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(-) Description

Title :  E. COLI DIHYDROURIDINE SYNTHASE C (DUSC) IN COMPLEX WITH TRNATRP
 
Authors :  R. T. Byrne, H. T. Jenkins, D. T. Peters, F. Whelan, J. Stowell, N. Aziz, P. Kasatsky, M. V. Rodnina, E. V. Koonin, A. L. Konevega, A. A. Antson
Date :  20 Feb 15  (Deposition) - 22 Apr 15  (Release) - 20 May 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.55
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Trna Modification, Oxidoreductase-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. T. Byrne, H. T. Jenkins, D. T. Peters, F. Whelan, J. Stowell, N. Aziz, P. Kasatsky, M. V. Rodnina, E. V. Koonin, A. L. Konevega, A. A. Antson
Major Reorientation Of Trna Substrates Defines Specificity Of Dihydrouridine Synthases.
Proc. Natl. Acad. Sci. Usa V. 112 6033 2015
PubMed-ID: 25902496  |  Reference-DOI: 10.1073/PNAS.1500161112

(-) Compounds

Molecule 1 - TRNA-DIHYDROURIDINE SYNTHASE C
    Chains: A
    EC Number: 1.-.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET28A
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 1-315
    Gene: DUSC, YOHI, B2140, JW2128
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI K-12
    Organism Taxid: 83333
    Synonym: DUSC
 
Molecule 2 - TRNATRP
    Chains: B
    Engineered: YES
    Organism Scientific: ESCHERICHIA COLI K-12
    Organism Taxid: 83333
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
1FMN1Ligand/IonFLAVIN MONONUCLEOTIDE
2MG1Ligand/IonMAGNESIUM ION
3SO42Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:6 , PRO A:7 , MET A:8 , GLU A:9 , PHE A:33 , GLN A:68 , ASN A:95 , 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:540 , HOH A:541 , U B:16 , U B:17binding site for residue FMN A 401
2AC2SOFTWAREARG A:281 , PHE A:291 , ARG A:295binding site for residue SO4 A 402
3AC3SOFTWAREARG A:243 , PRO A:245 , TRP A:246binding site for residue SO4 A 403
4AC4SOFTWAREHOH A:542 , HOH A:543 , U B:17 , G B:19 , HOH B:207 , HOH B:208binding site for residue MG B 101

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4YCP)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4YCP)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4YCP)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4YCP)

(-) Exons   (0, 0)

(no "Exon" information available for 4YCP)

(-) 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:308
                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.......hhhhhhhhhhh....eee...ee......hhhhhhhhhhhhhhh........eeeeee..hhhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhhhhhhhhhh.....eeeeee.......hhhhhhhhhhhhh..eeeee........hhhhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhh..eeee.hhhhhh.hhhhhhhhh....hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhh.hhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ycp A   1 MRVLLAPMEGVLDSLVRELLTEVNDYDLCITEFVRVVDQLLPVKVFHRICPELQNASRTPSGTLVRVQLLGQFPQWLAENAARAVELGSWGVDLNCGAPGGGATLLKDPELIYQGAKAMREAVPAHLPVSVKVRLGWDSGEKKFEIADAVQQAGATELVVHGRTKEQGYRAEHIDWQAIGDIRQRLNIPVIANGEIWDWQSAQQCMAISGCDAVMIGRGALNIPNLSRVVKYNEPRMPWPEVVALLQKYTRLEKQGDTGLYHVARIKQWLSYLRKEYDEATELFQHVRVLNNSPDIARAIQAIDIEKL 315
                                    10        20        30        40        50        60        70        80        90       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307        
                                                                                                                             99|                                                                                                                                                                                                                
                                                                                                                             107                                                                                                                                                                                                                


Chain B from PDB  Type:DNA/RNA  Length:62
                                                                                              
                 4ycp B   5 GCGUAGUUCAAUUGGUAGAGCACCGGUCAAAACCGGGUGUUGGGAGUUCGAGUCUCUCCGCC  69
                                    14        24       |37        47        57        67  
                                                      32|                                 
                                                       36
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  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 4YCP)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4YCP)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4YCP)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)

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  4ycp
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  DUSC_ECOLI | P33371
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 Related Entries

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

UniProtKB/Swiss-Prot
        DUSC_ECOLI | P33371: 3w9z 4bf9 4bfa 4yco

(-) Related Entries Specified in the PDB File

4bf9 4BFA CONTAINS WILD-TYPE PROTEIN IN THE ABSENCE OF RNA.
4bfa 4BFA CONTAINS WILD-TYPE PROTEIN IN THE ABSENCE OF RNA.
4yco CONTAINS THE SAME PROTEIN COMPLEXED WITH TRNAPHE