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(-) Description

Title :  CRYSTAL STRUCTURE OF DUSC
 
Authors :  M. Chen, J. Yu, Y. Tanaka, I. Tanaka, M. Yao
Date :  19 Apr 13  (Deposition) - 31 Jul 13  (Release) - 21 Aug 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A
Keywords :  Tim Barrel, Reductase, Trna, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Chen, J. Yu, Y. Tanaka, M. Tanaka, I. Tanaka, M. Yao
Structure Of Dihydrouridine Synthase C (Dusc) From Escherichia Coli
Acta Crystallogr. , Sect. F V. 69 834 2013
PubMed-ID: 23908023  |  Reference-DOI: 10.1107/S1744309113019489

(-) Compounds

Molecule 1 - TRNA-DIHYDROURIDINE SYNTHASE C
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-26(B)
    Expression System Strain: B834(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: B2140, DUSC, JW2128, YOHI
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1FMN1Ligand/IonFLAVIN MONONUCLEOTIDE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:6 , PRO A:7 , MET A:8 , GLU A:9 , PHE A:33 , GLN A:68 , ASN A:95 , CYS A:98 , LYS A:139 , HIS A:168 , TYR A:176 , ASN A:200 , GLY A:201 , GLU A:202 , GLY A:224 , ARG A:225 , HOH A:501 , HOH A:513BINDING SITE FOR RESIDUE FMN A 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3W9Z)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Glu A:313 -Lys A:314

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3W9Z)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UPF0034PS01136 Uncharacterized protein family UPF0034 signature.DUSC_ECOLI92-110  1A:92-98

(-) Exons   (0, 0)

(no "Exon" information available for 3W9Z)

(-) 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:290
 aligned with DUSC_ECOLI | P33371 from UniProtKB/Swiss-Prot  Length:315

    Alignment length:314
                                    10        20        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    
           DUSC_ECOLI     1 MRVLLAPMEGVLDSLVRELLTEVNDYDLCITEFVRVVDQLLPVKVFHRICPELQNASRTPSGTLVRVQLLGQFPQWLAENAARAVELGSWGVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAMREAVPAHLPVSVKVRLGWDSGEKKFEIADAVQQAGATELVVHGRTKEQGYRAEHIDWQAIGDIRQRLNIPVIANGEIWDWQSAQQCMAISGCDAVMIGRGALNIPNLSRVVKYNEPRMPWPEVVALLQKYTRLEKQGDTGLYHVARIKQWLSYLRKEYDEATELFQHVRVLNNSPDIARAIQAIDIEK 314
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.......hhhhhhhhhhh....eeeeeeee......hhhhhhhhhhhhhhh........eeeeee..hhhhhhhhhhhhhhh....eeeee..-------------...hhhhhhhhhhhhhhhh.....eeeeee.......hhhhhhhhhhhh...eeeee........hhhhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhh..eeee.hhhhhh.hhhhhhhhh....hhhhhhhhhhhhhhh.--------..hhhhhhhhhhhhhhhhhhhhhhhhh.---..hhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------UPF0034            ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3w9z A   1 MRVLLAPMEGVLDSLVRELLTEVNDYDLCITEFVRVVDQLLPVKVFHRICPELQNASRTPSGTLVRVQLLGQFPQWLAENAARAVELGSWGVDLNCGC-------------LLKDPELIYQGAKAMREAVPAHLPVSVKVRLGWDSGEKKFEIADAVQQAGATELVVHGRTKEQGYRAEHIDWQAIGDIRQRLNIPVIANGEIWDWQSAQQCMAISGCDAVMIGRGALNIPNLSRVVKYNEPRMPWPEVVALLQKYTRLE--------HVARIKQWLSYLRKEYDEATELFQHVRV---SPDIARAIQAIDIEK 314
                                    10        20        30        40        50        60        70        80        90       | -         - |     120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290     | 300       310    
                                                                                                                            98           112                                                                                                                                                 260      269                        296 300
   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  (0, 0)

(no "SCOP Domain" information available for 3W9Z)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3W9Z)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3W9Z)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (DUSC_ECOLI | P33371)
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:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    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:0050660    flavin adenine dinucleotide binding    Interacting selectively and non-covalently with FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.
    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:0000049    tRNA binding    Interacting selectively and non-covalently with transfer RNA.
    GO:0017150    tRNA dihydrouridine synthase activity    Catalysis of the reaction: tRNA-uracil + acceptor = tRNA-dihydrouridine + reduced acceptor.
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:0002943    tRNA dihydrouridine synthesis    The process whereby a uridine in a transfer RNA is converted to dihydrouridine.
    GO:0008033    tRNA processing    The process in which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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 Related Entries

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

UniProtKB/Swiss-Prot
        DUSC_ECOLI | P33371: 4bf9 4bfa 4yco 4ycp

(-) Related Entries Specified in the PDB File

1vhn HOMOLOGOUS PROTEIN FROM THERMOTOGA MARITIMA
3b0p HOMOLOGOUS PROTEIN FROM THERMUS THERMOPHILUS
3b0u HOMOLOGOUS PROTEIN FROM THERMUS THERMOPHILUS IN COMPLEX WITH TRNA FRAGMENT
3b0v HOMOLOGOUS PROTEIN FROM THERMUS THERMOPHILUS IN COMPLEX WITH TRNA