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(-) Description

Title :  TRNA-DIHYDROURIDINE SYNTHASE FROM THERMUS THERMOPHILUS IN COMPLEX WITH TRNA FRAGMENT
 
Authors :  F. Yu, Y. Tanaka, K. Yamashita, A. Nakamura, M. Yao, I. Tanaka
Date :  14 Jun 11  (Deposition) - 14 Dec 11  (Release) - 21 Dec 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym. Unit :  A,B,X,Y
Biol. Unit 1:  A,X  (1x)
Biol. Unit 2:  B,Y  (1x)
Keywords :  Tim Barrel, Oxidoreductase-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Yu, Y. Tanaka, K. Yamashita, T. Suzuki, A. Nakamura, N. Hirano, T. Suzuki, M. Yao, I. Tanaka
Molecular Basis Of Dihydrouridine Formation On Trna
Proc. Natl. Acad. Sci. Usa V. 108 19593 2011
PubMed-ID: 22123979  |  Reference-DOI: 10.1073/PNAS.1112352108

(-) Compounds

Molecule 1 - RNA (5'-R(*GP*GP*(H2U)P*A)-3')
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PUC19
    Expression System Strain: B834(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: TRNA FRAGMENT
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 300852
    Other Details: THE FULL LENGTH TRNA WAS TRANSCRIPTED IN E. COLI EXPRESSION SYSTEM AND AFTER BINDING TO PROTEIN THE RNA WAS PROCESSED BY RNASE
    Strain: HB8
 
Molecule 2 - TRNA-DIHYDROURIDINE SYNTHASE
    Chains: X, Y
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: CDFDUET-1
    Expression System Strain: B834(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TTHA0016
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 300852
    Strain: HB8

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABXY
Biological Unit 1 (1x): A X 
Biological Unit 2 (1x):  B Y

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1FMN2Ligand/IonFLAVIN MONONUCLEOTIDE
2H2U2Mod. Nucleotide5,6-DIHYDROURIDINE-5'-MONOPHOSPHATE
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1FMN1Ligand/IonFLAVIN MONONUCLEOTIDE
2H2U1Mod. Nucleotide5,6-DIHYDROURIDINE-5'-MONOPHOSPHATE
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1FMN1Ligand/IonFLAVIN MONONUCLEOTIDE
2H2U1Mod. Nucleotide5,6-DIHYDROURIDINE-5'-MONOPHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREH2U A:20 , ALA X:9 , PRO X:10 , MET X:11 , VAL X:12 , MET X:36 , GLN X:63 , ASN X:90 , LYS X:132 , HIS X:164 , ARG X:178 , ASN X:203 , GLY X:204 , GLY X:205 , GLY X:225 , ARG X:226 , HOH X:351 , HOH X:364 , HOH X:367 , HOH X:417BINDING SITE FOR RESIDUE FMN X 400
2AC2SOFTWAREH2U B:20 , ALA Y:9 , PRO Y:10 , MET Y:11 , VAL Y:12 , MET Y:36 , GLN Y:63 , ASN Y:90 , LYS Y:132 , HIS Y:164 , ARG Y:178 , ASN Y:203 , GLY Y:205 , GLY Y:225 , ARG Y:226 , HOH Y:352 , HOH Y:355 , HOH Y:402 , HOH Y:423BINDING SITE FOR RESIDUE FMN Y 400

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3B0U)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1His X:58 -Pro X:59
2His Y:58 -Pro Y:59

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3B0U)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UPF0034PS01136 Uncharacterized protein family UPF0034 signature.DUSAL_THET887-105
 		  2X:87-105
Y:87-105
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UPF0034PS01136 Uncharacterized protein family UPF0034 signature.DUSAL_THET887-105
 		  1X:87-105
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UPF0034PS01136 Uncharacterized protein family UPF0034 signature.DUSAL_THET887-105
 		  1-
Y:87-105

(-) Exons   (0, 0)

(no "Exon" information available for 3B0U)

(-) Sequences/Alignments

Asymmetric 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:RNA  Length:4
                                    
                 3b0u A  18 GGuA  21
                              | 
                             20-H2U


Chain B from PDB  Type:RNA  Length:4
                                    
                 3b0u B  18 GGuA  21
                              | 
                              | 
                             20-H2U


Chain X from PDB  Type:PROTEIN  Length:312
 aligned with DUSAL_THET8 | Q5SMC7 from UniProtKB/Swiss-Prot  Length:342

