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(-) Description

Title :  ISOLEUCYL-TRNA SYNTHETASE EDITING DOMAIN COMPLEXED WITH L-VALINE
 
Authors :  R. Fukunaga, S. Fukai, R. Ishitani, O. Nureki, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  08 May 03  (Deposition) - 23 Mar 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Aminoacyl-Trna Synthetase, Cp1, Editing, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Fukunaga, S. Fukai, R. Ishitani, O. Nureki, S. Yokoyama
Crystal Structures Of The Cp1 Domain From Thermus Thermophilus Isoleucyl-Trna Synthetase And Its Complex With L-Valine.
J. Biol. Chem. V. 279 8396 2004
PubMed-ID: 14672940  |  Reference-DOI: 10.1074/JBC.M312830200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ISOLEUCYL-TRNA SYNTHETASE
    Chains: A, B
    EC Number: 6.1.1.5
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET26B
    Expression System Strain: JM109(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: CP1 DOMAIN
    Gene: ILES
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 274

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1VAL1Mod. Amino AcidVALINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:23 , HOH A:36 , HOH A:66 , HOH A:96 , THR A:233 , VAL A:318 , HIS A:319 , ALA A:321 , ASP A:328BINDING SITE FOR RESIDUE VAL A 400

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1UE0)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Asp A:202 -Pro A:203
2Glu A:352 -Pro A:353
3Glu B:352 -Pro B:353

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1UE0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1UE0)

(-) Exons   (0, 0)

(no "Exon" information available for 1UE0)

(-) 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:182
 aligned with SYI_THET8 | P56690 from UniProtKB/Swiss-Prot  Length:1043

    Alignment length:200
                                   210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400
            SYI_THET8   201 QDPSVYVRFPLKEPKKLGLEKASLLIWTTTPWTLPGNVAAAVHPEYTYAAFQVGDEALILEEGLGRKLLGEGTPVLKTFPGKALEGLPYTPPYPQALEKGYFVVLADYVSQEDGTGIVHQAPAFGAEDLETARVYGLPLLKTVDEEGKLLVEPFKGLYFREANRAILRDLRGRGLLFKEESYLHSYPHCWRCSTPLMYYA 400
               SCOP domains d1ue0a_ A: Isoleucyl-tRNA synthetase (IleRS)                                                                                                                                                             SCOP domains
               CATH domains 1ue0A00 A:201-381 Isoleucyl-tRNA Synthetase; Domain 2                                                                                                                                ------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee...........eeeeeee.hhhhhhhh.eeee....eeeeeee..eeeeeehhhhhhhhh......eeee.hhhh................eeee...........eeeehhhhhhhhhhhhhhhh.....................hhhhhhhhhhhhhhhh..eeeee.------------------. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ue0 A 201 QDPSVYVRFPLKEPKKLGLEKASLLIWTTTPWTLPGNVAAAVHPEYTYAAFQVGDEALILEEGLGRKLLGEGTQVLKTFPGKALEGLPYTPPYPQALEKGYFVVLADYVSQEDGTGIVHQAPAFGAEDLETARVYGLPLLKTVDEEGKLLVEPFKGLYFREANRAILRDLRGRGFLFKEES------------------V 400
                                   210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380|        -       400
                                                                                                                                                                                                              381                400


Chain B from PDB  Type:PROTEIN  Length:180
 aligned with SYI_THET8 | P56690 from UniProtKB/Swiss-Prot  Length:1043

    Alignment length:180
                                   211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381
            SYI_THET8   202 DPSVYVRFPLKEPKKLGLEKASLLIWTTTPWTLPGNVAAAVHPEYTYAAFQVGDEALILEEGLGRKLLGEGTPVLKTFPGKALEGLPYTPPYPQALEKGYFVVLADYVSQEDGTGIVHQAPAFGAEDLETARVYGLPLLKTVDEEGKLLVEPFKGLYFREANRAILRDLRGRGLLFKEES 381
               SCOP domains d1ue0b_ B: Isoleucyl-tRNA synthetase (IleRS)                                                                                                                                         SCOP domains
               CATH domains 1ue0B00 B:202-381 Isoleucyl-tRNA Synthetase; Domain 2                                                                                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeee..hhhhhh...eeeeeee.hhhhhhhh.eeee....eeeeeee..eeeeee.hhhhhhhh......eeeehhhhh.................eee...........eeee....hhhhhhhhhhhh.....................hhhhhhhhhhhhhhhh..eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1ue0 B 202 DPSVYVRFPLKEPKKLGLEKASLLIWTTTPWTLPGNVAAAVHPEYTYAAFQVGDEALILEEGLGRKLLGEGTQVLKTFPGKALEGLPYTPPYPQALEKGYFVVLADYVSQEDGTGIVHQAPAFGAEDLETARVYGLPLLKTVDEEGKLLVEPFKGLYFREANRAILRDLRGRGFLFKEES 381
                                   211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381
   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  (1, 2)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1UE0)

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (SYI_THET8 | P56690)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0002161    aminoacyl-tRNA editing activity    The hydrolysis of an incorrectly aminoacylated tRNA.
    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:0004822    isoleucine-tRNA ligase activity    Catalysis of the reaction: L-isoleucine + ATP + tRNA(Ile) = L-isoleucyl-tRNA(Ile) + AMP + diphosphate + 2 H(+).
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0006428    isoleucyl-tRNA aminoacylation    The process of coupling isoleucine to isoleucyl-tRNA, catalyzed by isoleucyl-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:0006450    regulation of translational fidelity    Any process that modulates the ability of the translational apparatus to interpret the genetic 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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        SYI_THET8 | P56690: 1ile 1jzq 1jzs 1udz 1wk8 1wny 1wnz

(-) Related Entries Specified in the PDB File

1udz THE SAME PROTEIN WITHOUT LIGAND. RELATED ID: TTK003000883.4 RELATED DB: TARGETDB