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(-) Description

Title :  CRYSTAL STRUCTURE OF THE WILD TYPE CP1 HYDROLITIC DOMAIN FROM AQUIFEX AEOLICUS LEUCYL-TRNA
 
Authors :  V. Cura, N. Olieric, E. -D. Wang, D. Moras, G. Eriani, J. Cavarelli
Date :  19 Jul 10  (Deposition) - 17 Nov 10  (Release) - 17 Nov 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.77
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Aquifex Aeolicus, Leucyl-Trna Synthetase, Cp1 Hydrolytic Domain, Ligase, Aminoacyl-Trna Synthetase, Atp-Binding, Nucleotide-Binding, Protein Biosynthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. Cura, N. Olieric, A. Guichard, E. -D. Wang, D. Moras, G. Eriani, J. Cavarelli
Crystal Structure Of The Wild Type And Two Mutants Of The Cp1 Hydrolytic Domain From Aquifex Aeolicus Leucyl-Trna Synthetase
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - LEUCYL-TRNA SYNTHETASE SUBUNIT ALPHA
    Chains: A, B
    EC Number: 6.1.1.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11C
    Expression System Strain: ROSETTA DE3
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: HYDROLYTIC DOMAIN (UNP RESIDUES 225-443)
    Gene: LEUS, AQ_351
    Organism Scientific: AQUIFEX AEOLICUS
    Organism Taxid: 63363
    Synonym: LEUCINE--TRNA LIGASE SUBUNIT ALPHA, 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 3O0A)

(-) Sites  (0, 0)

(no "Site" information available for 3O0A)

(-) SS Bonds  (3, 3)

Asymmetric Unit
No.Residues
1A:247 -A:294
2A:303 -B:303
3B:247 -B:294

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3O0A)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3O0A)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3O0A)

(-) Exons   (0, 0)

(no "Exon" information available for 3O0A)

(-) 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:211
 aligned with SYLA_AQUAE | O66680 from UniProtKB/Swiss-Prot  Length:634

    Alignment length:211
                                   237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437 
           SYLA_AQUAE   228 EGALIRFYVEIEEPEKFLNCVPEELKETLLKEKRIYIDVFTTRPDTVFGATFVVLAPEHPLVPVLACIGERLGNACYSDVENFVEKMKKMSTRERTMEEDKEGVFLGVYATNPANGEKIPVWSANYVLYEYGTGAIMCVPAHDQRDWEFAKKYDLPIKVVVKPEGAWDFEKGAYEGKGTLVNSDGFDGLDSETAKRKITEWLQDRGLGEKK 438
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee..hhhhhhhhhhhhhhhhhhhhheeeeeeee.hhhhhhhh.eeee....hhhhhhhhhhhhh...hhhhhhhhhhhhhh.hhhhhhh.....eeeeeeeee......eeeeeee..........eeee....hhhhhhhhhhhh......ee................ee..hhhhh..hhhhhhhhhhhhhhhh..eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3o0a A 228 EGALIRFYVEIEEPEKFLNCVPEELKETLLKEKRIYIDVFTTRPDTVFGATFVVLAPEHPLVPVLACIGERLGNACYSDVENFVEKMKKMSTRERTMEEDKEGVFLGVYATNPANGEKIPVWSANYVLYEYGTGAIMCVPAHDQRDWEFAKKYDLPIKVVVKPEGAWDFEKGAYEGKGTLVNSDGFDGLDSETAKRKITEWLQDRGLGEKK 438
                                   237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437 


Chain B from PDB  Type:PROTEIN  Length:214
 aligned with SYLA_AQUAE | O66680 from UniProtKB/Swiss-Prot  Length:634

    Alignment length:214
                                   237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437    
           SYLA_AQUAE   228 EGALIRFYVEIEEPEKFLNCVPEELKETLLKEKRIYIDVFTTRPDTVFGATFVVLAPEHPLVPVLACIGERLGNACYSDVENFVEKMKKMSTRERTMEEDKEGVFLGVYATNPANGEKIPVWSANYVLYEYGTGAIMCVPAHDQRDWEFAKKYDLPIKVVVKPEGAWDFEKGAYEGKGTLVNSDGFDGLDSETAKRKITEWLQDRGLGEKKVSY 441
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) tRNA-synt_1_2-3o0aB02 B:228-430                                                                                                                                                                            --------tRN Pfam domains (1)
           Pfam domains (2) tRNA-synt_1_2-3o0aB03 B:228-430                                                                                                                                                                            ----------- Pfam domains (2)
         Sec.struct. author .eeeeeeeee..hhhhhhhhhhhhhhhhhhhhheeeeeeee.hhhhhhhh.eeee....hhhhhhhhhhhhh...hhhhhhhhhhhhhh.hhhhhhh.....eeeeeeeee......eeeeeee..........eeee....hhhhhhhhhhhh......ee................ee..hhhhh..hhhhhhhhhhhhhhhh..eeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3o0a B 228 EGALIRFYVEIEEPEKFLNCVPEELKETLLKEKRIYIDVFTTRPDTVFGATFVVLAPEHPLVPVLACIGERLGNACYSDVENFVEKMKKMSTRERTMEEDKEGVFLGVYATNPANGEKIPVWSANYVLYEYGTGAIMCVPAHDQRDWEFAKKYDLPIKVVVKPEGAWDFEKGAYEGKGTLVNSDGFDGLDSETAKRKITEWLQDRGLGEKKVSY 441
                                   237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437
   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 3O0A)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3O0A)

(-) Pfam Domains  (2, 3)

Asymmetric Unit
(-)
Clan: HUP (230)

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (SYLA_AQUAE | O66680)
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
        SYLA_AQUAE | O66680: 3pz0 3pz5

(-) Related Entries Specified in the PDB File

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