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(-) Description

Title :  TERNARY COMPLEX OF E. COLI LEUCYL-TRNA SYNTHETASE, TRNA(LEU) AND THE BENZOXABOROLE AN2679 IN THE EDITING CONFORMATION
 
Authors :  A. Palencia, T. Crepin, M. T. Vu, T. L. Lincecum Jr, S. A. Martinis, S. Cu
Date :  24 Apr 12  (Deposition) - 13 Jun 12  (Release) - 25 Jul 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.08
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Ligase-Rna Complex, Ligase, Nucleotide(Atp)-Binding, Protein Biosynthesis, Class I Aminoacyl-Trna Synthetase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Palencia, T. Crepin, M. T. Vu, T. L. Lincecum Jr, S. A. Martinis, S. Cusack
Structural Dynamics Of The Aminoacylation And Proofreading Functional Cycle Of Bacterial Leucyl-Trna Synthetase
Nat. Struct. Mol. Biol. V. 19 677 2012
PubMed-ID: 22683997  |  Reference-DOI: 10.1038/NSMB.2317

(-) Compounds

Molecule 1 - LEUCINE--TRNA LIGASE
    Chains: A
    EC Number: 6.1.1.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector: PET-15B
    Expression System Vector Type: PLASMID
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K-12
    Synonym: LEUCYL-TRNA SYNTHETASE, LEURS
 
Molecule 2 - TRNA-LEU5 (UAA ISOACEPTOR)
    Chains: B
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Other Details: UNMODIFIED T7 TRANSCRIPT
    Strain: K-12
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric/Biological Unit (3, 7)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2MG2Ligand/IonMAGNESIUM ION
3N791Mod. Nucleotide[(1S,5R,6R,8R)-6-(6-AMINOPURIN-9-YL)SPIRO[2,4,7-TRIOXA-3-BORANUIDABICYCLO[3.3.0]OCTANE-3,9'-8-OXA-9-BORANUIDABICYCLO[4.3.0]NONA-1(6),2,4-TRIENE]-8-YL]METHYL DIHYDROGEN PHOSPHATE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:196 , ALA A:197 , ALA A:199 , ASP A:200 , ASP A:819 , ALA A:820 , GOL A:1862 , HOH A:2091BINDING SITE FOR RESIDUE GOL A1861
2AC2SOFTWAREALA A:197 , TYR A:198 , GLU A:201 , ALA A:820 , THR A:821 , GLU A:822 , TYR A:849 , GOL A:1861 , HOH A:2091BINDING SITE FOR RESIDUE GOL A1862
3AC3SOFTWAREARG A:759 , PRO A:786 , TRP A:787 , PRO A:788 , VAL A:789 , GOL A:1864BINDING SITE FOR RESIDUE GOL A1863
4AC4SOFTWAREHIS A:706 , GLU A:752 , ARG A:759 , VAL A:789 , GOL A:1863 , HOH A:2275BINDING SITE FOR RESIDUE GOL A1864
5AC5SOFTWAREVAL A:236 , TYR A:239 , HOH A:2108BINDING SITE FOR RESIDUE MG A1865
6AC6SOFTWAREU B:8 , G B:9 , HOH B:2003 , HOH B:2005BINDING SITE FOR RESIDUE MG B1076

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4ARI)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Leu A:450 -Pro A:451
2Leu A:522 -Pro A:523

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4ARI)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AA_TRNA_LIGASE_IPS00178 Aminoacyl-transfer RNA synthetases class-I signature.SYL_ECOLI42-53  1A:42-53

(-) Exons   (0, 0)

(no "Exon" information available for 4ARI)

(-) 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:821
 aligned with SYL_ECOLI | P07813 from UniProtKB/Swiss-Prot  Length:860

