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(-) Description

Title :  CRYSTAL STRUCTURE OF CLASS II AARS HOMOLOGUE (BLL0957) COMPLEXED WITH COENZYME A
 
Authors :  I. Weygand-Durasevic, M. Luic, M. Mocibob, N. Ivic, D. Subasic
Date :  14 Dec 10  (Deposition) - 19 Oct 11  (Release) - 19 Oct 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Ligase, Amino Acid:[Carrier Protein] Ligase, Seryl-Trna Synthetase, Carrier Protein, Coenzyme A (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Mocibob, N. Ivic, D. Subasic, M. Luic, I. Weygand-Durasevic
Substrate Recognition By Novel Family Of Amino Acid:[Carrie Protein] Ligases
Croatica Chemica Acta V. 84 149 2011
PubMed: search  |  Reference-DOI: 10.5562/CCA1818
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - AMINO ACID--[ACYL-CARRIER-PROTEIN] LIGASE 1
    Chains: A, B
    EC Number: 6.2.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: BLL0957
    Glycine: [ACYL-CARRIER-PROTEIN] LIGASE 1
    Organism Scientific: BRADYRHIZOBIUM JAPONICUM
    Organism Taxid: 375

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 9)

Asymmetric/Biological Unit (5, 9)
No.NameCountTypeFull Name
1ACT3Ligand/IonACETATE ION
2COA1Ligand/IonCOENZYME A
3GAP1Ligand/IonGLYCYL-ADENOSINE-5'-PHOSPHATE
4GOL2Ligand/IonGLYCEROL
5ZN2Ligand/IonZINC ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:131 , GLU A:176 , CYS A:279 , GAP A:1001BINDING SITE FOR RESIDUE ZN A 1000
2AC2SOFTWAREARG A:159 , GLU A:161 , LEU A:169 , PHE A:172 , MET A:174 , GLU A:176 , LYS A:235 , ALA A:250 , CYS A:251 , MET A:252 , SER A:253 , CYS A:279 , GLY A:283 , ARG A:286 , HOH A:352 , HOH A:432 , HOH A:444 , HOH A:457 , ZN A:1000 , GOL A:1011BINDING SITE FOR RESIDUE GAP A 1001
3AC3SOFTWAREARG A:39 , GLU A:44 , ARG A:173 , ASP A:285BINDING SITE FOR RESIDUE GOL A 1010
4AC4SOFTWAREARG A:168 , PRO A:216 , GLU A:237 , ARG A:286 , HOH A:352 , HOH A:432 , HOH A:475 , GAP A:1001BINDING SITE FOR RESIDUE GOL A 1011
5AC5SOFTWARECYS B:131 , GLU B:176 , CYS B:279 , ACT B:1002BINDING SITE FOR RESIDUE ZN B 1000
6AC6SOFTWAREARG B:159 , GLU B:161 , ASP B:167 , ARG B:168 , LEU B:169 , PHE B:172 , MET B:174 , LYS B:235 , GLU B:237 , SER B:253 , ASN B:255 , ALA B:281 , ARG B:286 , HOH B:327 , HOH B:340 , HOH B:461 , HOH B:480 , HOH B:494 , ACT B:1002 , ACT B:1003BINDING SITE FOR RESIDUE COA B 1001
7AC7SOFTWARESER B:45 , HOH B:491BINDING SITE FOR RESIDUE ACT B 1004
8AC8SOFTWAREMET B:174 , ALA B:250 , CYS B:251 , MET B:252 , SER B:253 , ALA B:281 , GLY B:283 , COA B:1001BINDING SITE FOR RESIDUE ACT B 1003
9AC9SOFTWAREGLU B:176 , ASN B:255 , HIS B:257 , CYS B:279 , HOH B:327 , ZN B:1000 , COA B:1001BINDING SITE FOR RESIDUE ACT B 1002

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3PZC)

