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(-) Description

Title :  LEUCYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS COMPLEXED WITH A PRE-TRANSFER EDITING SUBSTRATE ANALOGUE IN BOTH SYNTHETIC ACTIVE SITE AND EDITING SITE
 
Authors :  S. Cusack, A. Yaremchuk, M. Tukalo
Date :  31 Jan 03  (Deposition) - 09 May 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A
Keywords :  Synthetase, Aminoacyl-Trna Synthetase, Class I Aminoacyl-Trna Synthetase, Atp + L-Leucine + Trna (Leu) -> Amp + Ppi L- Leucyl-Trna(Leu) (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Lincecum, M. Tukalo, A. Yaremchuk, R. Mursinna, A. Williams, B. Sproat, W. Van Den Eynde, A. Link, S. Van Calenbergh, M. Grotli, S. Martinis, S. Cusack
Structural And Mechanistic Basis Of Pre- And Posttransfer Editing By Leucyl-Trna Synthetase
Mol. Cell V. 11 951 2003
PubMed-ID: 12718881  |  Reference-DOI: 10.1016/S1097-2765(03)00098-4
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - LEUCYL-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: 262724
    Other Details: ENZYME CONTAINS 878 RESIDUES
    Strain: HB27

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 11)

Asymmetric/Biological Unit (4, 11)
No.NameCountTypeFull Name
1HG1Ligand/IonMERCURY (II) ION
2LMS2Ligand/Ion[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDRO-2-FURANYL]METHYLSULFAMATE
3NVA2Ligand/IonNORVALINE
4SO46Ligand/IonSULFATE ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELEU A:714 , GLU A:715 , GLY A:716 , ARG A:719 , LYS A:760BINDING SITE FOR RESIDUE SO4 A1501
02AC2SOFTWAREGLY A:707 , ARG A:769 , ARG A:773 , TRP A:795BINDING SITE FOR RESIDUE SO4 A1502
03AC3SOFTWAREVAL A:564 , GLU A:565 , GLU A:566 , HOH A:2193 , HOH A:2194BINDING SITE FOR RESIDUE SO4 A1503
04AC4SOFTWAREARG A:759 , HOH A:2178BINDING SITE FOR RESIDUE SO4 A1504
05AC5SOFTWAREARG A:426 , ARG A:428 , ASP A:499BINDING SITE FOR RESIDUE SO4 A1505
06AC6SOFTWAREHIS A:49 , HIS A:52 , SER A:639 , LYS A:640 , HOH A:2134BINDING SITE FOR RESIDUE SO4 A1506
07AC7SOFTWARETYR A:102 , CYS A:128 , GLU A:129BINDING SITE FOR RESIDUE HG A1815
08AC8SOFTWAREPHE A:41 , TYR A:43 , ASP A:80 , TYR A:535 , HIS A:545 , LMS A:1817BINDING SITE FOR RESIDUE NVA A1816
09AC9SOFTWAREPRO A:42 , TYR A:43 , GLY A:51 , HIS A:52 , ASN A:55 , TYR A:56 , MET A:576 , VAL A:577 , MET A:638 , NVA A:1816 , HOH A:2196BINDING SITE FOR RESIDUE LMS A1817
10BC1SOFTWARETHR A:247 , THR A:252 , MET A:338 , VAL A:340 , ASP A:347 , LMS A:1819 , HOH A:2077BINDING SITE FOR RESIDUE NVA A1818
11BC2SOFTWARETHR A:247 , THR A:248 , ARG A:249 , TYR A:327 , VAL A:328 , LEU A:329 , TYR A:332 , ILE A:337 , ASP A:344 , NVA A:1818 , HOH A:2197BINDING SITE FOR RESIDUE LMS A1819

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:439 -A:484

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Lys A:153 -Glu A:190
2Glu A:371 -Pro A:372
3Leu A:452 -Pro A:453
4Met A:530 -Pro A:531

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1OBH)

