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(-) Description

Title :  LEUCYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS COMPLEXED WITH A SULPHAMOYL ANALOGUE OF LEUCYL-ADENYLATE IN THE SYNTHETIC SITE AND AN ADDUCT OF AMP WITH 5-FLUORO-1,3-DIHYDRO-1-HYDROXY-2,1-BENZOXABOROLE (AN2690) IN THE EDITING SITE
 
Authors :  F. Rock, W. Mao, A. Yaremchuk, M. Tukalo, T. Crepin, H. Zhou, Y. Zhang, V. Hernandez, T. Akama, S. Baker, J. Plattner, L. Shapiro, S. A. Martinis, S. J. Benkovic, S. Cusack, M. R. K. Alley
Date :  14 May 07  (Deposition) - 03 Jul 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym./Biol. Unit :  A
Keywords :  Ligase, Nucleotide-Binding, Protein Biosynthesis, Clss I Aminoacyl- Trna Synthetase, Atp + L-Leucine + Trna (Leu) Gives Amp + Ppi + L-Leucyl-Trna(Leu), Aminoacyl-Trna Synthetase, Zinc, Atp-Binding, Metal-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Rock, W. Mao, A. Yaremchuk, M. Tukalo, T. Crepin, H. Zhou, Y. Zhang, V. Hernandez, T. Akama, S. Baker, J. Plattner, L. Shapiro, S. A. Martinis, S. J. Benkovic, S. Cusack, M. R. K. Alley
An Antifungal Agent Inhibits An Aminoacyl-Trna Synthetase By Trapping Trna In The Editing Site.
Science V. 316 1759 2007
PubMed-ID: 17588934  |  Reference-DOI: 10.1126/SCIENCE.1142189

(-) Compounds

Molecule 1 - AMINOACYL-TRNA SYNTHETASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 274
    Strain: HB-27
    Synonym: LEUCYL-TRNA SYNTHETASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 10)

Asymmetric/Biological Unit (5, 10)
No.NameCountTypeFull Name
1ANZ1Ligand/Ion[(6-AMINO-9H-PURIN-9-YL)-[5-FLUORO-1,3-DIHYDRO-1-HYDROXY-2,1-BENZOXABOROLE]-4'YL]METHYLDIHYDROGEN PHOSPHATE
2LEU1Mod. Amino AcidLEUCINE
3LMS1Ligand/Ion[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDRO-2-FURANYL]METHYLSULFAMATE
4SO45Ligand/IonSULFATE ION
5ZN2Ligand/IonZINC ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPHE A:41 , TYR A:43 , ASP A:80 , TYR A:535 , HIS A:541 , HIS A:545 , LMS A:1814 , HOH A:2474BINDING SITE FOR RESIDUE LEU A1501
02AC2SOFTWAREMET A:40 , PHE A:41 , PRO A:42 , TYR A:43 , HIS A:49 , GLY A:51 , HIS A:52 , ASN A:55 , TYR A:56 , GLY A:537 , GLY A:538 , GLU A:540 , GLN A:574 , GLY A:575 , MET A:576 , VAL A:577 , MET A:638 , LEU A:1501 , HOH A:2544 , HOH A:2678BINDING SITE FOR RESIDUE LMS A1814
03AC3SOFTWARECYS A:439 , CYS A:442 , CYS A:484 , CYS A:487BINDING SITE FOR RESIDUE ZN A1815
04AC4SOFTWARECYS A:159 , CYS A:162 , CYS A:176 , HIS A:179BINDING SITE FOR RESIDUE ZN A1816
05AC5SOFTWAREPHE A:246 , THR A:247 , THR A:248 , ARG A:249 , THR A:252 , TYR A:327 , VAL A:328 , LEU A:329 , TYR A:332 , ILE A:337 , MET A:338 , HIS A:343 , ASP A:344 , ARG A:346 , HOH A:2335 , HOH A:2681 , HOH A:2682 , HOH A:2683BINDING SITE FOR RESIDUE ANZ A1817
06AC6SOFTWAREGLU A:715 , GLY A:716 , ARG A:719 , LYS A:760 , HOH A:2609BINDING SITE FOR RESIDUE SO4 A1818
07AC7SOFTWAREGLY A:707 , ARG A:769 , ARG A:773 , TRP A:795BINDING SITE FOR RESIDUE SO4 A1819
08AC8SOFTWARELEU A:207 , GLU A:208 , GLU A:214 , LYS A:217 , ARG A:221BINDING SITE FOR RESIDUE SO4 A1820
09AC9SOFTWAREGLU A:301 , LYS A:302 , LYS A:353BINDING SITE FOR RESIDUE SO4 A1821
10BC1SOFTWAREARG A:759 , HOH A:2684BINDING SITE FOR RESIDUE SO4 A1822

