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(-) Description

Title :  CRYSTAL STRUCTURE OF THE ARGINYL-TRNA SYNTHETASE COMPLEXED WITH THE TRNA(ARG) AND L-ARG
 
Authors :  B. Delagoutte, D. Moras, J. Cavarelli
Date :  28 Jun 00  (Deposition) - 27 Jun 01  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Rna-Protein Complex, Aminoacylation, Arginyl-Trna Synthetase, Ligase, Ligase-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Delagoutte, D. Moras, J. Cavarelli
Trna Aminoacylation By Arginyl-Trna Synthetase: Induced Conformations During Substrates Binding
Embo J. V. 19 5599 2000
PubMed-ID: 11060012  |  Reference-DOI: 10.1093/EMBOJ/19.21.5599
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TRNA(ARG)
    Chains: B
    Engineered: YES
    Other Details: THIS SEQUENCE OCCURS NATURALLY IN YEAST SACCHAROMYCES CEREVISAE
    Synthetic: YES
 
Molecule 2 - ARGINYL-TRNA SYNTHETASE
    Chains: A
    EC Number: 6.1.1.19
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PTRC99
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: CYTOPLASMIC ARGININE-TRNA LIGASE, ARGRS

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (10, 14)

Asymmetric/Biological Unit (10, 14)
No.NameCountTypeFull Name
11MA1Mod. Nucleotide6-HYDRO-1-METHYLADENOSINE-5'-MONOPHOSPHATE
21MG1Mod. Nucleotide1N-METHYLGUANOSINE-5'-MONOPHOSPHATE
32MG1Mod. Nucleotide2N-METHYLGUANOSINE-5'-MONOPHOSPHATE
45MC1Mod. Nucleotide5-METHYLCYTIDINE-5'-MONOPHOSPHATE
55MU1Mod. Nucleotide5-METHYLURIDINE 5'-MONOPHOSPHATE
6ARG1Mod. Amino AcidARGININE
7H2U3Mod. Nucleotide5,6-DIHYDROURIDINE-5'-MONOPHOSPHATE
8M2G1Mod. NucleotideN2-DIMETHYLGUANOSINE-5'-MONOPHOSPHATE
9PSU3Mod. NucleotidePSEUDOURIDINE-5'-MONOPHOSPHATE
10SO41Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREG B:907 , 5MC B:949 , HOH B:1314 , HOH B:1364BINDING SITE FOR RESIDUE SO4 B 900
2AC2SOFTWAREGLU A:148 , SER A:151 , ASN A:153 , TYR A:188 , TYR A:347 , ASP A:351 , TYR A:369 , ILE A:371 , GLN A:375 , HOH A:1321 , HOH A:1578 , A B:976BINDING SITE FOR RESIDUE ARG A 800

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1F7U)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1F7U)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1F7U)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AA_TRNA_LIGASE_IPS00178 Aminoacyl-transfer RNA synthetases class-I signature.SYRC_YEAST152-163  1A:152-163

(-) Exons   (1, 1)

Asymmetric/Biological Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YDR341C1YDR341C.1IV:1153621-11517981824SYRC_YEAST1-6076071A:2-607606

(-) 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:607
 aligned with SYRC_YEAST | Q05506 from UniProtKB/Swiss-Prot  Length:607

