Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  TERNARY COMPLEX OF E .COLI LEUCYL-TRNA SYNTHETASE, TRNA(LEU) AND THE BENZOXABOROLE AN3016 IN THE EDITING CONFORMATION
 
Authors :  S. Cusack, A. Palencia, T. Crepin, V. Hernandez, T. Akama, S. J. Baker, W L. Feng, Y. R. Freund, L. Liu, M. Meewan, M. Mohan, W. Mao, F. L. Rock, H. S A. Sheoran, Y. Zhang, Y. Zhang, Y. Zhou, J. A. Nieman, M. R. Anugula, E. M. Keramane, K. Savariraj, D. S. Reddy, R. Sharma, R. Subedi, R. Sing A. Oleary, N. L. Simon, P. L. Demarsh, S. Mushtaq, M. Warner, D. M. Liver M. R. K. Alley, J. J. Plattner
Date :  18 Jan 13  (Deposition) - 17 Apr 13  (Release) - 17 Apr 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Ligase-Rna Complex, Nucleotide (Atp) -Binding, Protein Biosynthesis, Class I Aminoacyl-Trna Synthetase, Aminoacyl Trna Synthetase, Atp Binding, Editing Synthetase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  V. Hernandez, T. Crepin, A. Palencia, S. Cusack, T. Akama, S. J. Baker, W. Bu, L. Feng, Y. R. Freund, L. Liu, M. Meewan, M. Mohan, W. Mao, F. L. Rock, H. Sexton, A. Sheoran, Y. Zhang, Y. Zhang, Y. Zhou, J. A. Nieman, M. R. Anugula, E. M. Keramane, K. Savariraj, D. S. Reddy, R. Sharma, R. Subedi, R. Singh, A. O'Leary, N. L. Simon, P. L. De Marsh, S. Mushtaq, M. Warner, D. M. Livermore, M. R. K. Alley, J. J. Plattner
Discovery Of A Novel Class Of Boron-Based Antibacterials With Activity Against Gram-Negative Bacteria.
Antimicrob. Agents Chemother. V. 57 1394 2013
PubMed-ID: 23295920  |  Reference-DOI: 10.1128/AAC.02058-12

(-) Compounds

Molecule 1 - LEUCYL-TRNA SYNTHETASE
    ChainsA
    EC Number6.1.1.4
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21
    Expression System Taxid83333
    Expression System VectorPET15B
    Expression System Vector TypePLASMID
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562
    SynonymLEUCYL-TRNA SYNTHETASE, LEURS
 
Molecule 2 - TRNALEU5 UAA ISOACCEPTOR
    ChainsB
    Organism ScientificESCHERICHIA COLI K-12
    Organism Taxid83333
    Other DetailsUNMODIFIED T7 TRANSCRIPT
    SyntheticYES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1DJF1Mod. Nucleotide[(1S,5R,6R,8R)-6-(6-AMINOPURIN-9-YL)-2'-(3-OXIDANYLPROPOXY)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]METHDIHYDROGEN PHOSPHATE
2MG2Ligand/IonMAGNESIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:651 , ASN A:723 , A B:14BINDING SITE FOR RESIDUE MG A1861
2AC2SOFTWAREU B:16 , G B:18 , G B:19 , G B:59 , U B:60BINDING SITE FOR RESIDUE MG A1862

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3ZJU)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Leu A:450 -Pro A:451
2Leu A:522 -Pro A:523
3Val A:859 -Gly A:860

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3ZJU)

(-) 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 3ZJU)

(-) 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:820
 aligned with SYL_ECOLI | P07813 from UniProtKB/Swiss-Prot  Length:860