(-) 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:762
 aligned with Q7SIE4_THETH | Q7SIE4 from UniProtKB/TrEMBL  Length:878

    Alignment length:814
                                    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    
         Q7SIE4_THETH     1 MEKYNPHAIEAKWQRFWEEKGFMKAKDLPGGRGKQYVLVMFPYPSGDLHMGHLKNYTMGDVLARFRRMQGYEVLHPMGWDAFGLPAENAALKFGVHPKDWTYANIRQAKESLRLMGILYDWDREVTTCEPEYYRWNQWIFLKMWEKGLAYRAKGLVNWCPKCQTVLANEQVVEGRCWRHEDTPVEKRELEQWYLRITAYAERLLKDLEGLNWPEKVKAMQRAWIGRSEGAEILFPVEGKEVRIPVFTTRPDTLFGATFLVLAPEHPLTLELAAPEKREEVLAYVEAAKRKTEIERQAEGREKTGVFLGAYALNPATGERIPIWTADYVLFGYGTGAIMAVPAHDQRDYEFARKFGLPIKKVIERPGEPLPEPLERAYEEPGIMVNSGPFDGTESEEGKRKVIAWLEEKGLGKGRVTYRLRDWLISRQRYWGTPIPMVHCEACGVVPVPEEELPVLLPDLKDVEDIRPKGKSPLEAHPEFYETTCPKCGGPAKRDTDTMDTFFDSSWYYLRYTDPHNDRLPFDPEKANAWMPVDQYIGGVEHAVLHLLYSRFFTKFLHDLGMVKVEEPFQGLFTQGMVLAWTDFGPVEVEGSVVRLPEPTRIRLEIPESALSLEDVRKMGAELRPHEDGTLHLWKPAVMSKSKGNGVMVGPFVKEQGADIARITILFAAPPENEMVWTEEGVQGAWRFLNRIYRRVAEDREALLETSGVFQAEALEGKDRELYGKLHETLKKVTEDLEALRFNTAIAALMEFLNALYEYRKDRPVTPVYRTAIRYYLQMLFPFAPHLAEELWHWFWPDSLFEAGWPELDEKALEK 814
               SCOP domains d1obha3 A:1-225,A:418-686 Leucy l-tRNA synthetase (LeuRS)                                                                                                                                                                        d1obha2 A:226-417 Leucyl-tRNA synthetase (LeuRS)                                                                                                                                                d1obha3 A:1-225,A:418-    686 Leucyl-tRNA synthe     tase (LeuRS)                                                                                                                                                                                                            d1obha1 A:687-814 Leucyl-tRNA synthetase (LeuRS)                                                                                 SCOP domains
               CATH domains ------------------------------1 obhA01 A:31-222,A:419-576,A:639-646 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                     ----1obhA02 A:227-418 Isoleucyl-tRNA Synthetase; Domain 2                                                                                                                                           1obhA01 A:31-222,A:41    9-576,A:639-646 Tyrosy     l-Transfer RNA       Synthetase , subunit E, domain 1                                                     1obhA03 A:577-638 Leucyl-tRNA synthetase, domain 3            1obhA01 --------1obhA04 A:655-814 Isoleucyl-tRNA Synthetase; Domain 1                                                                                                            CATH domains
           Pfam domains (1) ------------------------------- -------------------------------------------------------------------------------------------------------------------------                                    -------------------------------tRNA-synt_1_2-1obhA02 A:221-406                                                                                                                                                           ------tRNA-synt_1-1obhA01 A:413-5    81                                                                                                                                        ----------------------------------------------------------------------------------------------------------------------------------------Anticodon_1-1obhA04 A:718-814                                                                     Pfam domains (1)
