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(-) Description

Title :  CRYSTAL STRUCTURE OF THE EDITING DOMAIN OF E. COLI LEUCYL-TRNA SYNTHETASE
 
Authors :  Y. Liu, J. Liao, B. Zhu, E. D. Wang, J. Ding
Date :  01 Aug 05  (Deposition) - 24 Jan 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Editing Domain, Leucyl-Trna Synthetase, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Liu, J. Liao, B. Zhu, E. D. Wang, J. Ding
Crystal Structures Of The Editing Domain Of Escherichia Coli Leucyl-Trna Synthetase And Its Complexes With Met And Ile Reveal A Lock-And-Key Mechanism For Amino Acid Discrimination
Biochem. J. V. 394 399 2006
PubMed-ID: 16277600  |  Reference-DOI: 10.1042/BJ20051249
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - LEUCYL-TRNA SYNTHETASE
    Chains: A, B
    EC Number: 6.1.1.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET-3E-HIS
    Expression System Strain: BL-21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 228-413
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: LEUCINE--TRNA LIGASE, LEURS

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2AJG)

(-) Sites  (0, 0)

(no "Site" information available for 2AJG)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2AJG)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2AJG)

(-) Sequences/Alignments

Asymmetric 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:186
 aligned with SYL_ECOLI | P07813 from UniProtKB/Swiss-Prot  Length:860

    Alignment length:186
                                   237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407      
            SYL_ECOLI   228 EGVEITFNVNDYDNTLTVYTTRPDTFMGCTYLAVAAGHPLAQKAAENNPELAAFIDECRNTKVAEAEMATMEKKGVDTGFKAVHPLTGEEIPVWAANFVLMEYGTGAVMAVPGHDQRDYEFASKYGLNIKPVILAADGSEPDLSQQALTEKGVLFNSGEFNGLDHEAAFNAIADKLTAMGVGERKV 413
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 2ajgA00 A:228-413 Isoleucyl-tRNA Synthetase; Domain 2                                                                                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeee......eeeeee.hhhhhhhh.eeee...hhhhhhhhh.hhhhhhhhhhhhhh..hhhhhhhh...eeeeeeeee......eeeeeee..........eeee....hhhhhhhhhhhh..............................hhhhh..hhhhhhhhhhhhhhhh..eeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2ajg A 228 EGVEITFNVNDYDNTLTVYTTRPDTFMGCTYLAVAAGHPLAQKAAENNPELAAFIDECRNTKVAEAEMATMEKKGVDTGFKAVHPLTGEEIPVWAANFVLMEYGTGAVMAVPGHDQRDYEFASKYGLNIKPVILAADGSEPDLSQQALTEKGVLFNSGEFNGLDHEAAFNAIADKLTAMGVGERKV 413
                                   237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407      


Chain B from PDB  Type:PROTEIN  Length:174
 aligned with SYL_ECOLI | P07813 from UniProtKB/Swiss-Prot  Length:860

    Alignment length:185
                                   237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407     
            SYL_ECOLI   228 EGVEITFNVNDYDNTLTVYTTRPDTFMGCTYLAVAAGHPLAQKAAENNPELAAFIDECRNTKVAEAEMATMEKKGVDTGFKAVHPLTGEEIPVWAANFVLMEYGTGAVMAVPGHDQRDYEFASKYGLNIKPVILAADGSEPDLSQQALTEKGVLFNSGEFNGLDHEAAFNAIADKLTAMGVGERK 412
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2ajgB00 B:228-412 Isoleucyl-tRNA Synthetase; Domain 2                                                                                                                                     CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee......eeeeee.hhhhhhhh.eeee...hhhhhhhhh.hhhhhhhhhhhhh-----------...eeeeeeeee......eeeeeee..........eeee....hhhhhhhhhhhh..............................hhhhh..hhhhhhhhhhhhhhhh..eeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ajg B 228 EGVEITFNVNDYDNTLTVYTTRPDTFMGCTYLAVAAGHPLAQKAAENNPELAAFIDECRN-----------EKKGVDTGFKAVHPLTGEEIPVWAANFVLMEYGTGAVMAVPGHDQRDYEFASKYGLNIKPVILAADGSEPDLSQQALTEKGVLFNSGEFNGLDHEAAFNAIADKLTAMGVGERK 412
                                   237       247       257       267       277       287         - |     307       317       327       337       347       357       367       377       387       397       407     
                                                                                     287         299
   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 2AJG)

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2AJG)

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (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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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

2ajh THE SAME PROTEIN COMPLEXED WITH METHIONINE
2aji THE SAME PROTEIN COMPLEXED WITH ISOLEUCINE