    Alignment length:861
                             1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659       669       679       689       699       709       719       729       739       749       759       769       779       789       799       809       819       829       839       849       859 
            SYL_ECOLI     - -MQEQYRPEEIESKVQLHWDEKRTFEVTEDESKEKYYCLSMLPYPSGRLHMGHVRNYTIGDVIARYQRMLGKNVLQPIGWDAFGLPAEGAAVKNNTAPAPWTYDNIAYMKNQLKMLGFGYDWSRELATCTPEYYRWEQKFFTELYKKGLVYKKTSAVNWCPNDQTVLANEQVIDGCCWRCDTKVERKEIPQWFIKITAYADELLNDLDKLDHWPDTVKTMQRNWIGRSEGVEITFNVNDYDNTLTVYTTRPDTFMGCTYLAVAAGHPLAQKAAENNPELAAFIDECRNTKVAEAEMATMEKKGVDTGFKAVHPLTGEEIPVWAANFVLMEYGTGAVMAVPGHDQRDYEFASKYGLNIKPVILAADGSEPDLSQQALTEKGVLFNSGEFNGLDHEAAFNAIADKLTAMGVGERKVNYRLRDWGVSRQRYWGAPIPMVTLEDGTVMPTPDDQLPVILPEDVVMDGITSPIKADPEWAKTTVNGMPALRETDTFDTFMESSWYYARYTCPQYKEGMLDSEAANYWLPVDIYIGGIEHAIMHLLYFRFFHKLMRDAGMVNSDEPAKQLLCQGMVLADAFYYVGENGERNWVSPVDAIVERDEKGRIVKAKDAAGHELVYTGMSKMSKSKNNGIDPQVMVERYGADTVRLFMMFASPADMTLEWQESGVEGANRFLKRVWKLVYEHTAKGDVAALNVDALTENQKALRRDVHKTIAKVTDDIGRRQTFNTAIAAIMELMNKLAKAPTDGEQDRALMQEALLAVVRMLNPFTPHICFTLWQELKGEGDIDNAPWPVADEKAMVEDSTLVVVQVNGKVRAKITVPVDATEEQVRERAGQEHLVAKYLDGVTVRKVIYVPGKLLNLVVG 860
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhh............eeeeee.........hhhhhhhhhhhhhhhhhhhhh..eee...ee....hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh....hhhhhee..hhhhhhhhhhhhhhhhhh..eeeeee..------------------------------.eeeeee.hhhhhhhhhhhhhhh...hhhhhhhhhhhhheeeeeeeeee......eeeeee.hhhhhhhh.eeee...hhhhhhhhh.hhhhhhhhhhhhhh----------...eeeeeeeee......eeeeeee..........eeee....hhhhhhhhhhhh..............................hhhhh..hhhhhhhhhhhhhhhh..eeeeeee....ee.ee.........eeee....eee.hhhhh..............hhhhhh....eeee..eeeee...ee.hhhhhhhhhhhh..........hhhhhhhhh.eeeee.hhhhh.hhhhhhhhhhhhhhhh........eeeee....eeeeeeeee.....eeeehhhhheeee.....eeeee.....eeeeeeeee.........hhhhhhhhhhhhhhhhhhhhh......ee.hhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh....hhhhh.....hhhhhh..eeeeeeee..eeeeeeeee...hhhhhhhhhhhhhhhhh.....eeeeeeee...eeeeeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------AA_TRNA_LIGA--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ari A   0 HMQEQYRPEEIESKVQLHWDEKRTFEVTEDESKEKYYCLSMLPYPSGRLHMGHVRNYTIGDVIARYQRMLGKNVLQPIGWDAFGLPAEGAAVKNNTAPAPWTYDNIAYMKNQLKMLGFGYDWSRELATCTPEYYRWEQKFFTELYKKGLVYKKTSAV------------------------------EIPQWFIKITAYADELLNDLDKLDHWPDTVKTMQRNWIGRSEGVEITFNVNDYDNTLTVYTTRPDTFMGCTYLAVAAGHPLAQKAAENNPELAAFIDECRNT----------EKKGVDTGFKAVHPLTGEEIPVWAANFVLMEYGTGAVMAVPGHDQRDYEFASKYGLNIKPVILAADGSEPDLSQQALTEKGVLFNSGEFNGLDHEAAFNAIADKLTAMGVGERKVNYRLRDWGVSRQRYWGAPIPMVTLEDGTVMPTPDDQLPVILPEDVVMDGITSPIKADPEWAKTTVNGMPALRETDTFDTFMESSWYYARYTCPQYKEGMLDSEAANYWLPVDIYIGGIEHAIMHLLYFRFFHKLMRDAGMVNSDEPAKQLLCQGMVLADAFYYVGENGERNWVSPVDAIVERDEKGRIVKAKDAAGHELVYTGMSKMSKSKNNGIDPQVMVERYGADTVRLFMMFASPADMTLEWQESGVEGANRFLKRVWKLVYEHTAKGDVAALNVDALTENQKALRRDVHKTIAKVTDDIGRRQTFNTAIAAIMELMNKLAKAPTDGEQDRALMQEALLAVVRMLNPFTPHICFTLWQELKGEGDIDNAPWPVADEKAMVEDSTLVVVQVNGKVRAKITVPVDATEEQVRERAGQEHLVAKYLDGVTVRKVIYVPGKLLNLVVG 860
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149      |  -         -         -       189       199       209       219       229       239       249       259       269       279        |-       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659       669       679       689       699       709       719       729       739       749       759       769       779       789       799       809       819       829       839       849       859 
                                                                                                                                                                                      156                            187                                                                                                  288        299                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 