    Alignment length:607
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       607 
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601     | 
           SYRC_YEAST     2 ASTANMISQLKKLSIAEPAVAKDSHPDVNIVDLMRNYISQELSKISGVDSSLIFPALEWTNTMERGDLLIPIPRLRIKGANPKDLAVQWAEKFPCGDFLEKVEANGPFIQFFFNPQFLAKLVIPDILTRKEDYGSCKLVENKKVIIEFSSPNIAKPFHAGHLRSTIIGGFLANLYEKLGWEVIRMNYLGDWGKQFGLLAVGFERYGNEEALVKDPIHHLFDVYVRINKDIEEEGDSIPLEQSTNGKAREYFKRMEDGDEEALKIWKRFREFSIEKYIDTYARLNIKYDVYSGESQVSKESMLKAIDLFKEKGLTHEDKGAVLIDLTKFNKKLGKAIVQKSDGTTLYLTRDVGAAMDRYEKYHFDKMIYVIASQQDLHAAQFFEILKQMGFEWAKDLQHVNFGMVQGMSTRKGTVVFLDNILEETKEKMHEVMKKNENKYAQIEHPEEVADLVGISAVMIQDMQGKRINNYEFKWERMLSFEGDTGPYLQYAHSRLRSVERNASGITQEKWINADFSLLKEPAAKLLIRLLGQYPDVLRNAIKTHEPTTVVTYLFKLTHQVSSCYDVLWVAGQTEELATARLALYGAARQVLYNGMRLLGLTPVERM-   -
               SCOP domains d1f7ua3 A:2-135 Arginyl-tRNA synthetase (ArgRS), N-terminal 'additional' domain                                                       d1f7ua2 A:136-483 Arginyl-tRNA synthetase (ArgRS)                                                                                                                                                                                                                                                                                                           d1f7ua1 A:484-607 Arginyl-tRNA synthetase (ArgRS)                                                                           - SCOP domains
               CATH domains 1f7uA03 A:2-135  [code=3.30.1360.70, no name defined]                                                                                 1f7uA01 A:136-482 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                                                                                                                                                                                                    1f7uA02 A:483-607 Isoleucyl-tRNA Synthetase; Domain 1                                                                        - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh...hhhhhh......hhhhhhhhhhhhhhhhhhh.hhhhhhhhhee..hhhhh.eeee.hhhh....hhhhhhhhhhhh......eeeeeee..eeeeeehhhhhhhhhhhhhhhhhhhh.........eeeee.............hhhhhhhhhhhhhhhhhh..eeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeee.hhhhhhhhhhhhhhhhhh..eeee..eeeee.hhh.....eeeee......hhhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhhhhh.hhhhh.eeee....ee..........hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh......ee.hhhhhhh....hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------AA_TRNA_LIGA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:2-607 UniProt: 1-607 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            - Transcript 1
                 1f7u A   2 ASTANMISQLKKLSIAEPAVAKDSHPDVNIVDLMRNYISQELSKISGVDSSLIFPALEWTNTMERGDLLIPIPRLRIKGANPKDLAVQWAEKFPCGDFLEKVEANGPFIQFFFNPQFLAKLVIPDILTRKEDYGSCKLVENKKVIIEFSSPNIAKPFHAGHLRSTIIGGFLANLYEKLGWEVIRMNYLGDWGKQFGLLAVGFERYGNEEALVKDPIHHLFDVYVRINKDIEEEGDSIPLEQSTNGKAREYFKRMEDGDEEALKIWKRFREFSIEKYIDTYARLNIKYDVYSGESQVSKESMLKAIDLFKEKGLTHEDKGAVLIDLTKFNKKLGKAIVQKSDGTTLYLTRDVGAAMDRYEKYHFDKMIYVIASQQDLHAAQFFEILKQMGFEWAKDLQHVNFGMVQGMSTRKGTVVFLDNILEETKEKMHEVMKKNENKYAQIEHPEEVADLVGISAVMIQDMQGKRINNYEFKWERMLSFEGDTGPYLQYAHSRLRSVERNASGITQEKWINADFSLLKEPAAKLLIRLLGQYPDVLRNAIKTHEPTTVVTYLFKLTHQVSSCYDVLWVAGQTEELATARLALYGAARQVLYNGMRLLGLTPVERMR 800
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601     ||
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       607|
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        800


Chain B from PDB  Type:RNA  Length:75
                                                                                                           
                 1f7u B 901 uUCCUCGUggCCCAAuGGuCACGGCguCUGGCUCGAACCAGAAGAuUcCAGGuuCAaGUCCUGGCGGGGAAGCCA 976
                            |      910     | 920     ||930  ||   941     | 951  ||  |961       971     
                            |     909-1MG  |  |      ||   933|         947-H2U  ||  |                  
                          901-PSU  910-2MG |  |      ||    935           949-5MC||  |                  
                                         916-H2U     ||                       954-5MU                  
                                            919-H2U  ||                        955-PSU                 
                                                   926-M2G                        958-1MA              
                                                    927-PSU
   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  (3, 3)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (3, 3)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1F7U)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (SYRC_YEAST | Q05506)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0004812    aminoacyl-tRNA ligase activity    Catalysis of the formation of aminoacyl-tRNA from ATP, amino acid, and tRNA with the release of diphosphate and AMP.
    GO:0004814    arginine-tRNA ligase activity    Catalysis of the reaction: ATP + L-arginine + tRNA(Arg) = AMP + diphosphate + L-arginyl-tRNA(Arg).
    GO:0016874    ligase activity    Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
biological process
    GO:0006420    arginyl-tRNA aminoacylation    The process of coupling arginine to arginyl-tRNA, catalyzed by arginyl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'-adenosine residue of the tRNA.
    GO:0032543    mitochondrial translation    The chemical reactions and pathways resulting in the formation of a protein in a mitochondrion. This is a ribosome-mediated process in which the information in messenger RNA (mRNA) is used to specify the sequence of amino acids in the protein; the mitochondrion has its own ribosomes and transfer RNAs, and uses a genetic code that differs from the nuclear code.
    GO:0006418    tRNA aminoacylation for protein translation    The synthesis of aminoacyl tRNA by the formation of an ester bond between the 3'-hydroxyl group of the most 3' adenosine of the tRNA, to be used in ribosome-mediated polypeptide synthesis.
    GO:0006412    translation    The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

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  1f7u
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  SYRC_YEAST | Q05506
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  6.1.1.19
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 Related Entries

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

UniProtKB/Swiss-Prot
        SYRC_YEAST | Q05506: 1bs2 1f7v

(-) Related Entries Specified in the PDB File

1bs2 ARGINYL-TRNA SYNTHETASE WITHOUT TRNA
1f7v ARGINYL-TRNA SYNTHETASE COMPLEXED WITH TRNA(ARG) AT 2.9 A