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(-) Description

Title :  STRUCTURE OF RV0554 FROM MYCOBACTERIUM TUBERCULOSIS COMPLEXED WITH MALONIC ACID
 
Authors :  J. M. Johnston, E. N. Baker
Date :  23 Jun 09  (Deposition) - 02 Jun 10  (Release) - 29 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  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 - PROTEIN RV0554, PUTATIVE BROMOPEROXIDASE
    Chains: A, B
    EC Number: 1.11.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: BPOC, MT0580, RV0554
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 1773
    Synonym: POSSIBLE PEROXIDASE BPOC (NON-HAEM PEROXIDASE)

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 12)

Asymmetric/Biological Unit (4, 12)
No.NameCountTypeFull Name
1EDO7Ligand/Ion1,2-ETHANEDIOL
2MLA2Ligand/IonMALONIC ACID
3NA2Ligand/IonSODIUM ION
4TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETHR A:27 , ARG A:146 , TRP A:172 , LEU A:240 , EDO A:264 , HOH A:405BINDING SITE FOR RESIDUE MLA A 5188
02AC2SOFTWAREGLY A:20 , ARG A:21 , SER A:87 , MET A:88 , ARG A:113 , GLN A:183 , LEU A:184 , HOH A:476BINDING SITE FOR RESIDUE TRS A 263
03AC3SOFTWAREARG A:21 , GLY A:23 , HOH A:400 , MLA A:5188BINDING SITE FOR RESIDUE EDO A 264
04AC4SOFTWAREALA A:161 , ASP A:164 , TRP A:165BINDING SITE FOR RESIDUE EDO A 265
05AC5SOFTWAREPHE A:46 , ASN A:48 , ARG A:49 , MET A:65 , ASP A:68 , THR A:69BINDING SITE FOR RESIDUE EDO A 266
06AC6SOFTWAREALA A:223 , LEU A:226 , GLY A:229 , HOH A:308 , HOH A:309BINDING SITE FOR RESIDUE NA A 267
07AC7SOFTWAREGLY B:20 , ARG B:21 , SER B:87 , MET B:88 , ARG B:120 , PHE B:123 , HIS B:239 , HOH B:300 , HOH B:301 , HOH B:302BINDING SITE FOR RESIDUE MLA B 5188
08AC8SOFTWAREARG B:146 , HOH B:307 , HOH B:417BINDING SITE FOR RESIDUE EDO B 263
09AC9SOFTWAREGLY B:22 , ALA B:24 , ARG B:26 , TRP B:172 , PRO B:173 , HOH B:417 , HOH B:418BINDING SITE FOR RESIDUE EDO B 264
10BC1SOFTWAREALA B:119 , HOH B:295 , HOH B:296BINDING SITE FOR RESIDUE EDO B 265
11BC2SOFTWAREGLY B:12 , ASP B:13 , GLY B:40BINDING SITE FOR RESIDUE EDO B 266
12BC3SOFTWAREALA B:223 , ASP B:224 , LEU B:226 , GLY B:229 , HOH B:282BINDING SITE FOR RESIDUE NA B 267

(-) SS Bonds  (0, 0)

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

(-) 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 3HYS)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3HYS)

(-) 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: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 d3hysa_ A: automated matches                                                                                                                                                                                                                                                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee.....eeeeeeeee...eeeeee.....hhhhhh..hhhhhhhh.eeeeee....hhhhh.....hhhhhhhhhhhhhhhhh...eeeeeehhhhhhhhhhhhhh...eeeeeee......hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhh.......hhhhhh.....eeeeee......hhhhhhhhhhhh..eeeeee.....hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hys A -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 A 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 d3hysa_ A: automated matches                                                                                                                                                                                                                                                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee.....eeeeeeeee...eeeeee.....hhhhhh..hhhhhhhh.eeeeee....hhhhh.....hhhhhhhhhhhhhhhhh...eeeeeehhhhhhhhhhhhhh...eeeeeee......hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhh.......hhhhhh.....eeeeee......hhhhhhhhhhhh..eeeeee.....hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hys A -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:261
 aligned with BPOC_MYCTO | P9WNH0 from UniProtKB/Swiss-Prot  Length:262

