPEFRVINLAYDDNGTGDPVVFIAGRGGAGRTWHPHQVPAFLAAGYRCITFDNRGIGATENAEGFTTQTMVADTAALIETLDIAPARVVGVSMGAFIAQELMVVAPELVSSAVLMATRGRLDRARQFFNKAEAELYDSGVQLPPTYDARARLLENFSRKTLNDDVAVGDWIAMFSMWPIKSTPGLRCQLDCAPQTNRLPAYRNIAAPVLVIGFADDVVTPPYLGREVADALPNGRYLQIPDAGHLGFFERPEAVNTAMLKFFASVK 261
                                    -4         6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256
   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, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3E3A)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3E3A)

(-) Gene Ontology  (8, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (BPOC_MYCTO | P9WNH0)
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:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0004601    peroxidase activity    Catalysis of the reaction: donor + hydrogen peroxide = oxidized donor + 2 H2O.
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.

Chain A,B   (BPOC_MYCTU | P9WNH1)
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:0016298    lipase activity    Catalysis of the hydrolysis of a lipid or phospholipid.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0004601    peroxidase activity    Catalysis of the reaction: donor + hydrogen peroxide = oxidized donor + 2 H2O.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
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:0009062    fatty acid catabolic process    The chemical reactions and pathways resulting in the breakdown of a fatty acid, any of the aliphatic monocarboxylic acids that can be liberated by hydrolysis from naturally occurring fats and oils. Fatty acids are predominantly straight-chain acids of 4 to 24 carbon atoms, which may be saturated or unsaturated; branched fatty acids and hydroxy fatty acids also occur, and very long chain acids of over 30 carbons are found in waxes.
    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

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

UniProtKB/Swiss-Prot
        BPOC_MYCTO | P9WNH0: 3hss 3hys 3hzo
        BPOC_MYCTU | P9WNH1: 3hss 3hys 3hzo

(-) Related Entries Specified in the PDB File

3hss