Chain B from PDB  Type:RNA  Length:80
                                                                                                                
                 4ari B   1 GCCCGGAUGGUGGAAUCGGUAGACACAAGGGAUCCCUCGGCGUUCGCGCUGUGCGGGUUCAAGUCCCGCUCCGGGUACCa  76
                                    10        20|       29 ||     46 ||||||47I|       56        66        76
                                              20A         31|      47A||||||47J                           76-N79
                                                           39       47B|||||||                              
                                                                     47C||||||                              
                                                                      47D|||||                              
                                                                       47E||||                              
                                                                        47F|||                              
                                                                         47G||                              
                                                                          47H|                              
                                                                           47I
   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 4ARI)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4ARI)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4ARI)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (SYL_ECOLI | P07813)
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.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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  4ari
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  SYL_ECOLI | P07813
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  6.1.1.4
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 Related Entries

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

UniProtKB/Swiss-Prot
        SYL_ECOLI | P07813: 2ajg 2ajh 2aji 3zgz 3zjt 3zju 3zjv 4aq7 4arc 4as1 4cqn

(-) Related Entries Specified in the PDB File

2ajg CRYSTAL STRUCTURE OF THE EDITING DOMAIN OF E. COLI LEUCYL-TRNA SYNTHETASE
2ajh CRYSTAL STRUCTURE OF THE EDITING DOMAIN OF E. COLI LEUCYL-TRNA SYNTHETASE COMPLEXES WITH METHIONINE
2aji CRYSTAL STRUCTURE OF THE EDITING DOMAIN OF E. COLI LEUCYL-TRNA SYNTHETASE COMPLEXES WITH ISOLEUCINE
4aq7 TERNARY COMPLEX OF E. COLI LEUCYL-TRNA SYNTHETASE, TRNA(LEU) AND LEUCYL-ADENYLATE ANALOGUE IN THE AMINOACYLATION CONFORMATION
4arc TERNARY COMPLEX OF E. COLI LEUCYL-TRNA SYNTHETASE, TRNA(LEU) AND LEUCINE IN THE EDITING CONFORMATION
4as1 TERNARY COMPLEX OF E. COLI LEUCYL-TRNA SYNTHETASE, TRNA(LEU) AND THE BENZOXABOROLE AN2679 IN THE EDITING CONFORMATION