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(-) Description

Title :  STRUCTURE OF THE HUMAN CYTOSOLIC LEUCYL-TRNA SYNTHETASE EDITING DOMAIN
 
Authors :  E. Seiradake, W. Mao, V. Hernandez, S. J. Baker, J. J. Plattner, M. R. K. Alley, S. Cusack
Date :  03 Apr 09  (Deposition) - 19 May 09  (Release) - 23 Jun 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.25
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Aminoacyl-Trna Synthetase, Phosphoprotein, Editing Domain, Nucleotide-Binding, Hydrolysis Of Mis-Charged Trnas, Protein Biosynthesis, Leucyl-Trna Synthetase, Human, Ligase, Cytoplasm, Atp-Binding, Polymorphism (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  E. Seiradake, W. Mao, V. Hernandez, S. J. Baker, J. J. Plattner, M. R. K. Alley, S. Cusack
Crystal Structures Of The Human And Fungal Cytosolic Leucyl-Trna Synthetase Editing Domains: A Structural Basis For The Rational Design Of Antifungal Benzoxaboroles.
J. Mol. Biol. V. 390 196 2009
PubMed-ID: 19426743  |  Reference-DOI: 10.1016/J.JMB.2009.04.073

(-) Compounds

Molecule 1 - LEUCYL-TRNA SYNTHETASE, CYTOPLASMIC
    ChainsA, B
    EC Number6.1.1.4
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPPROEX HTB
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    FragmentEDITING OR CP1 DOMAIN, RESIDUES 260-509
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymLEUCINE--TRNA LIGASE, LEURS

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 20)

Asymmetric/Biological Unit (1, 20)
No.NameCountTypeFull Name
1MSE20Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 2WFD)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2WFD)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Gly A:260 -Pro A:261
2Glu A:273 -Pro A:274
3Gly B:260 -Pro B:261
4Glu B:273 -Pro B:274

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 2)

Asymmetric/Biological Unit (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_070438Y373CSYLC_HUMANDisease (ILFS1)201861847A/BY373C

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2WFD)

(-) Exons   (0, 0)

(no "Exon" information available for 2WFD)

(-) 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:252
 aligned with SYLC_HUMAN | Q9P2J5 from UniProtKB/Swiss-Prot  Length:1176

    Alignment length:252
                                   267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507  
           SYLC_HUMAN   258 GVGPQEYTLLKLKVLEPYPSKLSGLKGKNIFLVAATLRPETMFGQTNCWVRPDMKYIGFETVNGDIFICTQKAARNMSYQGFTKDNGVVPVVKELMGEEILGASLSAPLTSYKVIYVLPMLTIKEDKGTGVVTSVPSDSPDDIAALRDLKKKQALRAKYGIRDDMVLPFEPVPVIEIPGFGNLSAVTICDELKIQSQNDREKLAEAKEKIYLKGFYEGIMLVDGFKGQKVQDVKKTIQKKMIDAGDALIYME 509
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeeeeeee...hhhhhhhh...eeeeeee.hhhhh....eeee......eeee.....eeeehhhhhhhh.............eeee.........eee........eeeee............eee....hhhhhhhhhhhhhhhhhhhh........................hhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhh.....eeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------C---------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2wfd A 258 AmGPQEYTLLKLKVLEPYPSKLSGLKGKNIFLVAATLRPETmFGQTNCWVRPDmKYIGFETVNGDIFICTQKAARNmSYQGFTKDNGVVPVVKELmGEEILGASLSAPLTSYKVIYVLPmLTIKEDKGTGVVTSVPSDSPDDIAALRDLKKKQALRAKYGIRDDmVLPFEPVPVIEIPGFGNLSAVTICDELKIQSQNDREKLAEAKEKIYLKGFYEGImLVDGFKGQKVQDVKKTIQKKmIDAGDALIYmE 509
                             |     267       277       287       297 |     307   |   317       327      |337       347     | 357       367       377       387       397       407       417    |  427       437       447       457       467       477       487       497|      507| 
                             |                                     299-MSE     311-MSE                334-MSE            353-MSE                 377-MSE                                      422-MSE                                                477-MSE              498-MSE   508-MSE
                           259-MSE                                                                                                                                                                                                                                                      

Chain B from PDB  Type:PROTEIN  Length:252
 aligned with SYLC_HUMAN | Q9P2J5 from UniProtKB/Swiss-Prot  Length:1176

    Alignment length:252
                                   267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507  
           SYLC_HUMAN   258 GVGPQEYTLLKLKVLEPYPSKLSGLKGKNIFLVAATLRPETMFGQTNCWVRPDMKYIGFETVNGDIFICTQKAARNMSYQGFTKDNGVVPVVKELMGEEILGASLSAPLTSYKVIYVLPMLTIKEDKGTGVVTSVPSDSPDDIAALRDLKKKQALRAKYGIRDDMVLPFEPVPVIEIPGFGNLSAVTICDELKIQSQNDREKLAEAKEKIYLKGFYEGIMLVDGFKGQKVQDVKKTIQKKMIDAGDALIYME 509
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) --tRNA-synt_1-2wfdB01 B:260-509                                                                                                                                                                                                                              Pfam domains (1)
           Pfam domains (2) --tRNA-synt_1-2wfdB02 B:260-509                                                                                                                                                                                                                              Pfam domains (2)
         Sec.struct. author ......eeeeeeeee...hhhhhhhh...eeeeeee.hhhhh....eeee......eeee.....eeeehhhhhhhh.............eeee.........eee........eeeee............eee....hhhhhhhhhhhhhhhhhhhhhh......................hhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhh.....eeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------C---------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2wfd B 258 AmGPQEYTLLKLKVLEPYPSKLSGLKGKNIFLVAATLRPETmFGQTNCWVRPDmKYIGFETVNGDIFICTQKAARNmSYQGFTKDNGVVPVVKELmGEEILGASLSAPLTSYKVIYVLPmLTIKEDKGTGVVTSVPSDSPDDIAALRDLKKKQALRAKYGIRDDmVLPFEPVPVIEIPGFGNLSAVTICDELKIQSQNDREKLAEAKEKIYLKGFYEGImLVDGFKGQKVQDVKKTIQKKmIDAGDALIYmE 509
                             |     267       277       287       297 |     307   |   317       327      |337       347     | 357       367       377       387       397       407       417    |  427       437       447       457       467       477       487       497|      507| 
                             |                                     299-MSE     311-MSE                334-MSE            353-MSE                 377-MSE                                      422-MSE                                                477-MSE              498-MSE   508-MSE
                           259-MSE                                                                                                                                                                                                                                                      

   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 2WFD)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2WFD)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: HUP (230)

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (SYLC_HUMAN | Q9P2J5)
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:0004823    leucine-tRNA ligase activity    Catalysis of the reaction: L-leucine + ATP + tRNA(Leu) = AMP + diphosphate + 2 H(+) + Leu-tRNA(Leu).
    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.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0006429    leucyl-tRNA aminoacylation    The process of coupling leucine to leucyl-tRNA, catalyzed by leucyl-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.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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