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(-) Description

Title :  CRYSTAL STRUCTURE OF CLASS II AARS HOMOLOGUE (BLL0957) COMPLEXED WITH ATP
 
Authors :  I. Weygand-Durasevic, M. Mocibob, N. Ivic, S. Bilokapic, T. Maier, M. L
Date :  01 Apr 10  (Deposition) - 28 Jul 10  (Release) - 13 Oct 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Aminoacyl-Trna Synthetase, Seryl-Trna Synthetase, Zinc Ion, Ligase, Amino Acid:[Carrier Protein] Ligase, Bll0957 (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Mocibob, N. Ivic, S. Bilokapic, T. Maier, M. Luic, N. Ban, I. Weygand-Durasevic
Homologs Of Aminoacyl-Trna Synthetases Acylate Carrier Proteins And Provide A Link Between Ribosomal And Nonribosomal Peptide Synthesis
Proc. Natl. Acad. Sci. Usa V. 107 14585 2010
PubMed-ID: 20663952  |  Reference-DOI: 10.1073/PNAS.1007470107
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BLL0957 PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: BLL0957
    Organism Scientific: BRADYRHIZOBIUM JAPONICUM
    Organism Taxid: 224911
    Strain: USDA110
    Synonym: CLASS II AARS HOMOLOGUE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1ATP2Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2MG2Ligand/IonMAGNESIUM ION
3ZN2Ligand/IonZINC ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:131 , GLU A:176 , CYS A:279 , HOH A:401BINDING SITE FOR RESIDUE ZN A 1000
2AC2SOFTWARELEU A:88 , ARG A:159 , PRO A:216 , HOH A:395 , ATP A:1010BINDING SITE FOR RESIDUE MG A 1001
3AC3SOFTWAREARG A:159 , GLU A:161 , ASP A:167 , ARG A:168 , LEU A:169 , PHE A:172 , MET A:174 , PRO A:216 , LYS A:235 , GLU A:237 , ALA A:250 , CYS A:251 , SER A:253 , ALA A:281 , GLY A:283 , ARG A:286 , HOH A:332 , HOH A:378 , HOH A:395 , HOH A:403 , MG A:1001BINDING SITE FOR RESIDUE ATP A 1010
4AC4SOFTWARECYS B:131 , GLU B:176 , CYS B:279 , HOH B:343 , HOH B:393BINDING SITE FOR RESIDUE ZN B 1000
5AC5SOFTWAREARG B:159 , HOH B:382 , HOH B:394 , HOH B:395 , HOH B:396 , ATP B:1010BINDING SITE FOR RESIDUE MG B 1001
6AC6SOFTWAREARG B:159 , GLU B:161 , ARG B:168 , LEU B:169 , PHE B:172 , MET B:174 , LYS B:235 , GLU B:237 , ALA B:250 , CYS B:251 , MET B:252 , SER B:253 , ASN B:255 , ALA B:281 , GLY B:283 , ARG B:286 , HOH B:344 , HOH B:348 , HOH B:358 , HOH B:381 , HOH B:382 , HOH B:394 , HOH B:395 , HOH B:396 , MG B:1001BINDING SITE FOR RESIDUE ATP B 1010

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:93 -B:93

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3MEY)

(-) 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:296
 aligned with AACL1_BRADU | Q89VT8 from UniProtKB/Swiss-Prot  Length:326