    Alignment length:312
                                    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       271       281       291       301       311  
          DUSAL_THET8     2 LDPRLSVAPMVDRTDRHFRFLVRQVSLGVRLYTEMTVDQAVLRGNRERLLAFRPEEHPIALQLAGSDPKSLAEAARIGEAFGYDEINLNLGCPSEKAQEGGYGACLLLDLARVREILKAMGEAVRVPVTVKMRLGLEGKETYRGLAQSVEAMAEAGVKVFVVHARSALLALSTKANREIPPLRHDWVHRLKGDFPQLTFVTNGGIRSLEEALFHLKRVDGVMLGRAVYEDPFVLEEADRRVFGLPRRPSRLEVARRMRAYLEEEVLKGTPPWAVLRHMLNLFRGRPKGRLWRRLLSEGRSLQALDRALRLME 313
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eee.......hhhhhhhhhhhh....ee...eehhhhhhhhhhhhhh.hhhhh.eeeeee..hhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeeee....hhhhhhhhhhhhhhh...eeeeeeeee......hhhhh....hhhhhhhhhhhh...eeeee....hhhhhhhhh....eeeehhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh..hhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------UPF0034            ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3b0u X   2 LDPRLSVAPMVDRTDRHFRFLVRQVSLGVRLYTEMTVDQAVLRGNRERLLAFRPEEHPIALQLAGSDPKSLAEAARIGEAFGYDEINLNLGCPSEKAQEGGYGACLLLDLARVREILKAMGEAVRVPVTVKMRLGLEGKETYRGLAQSVEAMAEAGVKVFVVHARSALLALSTKANREIPPLRHDWVHRLKGDFPQLTFVTNGGIRSLEEALFHLKRVDGVMLGRAVYEDPFVLEEADRRVFGLPRRPSRLEVARRMRAYLEEEVLKGTPPWAVLRHMLNLFRGRPKGRLWRRLLSEGRSLQALDRALRLME 313
                                    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       271       281       291       301       311  


Chain Y from PDB  Type:PROTEIN  Length:312
 aligned with DUSAL_THET8 | Q5SMC7 from UniProtKB/Swiss-Prot  Length:342

    Alignment length:312
                                    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       271       281       291       301       311  
          DUSAL_THET8     2 LDPRLSVAPMVDRTDRHFRFLVRQVSLGVRLYTEMTVDQAVLRGNRERLLAFRPEEHPIALQLAGSDPKSLAEAARIGEAFGYDEINLNLGCPSEKAQEGGYGACLLLDLARVREILKAMGEAVRVPVTVKMRLGLEGKETYRGLAQSVEAMAEAGVKVFVVHARSALLALSTKANREIPPLRHDWVHRLKGDFPQLTFVTNGGIRSLEEALFHLKRVDGVMLGRAVYEDPFVLEEADRRVFGLPRRPSRLEVARRMRAYLEEEVLKGTPPWAVLRHMLNLFRGRPKGRLWRRLLSEGRSLQALDRALRLME 313
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eee.......hhhhhhhhhhhh....ee...eehhhhhhhhhhhhhh.hhhhh.eeeeee..hhhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeeee....hhhhhhhhhhhhhhh...eeeeeeeee......hhhhh....hhhhhhhhhhhh...eeeee....hhhhhhhhh....eeeehhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh..hhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------UPF0034            ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3b0u Y   2 LDPRLSVAPMVDRTDRHFRFLVRQVSLGVRLYTEMTVDQAVLRGNRERLLAFRPEEHPIALQLAGSDPKSLAEAARIGEAFGYDEINLNLGCPSEKAQEGGYGACLLLDLARVREILKAMGEAVRVPVTVKMRLGLEGKETYRGLAQSVEAMAEAGVKVFVVHARSALLALSTKANREIPPLRHDWVHRLKGDFPQLTFVTNGGIRSLEEALFHLKRVDGVMLGRAVYEDPFVLEEADRRVFGLPRRPSRLEVARRMRAYLEEEVLKGTPPWAVLRHMLNLFRGRPKGRLWRRLLSEGRSLQALDRALRLME 313
                                    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       271       281       291       301       311
   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 3B0U)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3B0U)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3B0U)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain X,Y   (DUSAL_THET8 | Q5SMC7)
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:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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.

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        DUSAL_THET8 | Q5SMC7: 3b0p 3b0v

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3b0p APO FORM