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(-) Description

Title :  THE STRUCTURE OF GLUTAMINYL-TRNA SYNTHETASE FROM SACCHAROMYCES CEREVISIAE
 
Authors :  E. H. Snell, T. D. Grant
Date :  14 Sep 12  (Deposition) - 24 Apr 13  (Release) - 26 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym./Biol. Unit :  A
Keywords :  Rossmann Fold, Ligase, Appended Domain, Trna Synthetase, Beta Barrel Anticodon Binding Domain, Pseudo Zinc Finger Motif (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. D. Grant, J. R. Luft, J. R. Wolfley, M. E. Snell, H. Tsuruta, S. Corretore, E. Quartley, E. M. Phizicky, E. J. Grayhack, E. H. Snell
The Structure Of Yeast Glutaminyl-Trna Synthetase And Modeling Of Its Interaction With Trna.
J. Mol. Biol. V. 425 2480 2013
PubMed-ID: 23583912  |  Reference-DOI: 10.1016/J.JMB.2013.03.043

(-) Compounds

Molecule 1 - GLUTAMINE-TRNA LIGASE
    Chains: A
    EC Number: 6.1.1.18
    Engineered: YES
    Gene: GLN4, O3601, YOR168W
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 559292
    Strain: BCY123
    Synonym: GLUTAMINYL-TRNA SYNTHETASE, GLNRS

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 16)

Asymmetric/Biological Unit (6, 16)
No.NameCountTypeFull Name
1ACT4Ligand/IonACETATE ION
2BR1Ligand/IonBROMIDE ION
3CL1Ligand/IonCHLORIDE ION
4DTT1Ligand/Ion2,3-DIHYDROXY-1,4-DITHIOBUTANE
5GOL8Ligand/IonGLYCEROL
6ZN1Ligand/IonZINC ION

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:346 , CYS A:348 , CYS A:372 , HIS A:374BINDING SITE FOR RESIDUE ZN A 901
02AC2SOFTWAREPHE A:256 , HIS A:268 , ALA A:271 , GOL A:903 , BR A:910 , HOH A:1024 , HOH A:1078 , HOH A:1150BINDING SITE FOR RESIDUE GOL A 902
03AC3SOFTWAREHIS A:265 , GLY A:267 , HIS A:268 , ARG A:488 , LEU A:489 , GOL A:902BINDING SITE FOR RESIDUE GOL A 903
04AC4SOFTWARELEU A:574 , VAL A:781 , ARG A:799 , HOH A:1289BINDING SITE FOR RESIDUE GOL A 904
05AC5SOFTWARESER A:324 , ASP A:325 , PHE A:327 , ASP A:328 , GLU A:329 , THR A:430 , LYS A:433 , TRP A:434 , GOL A:909 , HOH A:1181BINDING SITE FOR RESIDUE GOL A 905
06AC6SOFTWAREHIS A:444 , PHE A:462 , SER A:465 , GLN A:483 , HOH A:1335 , HOH A:1408BINDING SITE FOR RESIDUE GOL A 906
07AC7SOFTWAREASP A:292 , ASN A:294 , PRO A:295 , GLU A:296 , PHE A:303 , HIS A:427 , PRO A:428 , ARG A:429 , HOH A:1325 , HOH A:1435BINDING SITE FOR RESIDUE GOL A 907
08AC8SOFTWARESER A:378 , GLU A:380 , ASN A:583 , SER A:585 , HOH A:1029 , HOH A:1053 , HOH A:1162BINDING SITE FOR RESIDUE GOL A 908
09AC9SOFTWAREARG A:387 , ARG A:390 , THR A:430 , LYS A:433 , GOL A:905 , HOH A:1181 , HOH A:1251BINDING SITE FOR RESIDUE GOL A 909
10BC1SOFTWARECYS A:458 , THR A:459 , GOL A:902BINDING SITE FOR RESIDUE BR A 910
11BC2SOFTWAREPRO A:728 , SER A:730 , GLU A:731BINDING SITE FOR RESIDUE CL A 911
12BC3SOFTWARELYS A:771 , SER A:790 , THR A:791BINDING SITE FOR RESIDUE ACT A 912
13BC4SOFTWAREHIS A:228 , LYS A:229 , TYR A:278 , HIS A:282 , HIS A:455 , HOH A:1391BINDING SITE FOR RESIDUE ACT A 913
14BC5SOFTWARETYR A:263 , LEU A:496 , LYS A:498 , THR A:520 , HOH A:1115BINDING SITE FOR RESIDUE ACT A 914
15BC6SOFTWARELYS A:643 , TYR A:684 , HOH A:1441BINDING SITE FOR RESIDUE ACT A 915
16BC7SOFTWAREARG A:390 , ASP A:391 , LYS A:433 , TRP A:434 , ARG A:435 , HOH A:1021 , HOH A:1390BINDING SITE FOR RESIDUE DTT A 916

