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(-) Description

Title :  CRYSTAL STRUCTURE OF E. COLI GLUTAMINYL-TRNA SYNTHETASE BOUND TO ATP AND NATIVE TRNA(GLN) CONTAINING THE CMNM5S2U34 ANTICODON WOBBLE BASE
 
Authors :  J. J. Perona, A. Rodriguez-Hernandez
Date :  01 Apr 13  (Deposition) - 29 May 13  (Release) - 23 Oct 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Rossmann Fold, Protein-Rna Complex, Aminoacyl-Trna Synthetase, Ligase, Ligase-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Rodriguez-Hernandez, J. L. Spears, K. W. Gaston, P. A. Limbach, H. Gamper, Y. M. Hou, R. Kaiser, P. F. Agris, J. J. Perona
Structural And Mechanistic Basis For Enhanced Translational Efficiency By 2-Thiouridine At The Trna Anticodon Wobble Position.
J. Mol. Biol. V. 425 3888 2013
PubMed-ID: 23727144  |  Reference-DOI: 10.1016/J.JMB.2013.05.018

(-) Compounds

Molecule 1 - GLUTAMINE--TRNA LIGASE
    Chains: A
    EC Number: 6.1.1.18
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: GLNS, B0680, JW0666
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12
    Synonym: GLUTAMINYL-TRNA SYNTHETASE, GLNRS
 
Molecule 2 - RNA (72-MER)
    Chains: B
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (10, 12)

Asymmetric/Biological Unit (10, 12)
No.NameCountTypeFull Name
11RN1Mod. Nucleotide(E)-N-{[4-OXO-1-(5-O-PHOSPHONO-BETA-D-ARABINOFURANOSYL)-2-THIOXO-1,2,3,4-TETRAHYDROPYRIMIDIN-5-YL]METHYLIDENE}GLYCINE
22MA1Mod. Nucleotide2-METHYLADENOSINE-5'-MONOPHOSPHATE
34SU1Mod. Nucleotide4-THIOURIDINE-5'-MONOPHOSPHATE
45MU1Mod. Nucleotide5-METHYLURIDINE 5'-MONOPHOSPHATE
5ATP1Ligand/IonADENOSINE-5'-TRIPHOSPHATE
6H2U1Mod. Nucleotide5,6-DIHYDROURIDINE-5'-MONOPHOSPHATE
7OMG1Mod. NucleotideO2'-METHYLGUANOSINE-5'-MONOPHOSPHATE
8OMU1Mod. NucleotideO2'-METHYLURIDINE 5'-MONOPHOSPHATE
9PSU2Mod. NucleotidePSEUDOURIDINE-5'-MONOPHOSPHATE
10SO42Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:32 , GLU A:34 , HIS A:40 , GLY A:42 , HIS A:43 , SER A:46 , THR A:230 , ARG A:260 , LEU A:261 , MET A:268 , LYS A:270 , HOH A:705 , A B:976BINDING SITE FOR RESIDUE ATP A 601
2AC2SOFTWAREVAL A:267 , MET A:268 , SER A:269 , LYS A:272 , GLY A:482 , HOH A:771BINDING SITE FOR RESIDUE SO4 A 602
3AC3SOFTWAREMET A:290 , LEU A:296 , MET A:324BINDING SITE FOR RESIDUE SO4 A 603

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4JYZ)

(-) 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:542
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains d4jyza1 A:7-338 Glutaminyl-tRNA synthetase (GlnRS)                                                                                                                                                                                                                                                                                          d4jyza2 A:339-548 Gln-tRNA synthetase (GlnRS), C-terminal (anticodon-binding) domain                                                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh......eeee........hhhhhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhhhhhhh........ee...hhhhhhhhhhhhhhh..eeee..hhhhhhhhhh..............hhhhhhhhhhhhhhh.......eeee.......hhhhh..eeeee.............eeehhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhh......eeeee..........hhhhhhhhhhh............hhhhhhhhh.hhhhhhhhhhhhh........hhhhhhhhhhhhhhh...ee.ee..eee..........eeeeee....hhhh.eeeeee....eee...ee.........ee.....ee.....eeeeeeee.....eeeeeeee.................ee........eeeeeeee.......hhhhh.hhhhhh....eeeeeeee.hhhhhh.....eee...eeeee..........eeeeeee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jyz A   7 PTNFIRQIIDEDLASGKHTTVHTRFPPEPNGYLHIGHAKSICLNFGIAQDYKGQCNLRFDDTNPVKEDIEYVESIKNDVEWLGFHWSGNVRYSSDYFDQLHAYAIELINKGLAYVDELTPEQIREYRGTLTQPGKNSPYRDRSVEENLALFEKMRAGGFEEGKACLRAKIDMASPFIVMRDPVLYRIKFAEHHQTGNKWCIYPMYDFTHCISDALEGITHSLCTLEFQDNRRLYDWVLDNITIPVHPRQYEFSRLNLEYTVMSKRKLNLLVTDKHVEGWDDPRMPTISGLRRRGYTAASIREFCKRIGVTKQDNTIEMASLESCIREDLNENAPRAMAVIDPVKLVIENYQGEGEMVTMPNHPNKPEMGSRQVPFSGEIWIDRADFREEANKQYKRLVLGKEVRLRNAYVIKAERVEKDAEGNITTIFCTYDADTLSKDPADGRKVKGVIHWVSAAHALPVEIRLYDRLFSVPNPGAADDFLSVINPESLVIKQGFAEPSLKDAVAGKAFQFEREGYFCLDSRHSTAEKPVFNRTVGLRDTW 548
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546  


Chain B from PDB  Type:RNA  Length:72
                                                                                                        
                 4jyz B 902 GGGGUAuCGCCAAGCgGuAAGGCACCGGUuUuUGauACCGGCACGCAGGuuCGAAUCCUGCUACCCCAGCCA 976
                                  |911    || 922       932 |  || 942  ||   954|      964       974  
                                908-4SU 916| |         932-OMU||    945|     ||                     
                                         918-OMG         934-1RN     948     ||                     
                                           920-H2U          937-2MA        954-5MU                  
                                                             938-PSU        955-PSU
   Legend:   → Mismatch (orange background)
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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  (2, 2)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)

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  6.1.1.18
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 Related Entries

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

UniProtKB/Swiss-Prot
        SYQ_ECOLI | P00962: 1euq 1euy 1exd 1gsg 1gtr 1gts 1nyl 1o0b 1o0c 1qrs 1qrt 1qru 1qtq 1zjw 2rd2 2re8 4jxx 4jxz

(-) Related Entries Specified in the PDB File

4jxx
4jxz THE SAME STRUCTURE WITH AN UNMODIFIED TRNA(GLN) TRANSCRIPT CONTAINING THE UUG ANTICODON