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(-) Description

Title :  CRYSTAL STRUCTURE OF E COLI E. COLI GLUTAMINYL-TRNA SYNTHETASE BOUND TO TRNA(GLN)(CUG) AND ATP FROM NOVEL CRYOSTABILIZATION CONDITIONS
 
Authors :  J. J. Perona, A. Rodriguez-Hernandez
Date :  28 Mar 13  (Deposition) - 01 May 13  (Release) - 23 Oct 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Rossmann Fold, Protein-Rna Complex, Transfer Rna, Trna Aminoacylation, Trna(Gln), 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 (71-MER)
    Chains: B
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1ATP1Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2SO41Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:31 , PRO A:33 , 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:704 , HOH A:800 , HOH A:814 , HOH A:832 , HOH A:877 , A B:976BINDING SITE FOR RESIDUE ATP A 601
2AC2SOFTWAREVAL A:267 , MET A:268 , SER A:269BINDING SITE FOR RESIDUE SO4 A 602

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4JXX)

(-) 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:536
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains d4jxxa1 A:7-338 Glutaminyl-tRNA synthetase (GlnRS)                                                                                                                                                                                                                                                                                          d4jxxa2 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.............eeehhhhhhhhhhhhh...eeeee.hhhhhhhhhhhhhhhh......eeeee..........hhhhhhhhhhh............hhhhhhhhh.hhhhhhhhhhhhh........hhhhhhhhhhhhhhhhh.ee.ee..eeeeee........eeeee....hhhh.eeeee...eeeee...ee.........ee...eeee....eeeeeeeee.....eeeeeeee...........ee..ee....eeeeeeee.......hhhhh.hhhhhh....eeeeeeee.hhhh......eeee...eeeee..........eeeeeee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jxx A   7 PTNFIRQIIDEDLASGKHTTVHTRFPPEPNGYLHIGHAKSICLNFGIAQDYKGQCNLRFDDTNPVKEDIEYVESIKNDVEWLGFHWSGNVRYSSDYFDQLHAYAIELINKGLAYVDELTPEQIREYRGTLTQPGKNSPYRDRSVEENLALFEKMRAGGFEEGKACLRAKIDMASPFIVMRDPVLYRIKFAEHHQTGNKWCIYPMYDFTHCISDALEGITHSLCTLEFQDNRRLYDWVLDNITIPVHPRQYEFSRLNLEYTVMSKRKLNLLVTDKHVEGWDDPRMPTISGLRRRGYTAASIREFCKRIGVTKQDNTIEMASLESCIREDLNENAPRAMAVIDPVKLVIENYQGEGEMVTMPNHPNKPEMGSRQVPFSGEIWIDRADFREEANKQYKRLVLGKEVRLRNAYVIKAERVEKDAEGNITTIFCTYDADTLSRKVKGVIHWVSAAHALPVEIRLYDRLFSVPNPGAADDFLSVINPESLVIKQGFAEPSLKDAVAGKAFQFEREGYFCLDSRHSTAEKPVFNRTVGLRDTW 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      |452       462       472       482       492       502       512       522       532       542      
                                                                                                                                                                                                                                                                                                                                                                                                                                                                              443|                                                                                                  
                                                                                                                                                                                                                                                                                                                                                                                                                                                                               450                                                                                                  


Chain B from PDB  Type:RNA  Length:71
                                                                                                       
                 4jxx B 902 GGGGUAUCGCCAAGCGGUAAGGCACCGGAUUCUGAUUCCGGCCCGAGGUUCGAAUCCUCGUACCCCAGCCA 976
                                   911    || 922       932       942 ||    955       965       975 
                                        916|                       944|                            
                                         918                        948
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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 4JXX)

(-) Pfam Domains  (0, 0)

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

(-) 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 4jxz 4jyz

(-) Related Entries Specified in the PDB File

1gtr THE SAME COMPLEX DETERMINED USING TRNA OVERPRODUCED IN VIVO AND COOLED TO 8 DEGREES C
4jxz
4jyz