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4H3S)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ser A:696 -Pro A:697
2Ser A:750 -Pro A:751

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4H3S)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4H3S)

(-) Exons   (0, 0)

(no "Exon" information available for 4H3S)

(-) 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:585
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhh..........hhhhhhhhhhhhh...eeee.........hhhhhhhhhhhhhhhhh..eeeeee........hhhhhhhhhhhhhhh.....eeee...hhhhhhhhhhhhhhh..eeee..hhhhhhhhh...........hhhhhhhhhhhhhhhhhhhh........eeee.......hhhhh..eeeee.............eeehhhhhhhhhhhhh....eeee.hhhhhhhhhhhhhhhh......eeee..eeee....hhhhhhhhhhh............hhhhhhhhh.hhhhhhhhhhhhh.....eeeehhhhhhhhhhhhhhhh.ee.ee..eeeeee........eeeeee....hhhh.eeeeee..eeeee.hhh..................ee......eeeeeeee.....eeeeeeee........ee..ee.hhhhh..eeeeeeeee.......hhhhh..hhhhhh....eeeeeeeee..hhhhhhhh....hhhhhh..........hhhhh.eee...eeeee.........eeeeee........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4h3s A 215 KRTMFNEGFLGDLHKVGENPQAYPELMKEHLEVTGGKVRTRFPPEPNGYLHIGHSKAIMVNFGYAKYHNGTCYLRFDDTNPEKEAPEYFESIKRMVSWLGFKPWKITYSSDYFDELYRLAEVLIKNGKAYVCHCTAEEIKRGRGIGTPGGERYACKHRDQSIEQNLQEFRDMRDGKYKPGEAILRMKQDLNSPSPQMWDLIAYRVLNAPHPRTGTKWRIYPTYDFTHCLVDSMENITHSLCTTEFYLSRESYEWLCDQVHVFRPAQREYGRLNITGTVLSKRKIAQLVDEKFVRGWDDPRLFTLEAIRRRGVPPGAILSFINTLGVTTSTTNIQVVRFESAVRKYLEDTTPRLMFVLDPVEVVVDNLSDDYEELATIPYRPGTPEFGERTVPFTNKFYIERSDFSENVDDKEFFRLTPNQPVGLIKVSHTVSFKSLEKDEAGKIIRIHVNYDNKKKPKTYIQWVPISSKYNSPLRVTETRVYNQLFKSENPSSHPEGFLKDINPESEVVYKESVMEHNFGDVVKNSPWVVDSVKNSEFYVEEDKDSKEVCRFQAMRVGYFTLDKESTTSKVILNRIVSLKDATSK 809
                                   224       234       244       254       264       274       284       294       304       314       324       334       344       354    || 367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597       607       617       627       637       647       657       667   ||  684       694       704       714       724       734       744       754       764       774       784       794       804     
                                                                                                                                                                          359|                                                                                                                                                                                                                                                                                                                 671|                                                                                                                                  
                                                                                                                                                                           363                                                                                                                                                                                                                                                                                                                  679
   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  (0, 0)

(no "SCOP Domain" information available for 4H3S)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4H3S)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4H3S)

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)

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        SYQ_YEAST | P13188: 3tl4

(-) Related Entries Specified in the PDB File

3tl4 THE N-TERMINAL ARM OF THE COMPLETE PROTEIN