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2V0C)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Glu A:371 -Pro A:372
2Leu A:452 -Pro A:453
3Met A:530 -Pro A:531

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2V0C)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2V0C)

(-) Exons   (0, 0)

(no "Exon" information available for 2V0C)

(-) 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:811
 aligned with Q7SIE4_THETH | Q7SIE4 from UniProtKB/TrEMBL  Length:878

    Alignment length:839
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       770       780       790       800       810       820       830         
        Q7SIE4_THETH      1 MEKYNPHAIEAKWQRFWEEKGFMKAKDLPGGRGKQYVLVMFPYPSGDLHMGHLKNYTMGDVLARFRRMQGYEVLHPMGWDAFGLPAENAALKFGVHPKDWTYANIRQAKESLRLMGILYDWDREVTTCEPEYYRWNQWIFLKMWEKGLAYRAKGLVNWCPKCQTVLANEQVVEGRCWRHEDTPVEKRELEQWYLRITAYAERLLKDLEGLNWPEKVKAMQRAWIGRSEGAEILFPVEGKEVRIPVFTTRPDTLFGATFLVLAPEHPLTLELAAPEKREEVLAYVEAAKRKTEIERQAEGREKTGVFLGAYALNPATGERIPIWTADYVLFGYGTGAIMAVPAHDQRDYEFARKFGLPIKKVIERPGEPLPEPLERAYEEPGIMVNSGPFDGTESEEGKRKVIAWLEEKGLGKGRVTYRLRDWLISRQRYWGTPIPMVHCEACGVVPVPEEELPVLLPDLKDVEDIRPKGKSPLEAHPEFYETTCPKCGGPAKRDTDTMDTFFDSSWYYLRYTDPHNDRLPFDPEKANAWMPVDQYIGGVEHAVLHLLYSRFFTKFLHDLGMVKVEEPFQGLFTQGMVLAWTDFGPVEVEGSVVRLPEPTRIRLEIPESALSLEDVRKMGAELRPHEDGTLHLWKPAVMSKSKGNGVMVGPFVKEQGADIARITILFAAPPENEMVWTEEGVQGAWRFLNRIYRRVAEDREALLETSGVFQAEALEGKDRELYGKLHETLKKVTEDLEALRFNTAIAALMEFLNALYEYRKDRPVTPVYRTAIRYYLQMLFPFAPHLAEELWHWFWPDSLFEAGWPELDEKALEKDVVEVAVQVNGRVRGTIHIPKDAPL  839
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----------------------------   --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------tRNA-synt_1_2-2v0cA02 A:221-406                                                                                                                                                           ------tRNA-synt_1-2v0cA01 A:413-581                                                                                                                                            ----------------------------------------------------------------------------------------------------------------------------------------Anticodon_1-2v0cA04 A:718-1501                                                                                             Pfam domains (1)
           Pfam domains (2) ----------------------------------tRNA-synt_1g-2v0cA03 A:35-229                                                                                                                                                                      ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ....hhhhhhhhhhhhhhhhh........