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(-) Description

Title :  CRYSTAL STRUCTURE OF RV1155 FROM MYCOBACTERIUM TUBERCULOSIS
 
Authors :  S. Canaan, G. Sulzenbacher, V. Roig-Zamboni, L. Scappuccini, F. Frassinetti-Calvo, D. Maurin, C. Cambillau, Y. Bourne
Date :  07 Oct 04  (Deposition) - 06 Jan 05  (Release) - 06 Mar 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Oxidoreductase, Related To Fmn-Binding Proteins (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Canaan, G. Sulzenbacher, V. Roig-Zamboni, L. Scappuccini-Calvo, F. Frassinetti, D. Maurin, C. Cambillau, Y. Bourne
Crystal Structure Of The Conserved Hypothetical Protein Rv1155 From Mycobacterium Tuberculosis
Febs Lett. V. 579 215 2005
PubMed-ID: 15620716  |  Reference-DOI: 10.1016/J.FEBSLET.2004.11.069

(-) Compounds

Molecule 1 - PUTATIVE PYRIDOXINE/PYRIDOXAMINE 5'-PHOSPHATE OXIDASE
    Chains: A, B
    EC Number: 1.4.3.5
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: HISPKM596
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: PLYSS
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 83332
    Strain: H37RV
    Synonym: PNP/PMP OXIDASE, PNPOX, RV1155, PYRIDOXAL 5'-PHOSPHATE SYNTHASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 1W9A)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1W9A)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1W9A)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1W9A)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1W9A)

(-) Exons   (0, 0)

(no "Exon" information available for 1W9A)

(-) 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:142
 aligned with F420R_MYCTU | O06553 from UniProtKB/Swiss-Prot  Length:147

    Alignment length:142
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145  
          F420R_MYCTU     6 FDDKLLAVISGNSIGVLATIKHDGRPQLSNVQYHFDPRKLLIQVSIAEPRAKTRNLRRDPRASILVDADDGWSYAVAEGTAQLTPPAAAPDDDTVEALIALYRNIAGEHSDWDDYRQAMVTDRRVLLTLPISHVYGLPPGMR 147
               SCOP domains d1w9aa_ A: Hypothetical protein Rv1155                                                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh..eeeeeee.....eeeeeee.eee....eeeeeee..hhhhhhhhh..eeeeeee......eeeeeee...........hhhhhhhhhhhhhhhh...hhhhhhhhhhhh.eeeeeee..eeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1w9a A   6 FDDKLLAVISGNSIGVLATIKHDGRPQLSNVQYHFDPRKLLIQVSIAEPRAKTRNLRRDPRASILVDADDGWSYAVAEGTAQLTPPAAAPDDDTVEALIALYRNIAGEHSDWDDYRQAmVTDRRVLLTLPISHVYGLPPGmR 147
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145| 
                                                                                                                                                124-MSE               146-MSE


Chain B from PDB  Type:PROTEIN  Length:143
 aligned with F420R_MYCTU | O06553 from UniProtKB/Swiss-Prot  Length:147

    Alignment length:143
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144   
          F420R_MYCTU     5 VFDDKLLAVISGNSIGVLATIKHDGRPQLSNVQYHFDPRKLLIQVSIAEPRAKTRNLRRDPRASILVDADDGWSYAVAEGTAQLTPPAAAPDDDTVEALIALYRNIAGEHSDWDDYRQAMVTDRRVLLTLPISHVYGLPPGMR 147
               SCOP domains d1w9ab_ B: Hypothetical protein Rv1155                                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhh..eeeeeee.....eeeeeee.eee....eeeeeee..hhhhhhhhhh.eeeeeee......eeeeeee...........hhhhhhhhhhhhhhh....hhhhhhhhhhhh.eeeeeee..eeeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1w9a B   5 VFDDKLLAVISGNSIGVLATIKHDGRPQLSNVQYHFDPRKLLIQVSIAEPRAKTRNLRRDPRASILVDADDGWSYAVAEGTAQLTPPAAAPDDDTVEALIALYRNIAGEHSDWDDYRQAmVTDRRVLLTLPISHVYGLPPGmR 147
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144 | 
                                                                                                                                                 124-MSE               146-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, 2)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1W9A)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1W9A)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (F420R_MYCTU | O06553)
molecular function
    GO:0010181    FMN binding    Interacting selectively and non-covalently with flavin mono nucleotide. Flavin mono nucleotide (FMN) is the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes.
    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:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    GO:0030170    pyridoxal phosphate binding    Interacting selectively and non-covalently with pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6.
    GO:0004733    pyridoxamine-phosphate oxidase activity    Catalysis of the reaction: pyridoxamine 5'-phosphate + H2O + O2 = pyridoxal 5'-phosphate + NH3 + hydrogen peroxide.
biological process
    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.
    GO:0042823    pyridoxal phosphate biosynthetic process    The chemical reactions and pathways resulting in the formation of pyridoxal phosphate, pyridoxal phosphorylated at the hydroxymethyl group of C-5, the active form of vitamin B6.
    GO:0042816    vitamin B6 metabolic process    The chemical reactions and pathways involving any of the vitamin B6 compounds: pyridoxal, pyridoxamine and pyridoxine and the active form, pyridoxal phosphate.

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 Related Entries

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

UniProtKB/Swiss-Prot
        F420R_MYCTU | O06553: 1xxo 1y30 2aq6 4qvb

(-) Related Entries Specified in the PDB File

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