           Pfam domains (2) ------------------------------- --tRNA-synt_1g-1obhA03 A:35-229                                                                                                                                                                      ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------    ----------------------     ---------------      ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author .......hhhhhhhhhhhhhh..........-.eeeeee.........hhhhhhhhhhhhhhhhhhhhhh.eee........hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh....hhhhh....hhhhhhhhhhhhhhhhhh..eeee.------------------------------------.eeee.hhhhhhhhhhh......hhhhhhhhhhhhheeeeeeeeee......eeeeee.hhhhhhhh.eeee...........hhhhhhhhhhhhhhhhh.hhhhhh.......eeeeeeeee......eeeeeee..........eeeehhhhhhhhhhhhhhhh......ee..................ee..hhhhh..hhhhhhhhhhhhhhhh..eeeeeee....ee.ee.....ee..ee..----.ee.hhhhh.............-----hhhhhhhhhhh....------.....eehhhhhhhhhhhhh..........hhhhhhhhh...eeee....hhhhhhhhhhhhhhhhhh...........eee...eeeeeeeeeeeee..eee.hhhhhhhhh....eeehhhhhhh..eeee.....eeeeeeee.........hhhhhhhhhhhhhhhhhhhhhh.....eeehhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh..hhhhhhhhhh.....hhhhhh.....hhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1obh A   1 MEKYNPHAIEAKWQRFWEEKGFMKAKDLPGG-GKQYVLVMFPYPSGDLHMGHLKNYTMGDVLARFRRMQGYEVLHPMGWDAFGLPAENAALKFGVHPKDWTYANIRQAKESLRLMGILYDWDREVTTCEPEYYRWNQWIFLKMWEKGLAYRAK------------------------------------EQWYLRITAYAERLLKDLEGLNWPEKVKAMQRAWIGRSEGAEILFPVEGKEVRIPVFTTRPDTLFGATFLVLAPEHPLTLELAAPEKREEVLAYVEAAKRKTEIERQAEGREKTGVFLGAYALNPATGERIPIWTADYVLFGYGTGAIMAVPAHDQRDYEFARKFGLPIKKVIERPGEPLPEPLERAYEEPGIMVNSGPFDGTESEEGKRKVIAWLEEKGLGKGRVTYRLRDWLISRQRYWGTPIPMVHC----VVPVPEEELPVLLPDLKDVEDI-----SPLEAHPEFYETTCP------KRDTDTMDTFFDSSWYYLRYTDPHNDRLPFDPEKANAWMPVDQYIGGVEHAVLHLLYSRFFTKFLHDLGMVKVEEPFQGLFTQGMVLAWTDFGPVEVEGSVVRLPEPTRIRLEIPESALSLEDVRKMGAELRPHEDGTLHLWKPAVMSKSKGNGVMVGPFVKEQGADIARITILFAAPPENEMVWTEEGVQGAWRFLNRIYRRVAEDREALLETSGVFQAEALEGKDRELYGKLHETLKKVTEDLEALRFNTAIAALMEFLNALYEYRKDRPVTPVYRTAIRYYLQMLFPFAPHLAEELWHWFWPDSLFEAGWPELDEKALEK 814
                                    10        20        30| |     40        50        60        70        80        90       100       110       120       130       140       150  |      -         -         -       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        |-   |   450       460    |    -|      480    |    - |     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    
                                                         31 |                                                                                                                     153                                  190                                                                                                                                                                                                                                                      439  444                  465   471           485    492                                                                                                                                                                                                                                                                                                                                  
                                                           33
   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: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (4, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)
(-)
Class: Mainly Beta (13760)

(-) 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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  1obh
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 Related Entries

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

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        Q7SIE4_THETH | Q7SIE4: 1h3n 2bte 2byt 2v0c 2v0g

(-) Related Entries Specified in the PDB File

1h3n LEUCYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS COMPLEXED WITH A SULPHAMOYL ANALOGUE OF LEUCYL-ADENYLATE
1jzq ISOLEUCYL-TRNA SYNTHETASE COMPLEXED WITH ISOLEUCYL-ADENYLATE ANALOGUE
1jzs ISOLEUCYL-TRNA SYNTHETASE COMPLEXED WITH MUPIROCIN
1obc LEUCYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS COMPLEXED WITH A POST-TRANSFER EDITING SUBSTRATE ANALOGUE