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(-) Description

Title :  CRYSTAL STRUCTURE OF A 4-THIOURIDINE SYNTHETASE - RNA COMPLEX WITH BOUND ATP
 
Authors :  P. Neumann, R. Ficner, K. Lakomek
Date :  16 May 13  (Deposition) - 23 Apr 14  (Release) - 16 Jul 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.42
Chains :  Asym./Biol. Unit :  A,B,M,X
Keywords :  Trna Modification, Thiouridine, Sulfurtransferase, Adenylation, Thump Domain, Pp-Loop Motif, 4-Thiouridine Synthesis, Transferase-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Neumann, K. Lakomek, P. T. Naumann, W. M. Erwin, C. T. Lauhon, R. Ficner
Crystal Structure Of A 4-Thiouridine Synthetase-Rna Complex Reveals Specificity Of Trna U8 Modification.
Nucleic Acids Res. V. 42 6673 2014
PubMed-ID: 24705700  |  Reference-DOI: 10.1093/NAR/GKU249

(-) Compounds

Molecule 1 - PROBABLE TRNA SULFURTRANSFERASE
    Chains: A, B
    EC Number: 2.8.1.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-28A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: AAD36761, THII, TM_1694
    Mutation: YES
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 243274
    Strain: ATCC 43589
    Synonym: SULFUR CARRIER PROTEIN THIS SULFURTRANSFERASE, THIAMINE BIOSYNTHESIS PROTEIN THII, TRNA 4-THIOURIDINE SYNTHASE
 
Molecule 2 - RNA (39-MER)
    Chains: M, X
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABMX

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1ATP2Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2MG2Ligand/IonMAGNESIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:180 , LEU A:181 , SER A:182 , GLY A:184 , ILE A:185 , ASP A:186 , SER A:187 , VAL A:204 , THR A:205 , PHE A:206 , ARG A:264 , MET A:267 , THR A:285 , GLY A:286 , GLU A:287 , GLN A:291 , GLN A:295 , MG A:402BINDING SITE FOR RESIDUE ATP A 401
2AC2SOFTWAREATP A:401BINDING SITE FOR RESIDUE MG A 402
3AC3SOFTWARELEU B:180 , LEU B:181 , SER B:182 , ASP B:186 , SER B:187 , VAL B:204 , PHE B:206 , ARG B:264 , MET B:267 , GLY B:286 , GLU B:287 , ASN B:288 , LYS B:320 , MG B:402BINDING SITE FOR RESIDUE ATP B 401
4AC4SOFTWAREATP B:401BINDING SITE FOR RESIDUE MG B 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4KR7)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Pro A:209 -Pro A:210
2Pro B:209 -Pro B:210

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4KR7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4KR7)

(-) Exons   (0, 0)

(no "Exon" information available for 4KR7)

(-) 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:386
                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.......hhhhhhhhhhhhhhhhhhhh...eee..eeeee......hhhhhhh.....eeeeeeee..hhhhhhhhhhhhhhhhhhhh....eeeeeee.......hhhhhhhhhhhhhhhhh...........eeeeeeee..eeeee...ee...........eeeee....hhhhhhhhhhhhh..eeeeeeee.......hhhhhhhhhhhhhhhhh....eeeeeeehhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh..eee...........hhhhhhhhhh.....ee......hhhhhhhhhhhh.hhhhhhh....................hhhhhhhhhh.hhhhhhhhhhhh.eeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kr7 A   3 ELRVYIVRYSEIGLKGKNRKDFEEALRRNIERVTGMKVKRQWGRFLIPIDENVTLDDKLKKIFGIQNFSKGFLVSHDFEEVKKYSLIAVKEKLEKGNYRTFKVQAKKAYKEYKKGVYEINSELGALILKNFKELSVDVRNPDFVLGVEVRPEGVLIFTDRVECYGGLPVGTGGKAVLLLSGGIDSPVAGWYALKRGVLIESVTFVSPPFTSEGAVEKVRDILRVLREFSGGHPLRLHIVNLTKLQLEVKKRVPDKYSLIMYRRSMFRIAEKIAEETGAVAFYTGENIGQVASQTLENLWSIESVTTRPVIRPLSGFDKTEIVEKAKEIGTYEISIKPYQDSCVFFAPKNPATRSHPSILEKLEQQVPDLPVLEEEAFTSRKVEVIE 388
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382      


Chain B from PDB  Type:PROTEIN  Length:386
                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.........hhhhhhhhhhhhhhhhhh...eee..eeeee......hhhhhhh.....eeeeeeee..hhhhhhhhhhhhhhhhhhhh...eeeeeeee.......hhhhhhhhhhhhhhhhh...ee......eeeeeeee..eeeee...ee...........eeeee....hhhhhhhhhhhhh..eeeeeeee.....hhhhhhhhhhhhhhhhhhh....eeeeeeehhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh..eee.......hhhhhhhhhhhhhh.....ee......hhhhhhhhhhhh.hhhhhh...................hhhhhhhhhhhh.hhhhhhhhhhhh.eeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kr7 B   3 ELRVYIVRYSEIGLKGKNRKDFEEALRRNIERVTGMKVKRQWGRFLIPIDENVTLDDKLKKIFGIQNFSKGFLVSHDFEEVKKYSLIAVKEKLEKGNYRTFKVQAKKAYKEYKKGVYEINSELGALILKNFKELSVDVRNPDFVLGVEVRPEGVLIFTDRVECYGGLPVGTGGKAVLLLSGGIDSPVAGWYALKRGVLIESVTFVSPPFTSEGAVEKVRDILRVLREFSGGHPLRLHIVNLTKLQLEVKKRVPDKYSLIMYRRSMFRIAEKIAEETGAVAFYTGENIGQVASQTLENLWSIESVTTRPVIRPLSGFDKTEIVEKAKEIGTYEISIKPYQDSCVFFAPKNPATRSHPSILEKLEQQVPDLPVLEEEAFTSRKVEVIE 388
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382      


Chain M from PDB  Type:RNA  Length:39
                                                                       
                 4kr7 M   1 GCCCGGAUAGUGUCCUUGGGAAACCAAGUCCGGGCACCA  39
                                    10        20        30         


Chain X from PDB  Type:RNA  Length:39
                                                                       
                 4kr7 X   1 GCCCGGAUAGUGUCCUUGGGAAACCAAGUCCGGGCACCA  39
                                    10        20        30
   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 4KR7)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4KR7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4KR7)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        THII_THEMA | Q9X220: 4kr6 4kr9

(-) Related Entries Specified in the PDB File

4kr6 4kr9