---.eeeeee.........hhhhhhhhhhhhhhhhhhhhhh.eee........hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh....hhhhh....hhhhhhhhhhhhhhhhhh..eeeeeeeeeee....eeehhh.ee..ee........eeeeeeeeee.hhhhhhhhhhh......hhhhhhhhhhhhheeeeeeeeee......eeeeee.hhhhhhhh.eeee...hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh.......eeeeeeee......eeeeee...........eeee....hhhhhhhhhhhh......ee..................ee..hhhhh..hhhhhhhhhhhhhhhh..eeeeeee....ee.ee.....ee..eeee...eeee.hhhhh........hhhhhh....hhhhhhhhhheee......eeee...eehhhhhhhhhhhhh..........hhhhhhhhh...eee.hhhhh.hhhhhhhhhhhhhhhh...........ee....eeeeeeeeeeeee..eee.hhhhhhhhh....eeehhhhhhh..eeee.....eeeeeeee.hhhhh...hhhhhhhhhhhhhhhhhhhhh......eeehhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh..hhhhhhhhhhhhh..hhhhh.....hhhhhh-------------------------. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2v0c A    1 MEKYNPHAIEAKWQRFWEEKGFMKAKDLP---GKQYVLVMFPYPSGDLHMGHLKNYTMGDVLARFRRMQGYEVLHPMGWDAFGLPAENAALKFGVHPKDWTYANIRQAKESLRLMGILYDWDREVTTCEPEYYRWNQWIFLKMWEKGLAYRAKGLVNWCPKCQTVLANEQVVEGRCWRHEDTPVEKRELEQWYLRITAYAERLLKDLEGLNWPEKVKAMQRAWIGRSEGAEILFPVEGKEVRIPVFTTRPDTLFGATFLVLAPEHPLTLELAAPEKREEVLAYVEAAKRKTEIERQAEGREKTGVFLGAYALNPATGERIPIWTADYVLFGYGTGAIMAVPAHDQRDYEFARKFGLPIKKVIERPGEPLPEPLERAYEEPGIMVNSGPFDGTESEEGKRKVIAWLEEKGLGKGRVTYRLRDWLISRQRYWGTPIPMVHCEACGVVPVPEEELPVLLPDLKDVEDIRPKGKSPLEAHPEFYETTCPKCGGPAKRDTDTMDTFFDSSWYYLRYTDPHNDRLPFDPEKANAWMPVDQYIGGVEHAVLHLLYSRFFTKFLHDLGMVKVEEPFQGLFTQGMVLAWTDFGPVEVEGSVVRLPEPTRIRLEIPESALSLEDVRKMGAELRPHEDGTLHLWKPAVMSKSKGNGVMVGPFVKEQGADIARITILFAAPPENEMVWTEEGVQGAWRFLNRIYRRVAEDREALLETSGVFQAEALEGKDRELYGKLHETLKKVTEDLEALRFNTAIAALMEFLNALYEYRKDRPVTPVYRTAIRYYLQMLFPFAPHLAEELWHWFWPDSLFEAGWPELDEKALE-------------------------L 1501
                                    10        20        |-  |     40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       770       780       790       800       810  |      -         -        |
                                                       29  33                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         813                      1501
   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 2V0C)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2V0C)

(-) Pfam Domains  (4, 4)

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

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q7SIE4_THETH | Q7SIE4)
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: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.
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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 Related Entries

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

UniProtKB/TrEMBL
        Q7SIE4_THETH | Q7SIE4: 1h3n 1obh 2bte 2byt 2v0g

(-) Related Entries Specified in the PDB File

1h3n LEUCYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS COMPLEXED WITH A SULPHAMOYL ANALOGUE OF LEUCYL-ADENYLATE
1obc LEUCYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS COMPLEXED WITH A POST-TRANSFER EDITING SUBSTRATE ANALOGUE
1obh LEUCYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS COMPLEXED WITH A PRE-TRANSFER EDITING SUBSTRATE ANALOGUE
2bte THERMUS THERMOPHILUS LEUCYL-TRNA SYNTHETASE COMPLEXED WITH WITH A TRNALEU TRANSCRIPT IN THE POST-EDITING CONFORMATION AND A POST- TRANSFER EDITING SUBSRATE ANALOGUE
2byt THERMUS THERMOPHILUS LEUCYL-TRNA SYNTHETASE COMPLEXED WITH WITH A TRNALEU TRANSCRIPT IN THE POST-EDITING CONFORMATION