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(-) Description

Title :  CRYSTAL STRUCTURE OF LEUCYL-TRNA SYNTHETASE FROM THE ARCHAEON PYROCOCCUS HORIKOSHII REVEALS A NOVEL EDITING DOMAIN ORIENTATION
 
Authors :  R. Fukunaga, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  30 May 04  (Deposition) - 08 Feb 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym./Biol. Unit :  A
Keywords :  Leucyl-Trna Synthetase, Leucine, Aminoacyl-Trna, Editing, Amino Acid, Aminoacylation, Pyrococcus Horikoshii, Trnaleu, Structural Genomics, Riken Structural Genomics/Proteomics Initiative, Rsgi, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Fukunaga, S. Yokoyama
Crystal Structure Of Leucyl-Trna Synthetase From The Archaeon Pyrococcus Horikoshii Reveals A Novel Editing Domain Orientation
J. Mol. Biol. V. 346 57 2005
PubMed-ID: 15663927  |  Reference-DOI: 10.1016/J.JMB.2004.11.060
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - LEUCYL-TRNA SYNTHETASE
    Chains: A
    EC Number: 6.1.1.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET16B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: RESIDUE 1-810
    Organism Scientific: PYROCOCCUS HORIKOSHII
    Organism Taxid: 53953
    Synonym: LEUCINE--TRNA LIGASE, LEURS

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 8)

Asymmetric/Biological Unit (1, 8)
No.NameCountTypeFull Name
1SO48Ligand/IonSULFATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:84 , SER A:85 , PRO A:86 , HIS A:196 , ARG A:510 , HOH A:943 , HOH A:994 , HOH A:1059 , HOH A:1189BINDING SITE FOR RESIDUE SO4 A 901
2AC2SOFTWARESER A:652 , LYS A:653 , SER A:654 , HOH A:1715BINDING SITE FOR RESIDUE SO4 A 902
3AC3SOFTWAREARG A:93 , GLU A:200 , GLY A:201 , GLU A:202 , ASP A:203BINDING SITE FOR RESIDUE SO4 A 903
4AC4SOFTWAREARG A:492 , LYS A:611 , HOH A:1101 , HOH A:1235BINDING SITE FOR RESIDUE SO4 A 904
5AC5SOFTWARELYS A:506 , ARG A:510 , HOH A:1079 , HOH A:1260 , HOH A:1475BINDING SITE FOR RESIDUE SO4 A 905
6AC6SOFTWAREARG A:182 , ARG A:184 , ILE A:206 , HOH A:1046 , HOH A:1515BINDING SITE FOR RESIDUE SO4 A 906
7AC7SOFTWARETHR A:229 , LEU A:230 , ARG A:231 , TYR A:401 , HOH A:1488BINDING SITE FOR RESIDUE SO4 A 907
8AC8SOFTWARETRP A:185 , GLY A:190 , PHE A:275 , LYS A:459 , HOH A:971 , HOH A:1104 , HOH A:1484BINDING SITE FOR RESIDUE SO4 A 908

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Leu A:488 -Pro A:489
2Tyr A:602 -Pro A:603

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AA_TRNA_LIGASE_IPS00178 Aminoacyl-transfer RNA synthetases class-I signature.SYL_PYRHO43-54  1A:43-54

(-) Exons   (0, 0)

(no "Exon" information available for 1WKB)

(-) 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:791
 aligned with SYL_PYRHO | O58698 from UniProtKB/Swiss-Prot  Length:967

