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(-) Description

Title :  CRYSTAL STRUCTURE OF A 4-THIOURIDINE SYNTHETASE - RNA COMPLEX
 
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 :  2.85
Chains :  Asym./Biol. Unit :  A,B,C,D
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: C, D
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1HG4Ligand/IonMERCURY (II) ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:166 , GLU A:329BINDING SITE FOR RESIDUE HG A 401
2AC2SOFTWARECYS A:344 , ILE B:89 , LYS B:92BINDING SITE FOR RESIDUE HG A 403
3AC3SOFTWARECYS B:344BINDING SITE FOR RESIDUE HG B 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4KR6)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Pro A:209 -Pro A:210
2Lys A:338 -Pro A:339
3Pro B:209 -Pro B:210

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4KR6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4KR6)

(-) Exons   (0, 0)

(no "Exon" information available for 4KR6)

(-) 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:388
                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeehhhhh....hhhhhhhhhhhhhhhhhh...eee..eeeee......hhhhhh......eeeeeeee..hhhhhhhhhhhhhhhhhh.....eeeeeeee.......hhhhhhhhhhhhhhhhh...ee......eeeeeeee..eeeeeeee.............eeeee....hhhhhhhhhhhhh..eeeeeeee.......hhhhhhhhhhhhhhhhh....eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...ee.......hhhhhhhhhhhhhh.....ee......hhhhhhhhhhhh..........................hhhhhhhhhhhh.hhhhhhhhhhhh.eeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kr6 A   1 MEELRVYIVRYSEIGLKGKNRKDFEEALRRNIERVTGMKVKRQWGRFLIPIDENVTLDDKLKKIFGIQNFSKGFLVSHDFEEVKKYSLIAVKEKLEKGNYRTFKVQAKKAYKEYKKGVYEINSELGALILKNFKELSVDVRNPDFVLGVEVRPEGVLIFTDRVECYGGLPVGTGGKAVLLLSGGIDSPVAGWYALKRGVLIESVTFVSPPFTSEGAVEKVRDILRVLREFSGGHPLRLHIVNLTKLQLEVKKRVPDKYSLIMYRRSMFRIAEKIAEETGAVAFYTGENIGQVASQTLENLWSIESVTTRPVIRPLSGFDKTEIVEKAKEIGTYEISIKPYQDSCVFFAPKNPATRSHPSILEKLEQQVPDLPVLEEEAFTSRKVEVIE 388
                                    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       320       330       340       350       360       370       380        


Chain B from PDB  Type:PROTEIN  Length:388
                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee............hhhhhhhhhhhhhhh...eee..eeeee......hhhhhh......eeeeeeee..hhhhhhhhhhhhhhhhhh.....eeeeeeee.......hhhhhhhhhhhhhhhhh...ee......eeeeeeee..eeeeee..ee...........eeeee....hhhhhhhhhhhhh..eeeeeeee.......hhhhhhhhhhhhhhhhh....eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee.......hhhhhhhhhhhhhh.....ee......hhhhhhhhhhhhh.....hhhhh...............hhhhhhhhhhhh.hhhhhhhhhhhh.eeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kr6 B   1 MEELRVYIVRYSEIGLKGKNRKDFEEALRRNIERVTGMKVKRQWGRFLIPIDENVTLDDKLKKIFGIQNFSKGFLVSHDFEEVKKYSLIAVKEKLEKGNYRTFKVQAKKAYKEYKKGVYEINSELGALILKNFKELSVDVRNPDFVLGVEVRPEGVLIFTDRVECYGGLPVGTGGKAVLLLSGGIDSPVAGWYALKRGVLIESVTFVSPPFTSEGAVEKVRDILRVLREFSGGHPLRLHIVNLTKLQLEVKKRVPDKYSLIMYRRSMFRIAEKIAEETGAVAFYTGENIGQVASQTLENLWSIESVTTRPVIRPLSGFDKTEIVEKAKEIGTYEISIKPYQDSCVFFAPKNPATRSHPSILEKLEQQVPDLPVLEEEAFTSRKVEVIE 388
                                    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       320       330       340       350       360       370       380        


Chain C from PDB  Type:RNA  Length:39
                                                                       
                 4kr6 C   1 GCCCGGAUAGUGUCCUUGGGAAACCAAGUCCGGGCACCA  39
                                    10        20        30         


Chain D from PDB  Type:RNA  Length:39
                                                                       
                 4kr6 D   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 4KR6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4KR6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4KR6)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)

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  2.8.1.4
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 Related Entries

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

UniProtKB/Swiss-Prot
        THII_THEMA | Q9X220: 4kr7 4kr9

(-) Related Entries Specified in the PDB File

4kr7 4kr9