(-) 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
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306      
          AACL1_BRADU    17 ADPLDHLADKLFHSMGSDGVYARTALYESIVERLAALITSHREAGTEALRFPPVMSRAQLEKSGYLKSFPNLLGCVCGLHGTEREINAAVSRFDAGGDWTTSLSPADLVLSPAACYPVYPIAASRGPLPKGGLRFDVAADCFRREPSKHLDRLQSFRMREYVCIGTPDDVSDFRERWMVRAQAIARDLGLTFRVDYASDPFFGRVGQMKAVSQKQQQLKFELLIPLRSEEQPTACMSFNYHREHFGTTWGIQDANGEPAHTGCVAFGMDRLAVAMFHTHGTDLSAWPAKVRDILGL 312
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhheee......eeehhhhhhhhhhhhhhhhh.....eeeee...eeehhhhhhhhhhhhhhhhh.eeee...hhhhhhhhhhhhhh..hhhhhheeeeeee......hhhhhhhh........eeeeeeeeee............eeeeeeeeeeehhhhhhhhhhhhhhhhhhhhhhh....eeee.....hhhhhhhhhhhhhhh..eeeeee........eeeeeeee..hhhhhhhh.........eeeeeeeehhhhhhhhhhhhh.hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pzc A  17 ADPLDHLADKLFHSMGSDGVYARTALYESIVERLAALITSHREAGTEALRFPPVMSRAQLEKSGYLKSFPNLLGCVCGLHGTEREINAAVSRFDAGGDWTTSLSPADLVLSPAACYPVYPIAASRGPLPKGGLRFDVAADCFRREPSKHLDRLQSFRMREYVCIGTPDDVSDFRERWMVRAQAIARDLGLTFRVDYASDPFFGRVGQMKAVSQKQQQLKFELLIPLRSEEQPTACMSFNYHREHFGTTWGIQDANGEPAHTGCVAFGMDRLAVAMFHTHGTDLSAWPAKVRDILGL 312
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306      


Chain B from PDB  Type:PROTEIN  Length:276
 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..eeeeehhhhhhhhhhhhhhhhh....eeeee...eeehhhhhhhhhhhhhhhhheeeee...hhhhhhhhhhhhhh..hhhhhheeeeeee......hhhhhhhh........eeeeeeeeee............eeeeeeeeeeehhhhhhhhhhhhhhhhhhhhhhh....eee..--------------------..eeeee........eeeeeeee..hhhhhhhh.........eeeeeeeehhhhhhhhhhhhh.hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pzc B  18 DPLDHLADKLFHSMGSDGVYARTALYESIVERLAALITSHREAGTEALRFPPVMSRAQLEKSGYLKSFPNLLGCVCGLHGTEREINAAVSRFDAGGDWTTSLSPADLVLSPAACYPVYPIAASRGPLPKGGLRFDVAADCFRREPSKHLDRLQSFRMREYVCIGTPDDVSDFRERWMVRAQAIARDLGLTFRVDYA--------------------LKFELLIPLRSEEQPTACMSFNYHREHFGTTWGIQDANGEPAHTGCVAFGMDRLAVAMFHTHGTDLSAWPAKVRDILGLQ 313
                                    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      
                                                                                                                                                                                                                             213                  234
   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 3PZC)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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: 3mey 3mf1 3mf2 4h2s 4h2t 4h2u 4h2v 4h2w 4h2x 4h2y

(-) Related Entries Specified in the PDB File

2cja CRYSTAL STRUCTURE OF METHANOSARCINA BARKERI SERYL-TRNA SYNTHETASE COMPLEXED WITH ATP.
3mey THE SAME PROTEIN COMPLEXED WITH ATP.
3mf1 THE SAME PROTEIN COMPLEXED WITH AN ANALOGUE OF GLYCYL ADENYLATE.
3mf2 THE SAME PROTEIN COMPLEXED WITH AMP.