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(-) Description

Title :  CRYSTAL STRUCTURE OF VIOC IN COMPLEX WITH FE(II), (2S,3S)-HYDROXYARGININE, AND SUCCINATE
 
Authors :  V. Helmetag, S. A. Samel, M. G. Thomas, M. A. Marahiel, L. -O. Essen
Date :  02 Mar 09  (Deposition) - 23 Jun 09  (Release) - 08 May 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.16
Chains :  Asym./Biol. Unit :  A
Keywords :  Oxidoreductase, Non-Heme Fe(Ii) Hydroxylase, Cbeta-Hydroxylation, Nrps, Viomycin, Alpha-Ketoglutarate (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. Helmetag, S. A. Samel, M. G. Thomas, M. A. Marahiel, L. -O. Essen
Structural Basis For The Erythro-Stereospecificity Of The L-Arginine Oxygenase Vioc In Viomycin Biosynthesis.
Febs J. V. 276 3669 2009
PubMed-ID: 19490124  |  Reference-DOI: 10.1111/J.1742-4658.2009.07085.X

(-) Compounds

Molecule 1 - L-ARGININE BETA-HYDROXYLASE
    Atcc: 11861
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28VIOC
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET-28A
    Organism Scientific: STREPTOMYCES VINACEUS
    Organism Taxid: 1960
    Synonym: L-ARGININE OXYGENASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 5)

Asymmetric/Biological Unit (5, 5)
No.NameCountTypeFull Name
1ARG1Mod. Amino AcidARGININE
2FE21Ligand/IonFE (II) ION
3GOL1Ligand/IonGLYCEROL
4SIN1Ligand/IonSUCCINIC ACID
5ZZU1Ligand/Ion(2S,3S)-3-HYDROXYARGININE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:168 , GLU A:170 , HIS A:316 , ZZU A:1359 , SIN A:1360BINDING SITE FOR RESIDUE FE2 A1358
2AC2SOFTWAREGLN A:137 , LEU A:156 , VAL A:157 , SER A:158 , LEU A:165 , HIS A:168 , GLU A:170 , ASP A:222 , SER A:224 , ASP A:268 , ASP A:270 , PHE A:271 , ARG A:334 , FE2 A:1358 , SIN A:1360 , HOH A:2213 , HOH A:2272BINDING SITE FOR RESIDUE ZZU A1359
3AC3SOFTWAREVAL A:146 , LEU A:165 , HIS A:168 , GLU A:170 , THR A:194 , HIS A:316 , ARG A:318 , ARG A:330 , LEU A:332 , ARG A:334 , FE2 A:1358 , ZZU A:1359 , HOH A:2384BINDING SITE FOR RESIDUE SIN A1360
4AC4SOFTWAREARG A:47 , TYR A:48 , GLU A:55 , ASP A:59 , ARG A:77 , VAL A:238 , GLN A:245BINDING SITE FOR RESIDUE ARG A1361
5AC5SOFTWAREGLY A:166 , TRP A:167 , GLY A:269 , ARG A:289 , ASP A:293 , ARG A:328 , HOH A:2214 , HOH A:2363 , HOH A:2385 , HOH A:2386 , HOH A:2387BINDING SITE FOR RESIDUE GOL A1362

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2WBP)

(-) 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:334
 aligned with ARGHX_STRVI | Q6WZB0 from UniProtKB/Swiss-Prot  Length:358

    Alignment length:338
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350        
         ARGHX_STRVI     21 VRPWSEFRLTPAEAAAAAALAARCAQRYDETDGPEFLLDAPVIAHELPRRLRTFMARARLDAWPHALVVRGNPVDDAALGSTPVHWRTARTPGSRPLSFLLMLYAGLLGDVFGWATQQDGRVVTDVLPIKGGEHTLVSSSSRQELGWHTEDAFSPYRADYVGLLSLRNPDGVATTLAGVPLDDLDERTLDVLFQERFLIRPDDSHLQVNNSTAQQGRVEFEGIAQAADRPEPVAILTGHRAAPHLRVDGDFSAPAEGDEEAAAALGTLRKLIDASLYELVLDQGDVAFIDNRRAVHGRRAFQPRYDGRDRWLKRINITRDLHRSRKAWAGDSRVLGQR  358
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee.hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeee....hhhhhh....hhhhh.hhhhhhhhhhhhhhhhh..eeeee..hhhhh..eee..................eeee...........eeeeeeee.....eeeeee......hhhhhhhhh...ee...hhhhhhhhh..----..hhhhhhhhhhh......eeee..eeee.......ee...hhhhhhhhhhhhhhhhhhheeee.....eeeee...eeeee............eeeeeeee.hhhhhhh.eeee..ee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2wbp A   21 VRPWSEFRLTPAEAAAAAALAARCAQRYDETDGPEFLLDAPVIAHELPRRLRTFMARARLDAWPHALVVRGNPVDDAALGSTPVHWRTARTPGSRPLSFLLMLYAGLLGDVFGWATQQDGRVVTDVLPIKGGEHTLVSSSSRQELGWHTEDAFSPYRADYVGLLSLRNPDGVATTLAGVPLDDLDERTLDVLFQERFLIRPDDSHLQVNNST----RVEFEGIAQAADRPEPVAILTGHRAAPHLRVDGDFSAPAEGDEEAAAALGTLRKLIDASLYELVLDQGDVAFIDNRRAVHGRRAFQPRYDGRDRWLKRINITRDLHRSRKAWAGDSRVLGQR 1361
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230 |    |240       250       260       270       280       290       300       310       320       330       340       350      ||
                                                                                                                                                                                                                                             232  237                                                                                                                     357|
                                                                                                                                                                                                                                                                                                                                                                          1361
   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  (0, 0)

(no "SCOP Domain" information available for 2WBP)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (ARGHX_STRVI | Q6WZB0)
molecular function
    GO:0033758    clavaminate synthase activity    Catalysis of the reactions: deoxyamidinoproclavaminate + 2-oxoglutarate + O2 = amidinoproclavaminate + succinate + CO2 + H2O; proclavaminate + 2-oxoglutarate + O2 = dihydroclavaminate + succinate + CO2 + 2 H2O; and dihydroclavaminate + 2-oxoglutarate + O2 = clavaminate + succinate + CO2 + 2 H2O.
    GO:0005506    iron ion binding    Interacting selectively and non-covalently with iron (Fe) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0016706    oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors    Catalysis of the reaction: A + 2-oxoglutarate + O2 = B + succinate + CO2. This is an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from 2-oxoglutarate and one other donor, and one atom of oxygen is incorporated into each donor.
biological process
    GO:0017000    antibiotic biosynthetic process    The chemical reactions and pathways resulting in the formation of an antibiotic, a substance produced by or derived from certain fungi, bacteria, and other organisms, that can destroy or inhibit the growth of other microorganisms.
    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.
cellular component
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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 Related Entries

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

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        ARGHX_STRVI | Q6WZB0: 2wbo 2wbq

(-) Related Entries Specified in the PDB File

2wbo CRYSTAL STRUCTURE OF VIOC IN COMPLEX WITH L-ARGININE
2wbq CRYSTAL STRUCTURE OF VIOC IN COMPLEX WITH (2S,3S)-HYDROXYARGININE