    Alignment length:860
                                    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       840       850       860
            SYL_ECOLI     1 MQEQYRPEEIESKVQLHWDEKRTFEVTEDESKEKYYCLSMLPYPSGRLHMGHVRNYTIGDVIARYQRMLGKNVLQPIGWDAFGLPAEGAAVKNNTAPAPWTYDNIAYMKNQLKMLGFGYDWSRELATCTPEYYRWEQKFFTELYKKGLVYKKTSAVNWCPNDQTVLANEQVIDGCCWRCDTKVERKEIPQWFIKITAYADELLNDLDKLDHWPDTVKTMQRNWIGRSEGVEITFNVNDYDNTLTVYTTRPDTFMGCTYLAVAAGHPLAQKAAENNPELAAFIDECRNTKVAEAEMATMEKKGVDTGFKAVHPLTGEEIPVWAANFVLMEYGTGAVMAVPGHDQRDYEFASKYGLNIKPVILAADGSEPDLSQQALTEKGVLFNSGEFNGLDHEAAFNAIADKLTAMGVGERKVNYRLRDWGVSRQRYWGAPIPMVTLEDGTVMPTPDDQLPVILPEDVVMDGITSPIKADPEWAKTTVNGMPALRETDTFDTFMESSWYYARYTCPQYKEGMLDSEAANYWLPVDIYIGGIEHAIMHLLYFRFFHKLMRDAGMVNSDEPAKQLLCQGMVLADAFYYVGENGERNWVSPVDAIVERDEKGRIVKAKDAAGHELVYTGMSKMSKSKNNGIDPQVMVERYGADTVRLFMMFASPADMTLEWQESGVEGANRFLKRVWKLVYEHTAKGDVAALNVDALTENQKALRRDVHKTIAKVTDDIGRRQTFNTAIAAIMELMNKLAKAPTDGEQDRALMQEALLAVVRMLNPFTPHICFTLWQELKGEGDIDNAPWPVADEKAMVEDSTLVVVQVNGKVRAKITVPVDATEEQVRERAGQEHLVAKYLDGVTVRKVIYVPGKLLNLVVG 860
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhh...........eeeeee.........hhhhhhhhhhhhhhhhhhhhh..eee...ee....hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh....hhhhhee..hhhhhhhhhhhhhhhhhhh.eeeeee..------------------------------.eeeeee.hhhhhhhhhhhhhhh...hhhhhhhhhhhhheeeeeeeeeee.....eeeeee.hhhhhhhh.eeee...hhhhhhhh..hhhhhhhhhhh...----------...eeeeeeeee......eeeeeee..........eeee....hhhhhhhhhhh...............................hhhhh..hhhhhhhhhhhhhhhh..eeeeeee....ee.ee.........eeee....eee.hhhhh..............hhhhhhhhhheee....eeee...ee.hhhhhhhhhhhh..........hhhhhhhhh.eeeee.hhhhh.hhhhhhhhhhhhhhhh........eeeee....eeeeeeeee.....eeeehhhhheee........eee.....eeeeeeeee.........hhhhhhhhhhhhhhhhhhhhh......ee.hhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh....hhhhh.....hhhhhh..eeeeeeee..eeeeeeeee...hhhhhhhhhhhhhhhhh.....eeeeeeee...eeeeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------AA_TRNA_LIGA--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zju A   1 MQEQYRPEEIESKVQLHWDEKRTFEVTEDESKEKYYCLSMLPYPSGRLHMGHVRNYTIGDVIARYQRMLGKNVLQPIGWDAFGLPAEGAAVKNNTAPAPWTYDNIAYMKNQLKMLGFGYDWSRELATCTPEYYRWEQKFFTELYKKGLVYKKTSAV------------------------------EIPQWFIKITAYADELLNDLDKLDHWPDTVKTMQRNWIGRSEGVEITFNVNDYDNTLTVYTTRPDTFMGCTYLAVAAGHPLAQKAAENNPELAAFIDECRNT----------EKKGVDTGFKAVHPLTGEEIPVWAANFVLMEYGTGAVMAVPGHDQRDYEFASKYGLNIKPVILAADGSEPDLSQQALTEKGVLFNSGEFNGLDHEAAFNAIADKLTAMGVGERKVNYRLRDWGVSRQRYWGAPIPMVTLEDGTVMPTPDDQLPVILPEDVVMDGITSPIKADPEWAKTTVNGMPALRETDTFDTFMESSWYYARYTCPQYKEGMLDSEAANYWLPVDIYIGGIEHAIMHLLYFRFFHKLMRDAGMVNSDEPAKQLLCQGMVLADAFYYVGENGERNWVSPVDAIVERDEKGRIVKAKDAAGHELVYTGMSKMSKSKNNGIDPQVMVERYGADTVRLFMMFASPADMTLEWQESGVEGANRFLKRVWKLVYEHTAKGDVAALNVDALTENQKALRRDVHKTIAKVTDDIGRRQTFNTAIAAIMELMNKLAKAPTDGEQDRALMQEALLAVVRMLNPFTPHICFTLWQELKGEGDIDNAPWPVADEKAMVEDSTLVVVQVNGKVRAKITVPVDATEEQVRERAGQEHLVAKYLDGVTVRKVIYVPGKLLNLVVG 860
                                    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       | -       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       840       850       860
                                                                                                                                                                                     156                            187                                                                                                  288        299                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 

Chain B from PDB  Type:RNA  Length:80
                                                                                                                
                 3zju B   1 GCCCGGAUGGUGGAAUCGGUAGACACAAGGGAUCCCUCGGCGUUCGCGCUGUGCGGGUUCAAGUCCCGCUCCGGGUACCx  76
                                    10        20|       29 ||     46 ||||||47I|       56        66        76
                                              20A         31|      47A||||||47J                           76-DJF
                                                           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 3ZJU)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3ZJU)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3ZJU)

(-) 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.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    DJF  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Leu A:450 - Pro A:451   [ RasMol ]  
    Leu A:522 - Pro A:523   [ RasMol ]  
    Val A:859 - Gly A:860   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3zju
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  SYL_ECOLI | P07813
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  6.1.1.4
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  SYL_ECOLI | P07813
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        SYL_ECOLI | P078132ajg 2ajh 2aji 3zgz 3zjt 3zjv 4aq7 4arc 4ari 4as1 4cqn

(-) Related Entries Specified in the PDB File

3zjt TERNARY COMPLEX OF E .COLI LEUCYL-TRNA SYNTHETASE, TRNA(LEU) AND THE BENZOXABOROLE AN3017 IN THE EDITING CONFORMATION
3zjv TERNARY COMPLEX OF E .COLI LEUCYL-TRNA SYNTHETASE, TRNA(LEU) AND THE BENZOXABOROLE AN3213 IN THE EDITING CONFORMATION