    Alignment length:807
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723       733       743       753       763       773       783       793       803       
            SYL_PYRHO     4 LNFKAIEEKWQKRWLEAKIFEPNIRDKPKEKKFYITVAFPYLSGHLHVGHARTYTIPDVIARFKRMQGYNVLFPMAWHITGSPIVGIAERIKNRDPKTIWIYRDVYKVPEEILWTFEDPINIVKYFMKAAKETFIRAGFSVDWSREFYTTSLFPPFSKFIEWQFWKLKEKGYIVKGAHRVRWDPVVGTPLGDHDLMEGEDVPILDYIIIKFELRENGEVIYLPAATLRPETVYGVTNMWVNPNATYVKAKVRRKDKEETWIVSKEAAYKLSFQDREIEVIEEFKGEKLIGKYVRNPVSGDEVIILPAEFVDPDNATGVVMSVPAHAPFDHVALEDLKRETEILEKYDIDPRIVENITYISLIKLEGYGDFPAVEEVNKLGIKSQKDKEKLEQATKTIYKAEYHKGIFKVPPYEGKPVQEVKEAIAKEMLEKGIAEIMYEFAEKNVISRFGNRAVIKIIHDQWFIDYGNPEWKEKARKALERMKILPETRRAQFEAIIDWLDKKACARKIGLGTPLPWDPEWVIESLSDSTIYMAYYTISRHINKLRQEGKLDPEKLTPEFFDYIFLEEFSEDKEKELEKKTGIPAEIIHEMKEEFEYWYPLDWRCSGKDLIPNHLTFFIFNHVAIFREEHWPKGIAVNGFGTLEGQKMSKSKGNVLNFIDAIEENGADVVRLYIMSLAEHDSDFDWRRKEVGKLRKQIERFYELISQFAEYEVKGNVELKDIDRWMLHRLNKAIKETTNALEEFRTRTAVQWAFYSIMNDLRWYLRRTEGRDDEAKRYVLRTLADVWVRLMAPFTPHICEELWEKLG 810
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 1wkbA01 A:4-204,A:448-689 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                                          1wkbA02 A:205-447 Isoleucyl-tRNA Synthetase; Domain 2                                                                                                                                                                                              1wkbA01 A:4-204,A:448-689 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                                                                                   1wkbA03 A:690-810 Isoleucyl-tRNA Synthetase; Domain 1                                                                     CATH domains
               Pfam domains --------tRNA-synt_1-1wkbA01 A:12-690                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           -----------------------------------Anticodon_1-1wkbA02 A:726-810                                                         Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhh.....hhhhhhhh.eeeeee.........hhhhhhhhhhhhhhhhhhhhhh.eee.........hhhhhhhhhhhh.hhhhhhhhhhh...hhhhhhh..hhhhhhhhhhhhhhhhhhhh....hhhhh......hhhhhhhhhhhhhhhhhh..eeeeeeeeeee....ee.............eeeeeeeeee........eeeeee.hhhhhhhh.eeee.....eeeeeeee..eeeeeeeehhhhhhhh....eeeeeee.........eee......eeeeee............eee....hhhhhhhhh...................----------------......hhhhh.........hhhhhhhhhhhhhhh.ee.hhhhh.eehhhhhhhhhhhhhh...eeeeeee.............eeeeeeeeeee...hhhhhhhhhhhhhh.eeehhhhhhhhhhhhhhh..ee.ee......ee..eeeeee.......hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.hhhhhhhhhhhhhhhh...eeeee.hhh.hhhhhhhhhhhhhhhhhhh..eeeee..eee.............hhhhhhhhhhhhhhhhhhhhhh.....eeehhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------AA_TRNA_LIGA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wkb A   4 LNFKAIEEKWQKRWLEAKIFEPNIRDKPKEKKFYITVAFPYLSGHLHVGHARTYTIPDVIARFKRMQGYNVLFPMAWHITGSPIVGIAERIKNRDPKTIWIYRDVYKVPEEILWTFEDPINIVKYFMKAAKETFIRAGFSVDWSREFYTTSLFPPFSKFIEWQFWKLKEKGYIVKGAHRVRWDPVVGTPLGDHDLMEGEDVPILDYIIIKFELRENGEVIYLPAATLRPETVYGVTNMWVNPNATYVKAKVRRKDKEETWIVSKEAAYKLSFQDREIEVIEEFKGEKLIGKYVRNPVSGDEVIILPAEFVDPDNATGVVMSVPAHAPFDHVALEDLKRETEILEKYDIDPRIV----------------FPAVEEVNKLGIKSQKDKEKLEQATKTIYKAEYHKGIFKVPPYEGKPVQEVKEAIAKEMLEKGIAEIMYEFAEKNVISRFGNRAVIKIIHDQWFIDYGNPEWKEKARKALERMKILPETRRAQFEAIIDWLDKKACARKIGLGTPLPWDPEWVIESLSDSTIYMAYYTISRHINKLRQEGKLDPEKLTPEFFDYIFLEEFSEDKEKELEKKTGIPAEIIHEMKEEFEYWYPLDWRCSGKDLIPNHLTFFIFNHVAIFREEHWPKGIAVNGFGTLEGQKMSKSKGNVLNFIDAIEENGADVVRLYIMSLAEHDSDFDWRRKEVGKLRKQIERFYELISQFAEYEVKGNVELKDIDRWMLHRLNKAIKETTNALEEFRTRTAVQWAFYSIMNDLRWYLRRTEGRDDEAKRYVLRTLADVWVRLMAPFTPHICEELWEKLG 810
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353  |      -       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723       733       743       753       763       773       783       793       803       
                                                                                                                                                                                                                                                                                                                                                                                          356              373
   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 1WKB)

(-) CATH Domains  (3, 3)

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

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: HUP (230)
(-)
Clan: no clan defined [family: Anticodon_1] (10)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (SYL_PYRHO | O58698)
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.
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.

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        SYL_PYRHO | O58698: 1wz2

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