    Alignment length:261
                                    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 
           BPOC_MYCTO     2 INLAYDDNGTGDPVVFIAGRGGAGRTWHPHQVPAFLAAGYRCITFDNRGIGATENAEGFTTQTMVADTAALIETLDIAPARVVGVSMGAFIAQELMVVAPELVSSAVLMATRGRLDRARQFFNKAEAELYDSGVQLPPTYDARARLLENFSRKTLNDDVAVGDWIAMFSMWPIKSTPGLRCQLDCAPQTNRLPAYRNIAAPVLVIGFADDVVTPPYLGREVADALPNGRYLQIPDAGHLGFFERPEAVNTAMLKFFASVKA 262
               SCOP domains d3hysb_ B: automated matches                                                                                                                                                                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee....eeeee.....hhhhhh..hhhhhhhh..eeeee....hhhhh.....hhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhhhhh...eeeeeee......hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhh.......hhhhhh.....eeeeee......hhhhhhhhhhhh..eeeeee.....hhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hys B   2 INLAYDDNGTGDPVVFIAGRGGAGRTWHPHQVPAFLAAGYRCITFDNRGIGATENAEGFTTQTMVADTAALIETLDIAPARVVGVSMGAFIAQELMVVAPELVSSAVLMATRGRLDRARQFFNKAEAELYDSGVQLPPTYDARARLLENFSRKTLNDDVAVGDWIAMFSMWPIKSTPGLRCQLDCAPQTNRLPAYRNIAAPVLVIGFADDVVTPPYLGREVADALPNGRYLQIPDAGHLGFFERPEAVNTAMLKFFASVKA 262
                                    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 


Chain B from PDB  Type:PROTEIN  Length:261
 aligned with BPOC_MYCTU | P9WNH1 from UniProtKB/Swiss-Prot  Length:262

    Alignment length:261
                                    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 
           BPOC_MYCTU     2 INLAYDDNGTGDPVVFIAGRGGAGRTWHPHQVPAFLAAGYRCITFDNRGIGATENAEGFTTQTMVADTAALIETLDIAPARVVGVSMGAFIAQELMVVAPELVSSAVLMATRGRLDRARQFFNKAEAELYDSGVQLPPTYDARARLLENFSRKTLNDDVAVGDWIAMFSMWPIKSTPGLRCQLDCAPQTNRLPAYRNIAAPVLVIGFADDVVTPPYLGREVADALPNGRYLQIPDAGHLGFFERPEAVNTAMLKFFASVKA 262
               SCOP domains d3hysb_ B: automated matches                                                                                                                                                                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee....eeeee.....hhhhhh..hhhhhhhh..eeeee....hhhhh.....hhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhhhhh...eeeeeee......hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhh.......hhhhhh.....eeeeee......hhhhhhhhhhhh..eeeeee.....hhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hys B   2 INLAYDDNGTGDPVVFIAGRGGAGRTWHPHQVPAFLAAGYRCITFDNRGIGATENAEGFTTQTMVADTAALIETLDIAPARVVGVSMGAFIAQELMVVAPELVSSAVLMATRGRLDRARQFFNKAEAELYDSGVQLPPTYDARARLLENFSRKTLNDDVAVGDWIAMFSMWPIKSTPGLRCQLDCAPQTNRLPAYRNIAAPVLVIGFADDVVTPPYLGREVADALPNGRYLQIPDAGHLGFFERPEAVNTAMLKFFASVKA 262
                                    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
   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 3HYS)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 13)

Asymmetric/Biological Unit(hide GO term definitions)
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.

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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        BPOC_MYCTO | P9WNH0: 3e3a 3hss 3hzo
        BPOC_MYCTU | P9WNH1: 3e3a 3hss 3hzo

(-) Related Entries Specified in the PDB File

3e3a 3hss 3hzo