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(-) Description

Title :  CRYSTAL STRUCTURE OF ARGINYL-TRNA SYNTHETASE COMPLEXED WITH L-ARGININE
 
Authors :  H. S. Kim, C. H. Jo, S. Y. Cha, A. R. Han, K. Y. Hwang
Date :  09 Apr 14  (Deposition) - 23 Jul 14  (Release) - 23 Jul 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  High Region, Arginine-Trna Ligase Activity, Arginine Binding, Trna Binding, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. S. Kim, S. Y. Cha, C. H. Jo, A. R. Han, K. Y. Hwang
The Crystal Structure Of Arginyl-Trna Synthetase From Homo Sapiens
Febs Lett. V. 588 2328 2014
PubMed-ID: 24859084  |  Reference-DOI: 10.1016/J.FEBSLET.2014.05.027

(-) Compounds

Molecule 1 - ARGININE--TRNA LIGASE, CYTOPLASMIC
    Chains: A, B
    EC Number: 6.1.1.19
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: ROSETTA
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: RARS
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ARGINYL-TRNA SYNTHETASE, ARGRS

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1ARG2Mod. Amino AcidARGININE
2GOL2Ligand/IonGLYCEROL
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1ARG1Mod. Amino AcidARGININE
2GOL1Ligand/IonGLYCEROL
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1ARG1Mod. Amino AcidARGININE
2GOL1Ligand/IonGLYCEROL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:125 , SER A:128 , ASN A:130 , HIS A:139 , HIS A:165 , TYR A:312 , ASP A:316 , TYR A:334 , GLN A:340 , PHE A:344 , GOL A:602 , HOH A:703BINDING SITE FOR RESIDUE ARG A 601
2AC2SOFTWARESER A:127 , HIS A:136 , SER A:142 , VAL A:336 , ASP A:337 , PHE A:369 , ARG A:601BINDING SITE FOR RESIDUE GOL A 602
3AC3SOFTWAREASP B:125 , SER B:128 , ASN B:130 , HIS B:139 , HIS B:165 , TYR B:312 , ASP B:316 , TYR B:334 , VAL B:336 , GLN B:340 , PHE B:344 , GOL B:602 , HOH B:705BINDING SITE FOR RESIDUE ARG B 601
4AC4SOFTWARESER B:127 , HIS B:136 , SER B:142 , VAL B:336 , ASP B:337 , ARG B:601BINDING SITE FOR RESIDUE GOL B 602

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4Q2T)

(-) Cis Peptide Bonds  (5, 5)

Asymmetric Unit
No.Residues
1Arg A:383 -Ser A:384
2Ser A:384 -Gly A:385
3Glu A:407 -Lys A:408
4Gln A:551 -Thr A:552
5Glu B:407 -Lys B:408

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4Q2T)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4Q2T)

(-) Exons   (0, 0)

(no "Exon" information available for 4Q2T)

(-) Sequences/Alignments

Asymmetric 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:591
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhh.........eee..hhhhh.eeehhhhhhhhhhh......hhhhhhhhhhh.......eeeeeee...eeeeeehhhhhhhhhhhhhhh...........eeeee..........hhhhhhhhhhhhhhhhhhhhh..eeeeee........hhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh....ee.hhhhhhhhhhhhhhhhhhh...eee..eeee........eeee......hhhhhhhhhhhhhhhh....eeeeeee..hhhhhhhhhhhhhhh........eeeeeee..ee...............hhhhhhhhhhhhhhhhhh.hhhhh.......hhhhhhhhhhhhhhhhhh......ee.hhhhhhh....hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4q2t A  -1 ASMINIISRLQEVFGHAIKAAYPDLENPPLLVTPSQQAKFGDYQCNSAMGISQMLKTKEQKVNPREIAENITKHLPDNECIEKVEIAGPGFINVHLRKDFVSEQLTSLLVNGVQLPALGENKKVIVDFSSPNIAKEMHVGHLRSTIIGESISRLFEFAGYDVLRLNHVGDWGTQFGMLIAHLQDKFPDYLTVSPPIGDLQVFYKESKKRFDTEEEFKKRAYQCVVLLQGKNPDITKAWKLICDVSRQELNKIYDALDVSLIERGESFYQDRMNDIVKEFEDRGFVQVDDGRKIVFVPGCSIPLTIVKSDGGYTYDTSDLAAIKQRLFEEKADMIIYVVDNGQSVHFQTIFAAAQMIGWYDPKVTRVFHAGFGVVLGEDKKKFKTRSGETVRLMDLLGEGLKRSMDKLKEKERDKVLTAEELNAAQTSVAYGCIKYADLSRNRLNDYIFSFDKMLDDRGNTAAYLLYAFTRIRSIARLANIDEEMLQKAARETKILLDHEKEWKLGRCILRFPEILQKILDDLFLHTLCDYIYELATAFTEFYDSCYCVEKDRQTGKILKVNMWRMLLCEAVAAVMAKGFDILGIKPVQRMR 601
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588|
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       588|
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        601


Chain B from PDB  Type:PROTEIN  Length:589
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhh.........eee..hhhhh.eeehhhhhhhhhhh......hhhhhhhhhhh.......eeeeeee...eeeeeehhhhhhhhhhhhhhhh..........eeeee..........hhhhhhhhhhhhhhhhhhhhh..eeeeee......hhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh....ee.hhhhhhhhhhhhhhhhhhh...eee..eeee........eeee......hhhhhhhhhhhhhhhh....eeeee.hhhhhhhhhhhhhhhhhh........eeeee....ee.............hhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh......ee.hhhhhhh....hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh....ee.........eehhhhhhhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4q2t B  -1 ASMINIISRLQEVFGHAIKAAYPDLENPPLLVTPSQQAKFGDYQCNSAMGISQMLKTKEQKVNPREIAENITKHLPDNECIEKVEIAGPGFINVHLRKDFVSEQLTSLLVNGVQLPALGENKKVIVDFSSPNIAKEMHVGHLRSTIIGESISRLFEFAGYDVLRLNHVGDWGTQFGMLIAHLQDKFPDYLTVSPPIGDLQVFYKESKKRFDTEEEFKKRAYQCVVLLQGKNPDITKAWKLICDVSRQELNKIYDALDVSLIERGESFYQDRMNDIVKEFEDRGFVQVDDGRKIVFVPGCSIPLTIVKSDGGYTYDTSDLAAIKQRLFEEKADMIIYVVDNGQSVHFQTIFAAAQMIGWYDPKVTRVFHAGFGVVLGEDKKKFKTRETVRLMDLLGEGLKRSMDKLKEKERDKVLTAEELNAAQTSVAYGCIKYADLSRNRLNDYIFSFDKMLDDRGNTAAYLLYAFTRIRSIARLANIDEEMLQKAARETKILLDHEKEWKLGRCILRFPEILQKILDDLFLHTLCDYIYELATAFTEFYDSCYCVEKDRQTGKILKVNMWRMLLCEAVAAVMAKGFDILGIKPVQRMR 601
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378    || 390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       ||
                                                                                                                                                                                                                                                                                                                                                                                                                          383|                                                                                                                                                                                                       588|
                                                                                                                                                                                                                                                                                                                                                                                                                           386                                                                                                                                                                                                        601
   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 4Q2T)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4Q2T)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4Q2T)

(-) Gene Ontology  (18, 18)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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        SYRC_HUMAN | P54136: 4q2x 4q2y 4r3z 4zaj

(-) Related Entries Specified in the PDB File

4q2x 4q2y