    Alignment length:296
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307      
          AACL1_BRADU    18 DPLDHLADKLFHSMGSDGVYARTALYESIVERLAALITSHREAGTEALRFPPVMSRAQLEKSGYLKSFPNLLGCVCGLHGTEREINAAVSRFDAGGDWTTSLSPADLVLSPAACYPVYPIAASRGPLPKGGLRFDVAADCFRREPSKHLDRLQSFRMREYVCIGTPDDVSDFRERWMVRAQAIARDLGLTFRVDYASDPFFGRVGQMKAVSQKQQQLKFELLIPLRSEEQPTACMSFNYHREHFGTTWGIQDANGEPAHTGCVAFGMDRLAVAMFHTHGTDLSAWPAKVRDILGLQ 313
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhheeeeee..eeeehhhhhhhhhhhhhhhhh.....eeeee...eeehhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhh..hhhhhheeeeeee......hhhhhhhh........eeeeeeeeee............eeeeeeeeeeehhhhhhhhhhhhhhhhhhhhhhh....eeee.....hhhhhhhhhhhhhhhh.eeeeee........eeeeeeeeeehhhhhhhh.........eeeeeeeehhhhhhhhhhhhh.hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mey A  18 DPLDHLADKLFHSMGSDGVYARTALYESIVERLAALITSHREAGTEALRFPPVMSRAQLEKSGYLKSFPNLLGCVCGLHGTEREINAAVSRFDAGGDWTTSLSPADLVLSPAACYPVYPIAASRGPLPKGGLRFDVAADCFRREPSKHLDRLQSFRMREYVCIGTPDDVSDFRERWMVRAQAIARDLGLTFRVDYASDPFFGRVGQMKAVSQKQQQLKFELLIPLRSEEQPTACMSFNYHREHFGTTWGIQDANGEPAHTGCVAFGMDRLAVAMFHTHGTDLSAWPAKVRDILGLQ 313
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307      


Chain B from PDB  Type:PROTEIN  Length:274
 aligned with AACL1_BRADU | Q89VT8 from UniProtKB/Swiss-Prot  Length:326

    Alignment length:295
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307     
          AACL1_BRADU    18 DPLDHLADKLFHSMGSDGVYARTALYESIVERLAALITSHREAGTEALRFPPVMSRAQLEKSGYLKSFPNLLGCVCGLHGTEREINAAVSRFDAGGDWTTSLSPADLVLSPAACYPVYPIAASRGPLPKGGLRFDVAADCFRREPSKHLDRLQSFRMREYVCIGTPDDVSDFRERWMVRAQAIARDLGLTFRVDYASDPFFGRVGQMKAVSQKQQQLKFELLIPLRSEEQPTACMSFNYHREHFGTTWGIQDANGEPAHTGCVAFGMDRLAVAMFHTHGTDLSAWPAKVRDILGL 312
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhheeeeee..eeeehhhhhhhhhhhhhhhhhh....eeeee...eeehhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhh..hhhhhheeeeeee......hhhhhhhh........eeeeeeeeee............eeeeeeeeeeehhhhhhhhhhhhhhhhhhhhhhh....eee.---------------------.eeeeee........eeeeeeee..hhhhhhhh.........eeeeeeeehhhhhhhhhhhhh.hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mey B  18 DPLDHLADKLFHSMGSDGVYARTALYESIVERLAALITSHREAGTEALRFPPVMSRAQLEKSGYLKSFPNLLGCVCGLHGTEREINAAVSRFDAGGDWTTSLSPADLVLSPAACYPVYPIAASRGPLPKGGLRFDVAADCFRREPSKHLDRLQSFRMREYVCIGTPDDVSDFRERWMVRAQAIARDLGLTFRVDY---------------------LKFELLIPLRSEEQPTACMSFNYHREHFGTTWGIQDANGEPAHTGCVAFGMDRLAVAMFHTHGTDLSAWPAKVRDILGL 312
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207    |    -         -      |237       247       257       267       277       287       297       307     
                                                                                                                                                                                                                            212                   234
   Legend:   → Mismatch (orange background)
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  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 3MEY)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (AACL1_BRADU | Q89VT8)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016878    acid-thiol ligase activity    Catalysis of the joining of an acid and a thiol via a carbon-sulfur bond, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
    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: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: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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        AACL1_BRADU | Q89VT8: 3mf1 3mf2 3pzc 4h2s 4h2t 4h2u 4h2v 4h2w 4h2x 4h2y

(-) Related Entries Specified in the PDB File

3mf1 3mf2