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(-) Description

Title :  CRYSTAL STRUCTURE OF ENGINEERED BRADYRHIZOBIUM JAPONICUM GLYCINE:[CARRIER PROTEIN] LIGASE COMPLEXED WITH CARRIER PROTEIN FROM AGROBACTERIUM TUMEFACIENS AND ATP
 
Authors :  M. Luic, I. Weygand-Durasevic, N. Ivic, M. Mocibob
Date :  13 Sep 12  (Deposition) - 06 Mar 13  (Release) - 29 May 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Ligase, Atp Binding, Glycine Binding, Carrier Protein, Aminoacyl-Trna Synthetase, Seryl-Trna Synthetase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Mocibob, N. Ivic, M. Luic, I. Weygand-Durasevic
Adaptation Of Aminoacyl-Trna Synthetase Catalytic Core To Carrier Protein Aminoacylation.
Structure V. 21 614 2013
PubMed-ID: 23541895  |  Reference-DOI: 10.1016/J.STR.2013.02.017
(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 Plasmid: PET28
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: BLL0957
    Organism Scientific: BRADYRHIZOBIUM JAPONICUM
    Organism Taxid: 224911
    Strain: USDA 110
    Synonym: AMINOACYL-[ACYL-CARRIER-PROTEIN] SYNTHETASE 1
 
Molecule 2 - AMINOACYL CARRIER PROTEIN
    Chains: C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: AGR_C_4658, ATU2571
    Organism Scientific: AGROBACTERIUM TUMEFACIENS
    Organism Taxid: 176299
    Strain: C58

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 7)

Asymmetric/Biological Unit (4, 7)
No.NameCountTypeFull Name
1ATP2Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2MG1Ligand/IonMAGNESIUM ION
3PNS2Ligand/Ion4'-PHOSPHOPANTETHEINE
4ZN2Ligand/IonZINC ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:131 , GLU A:176 , CYS A:279 , HOH A:626 , PNS D:101BINDING SITE FOR RESIDUE ZN A 401
2AC2SOFTWAREARG A:159 , ARG A:168 , LEU A:169 , PHE A:172 , MET A:174 , ASP A:215 , PRO A:216 , LYS A:235 , ALA A:250 , CYS A:251 , SER A:253 , GLY A:283 , ARG A:286 , MG A:403 , HOH A:509 , HOH A:563 , HOH A:629 , HOH A:648 , HOH A:650BINDING SITE FOR RESIDUE ATP A 402
3AC3SOFTWAREGLU A:237 , ALA A:250 , ATP A:402BINDING SITE FOR RESIDUE MG A 403
4AC4SOFTWARECYS B:131 , GLU B:176 , CYS B:279 , HOH B:676 , PNS C:101BINDING SITE FOR RESIDUE ZN B 401
5AC5SOFTWAREARG B:159 , GLU B:161 , ARG B:168 , LEU B:169 , PHE B:172 , MET B:174 , PRO B:216 , LYS B:235 , GLU B:237 , ALA B:250 , CYS B:251 , SER B:253 , GLY B:283 , ARG B:286 , HOH B:505 , HOH B:579 , HOH B:622 , HOH B:677BINDING SITE FOR RESIDUE ATP B 402
6AC6SOFTWARETYR B:132 , ASP B:215 , PHE B:217 , ASN B:228 , GLN B:232 , LEU B:234 , HIS B:257 , HIS B:260 , ZN B:401 , SER C:35BINDING SITE FOR RESIDUE PNS C 101
7AC7SOFTWARETYR A:132 , ASP A:215 , ASN A:228 , GLN A:232 , ASN A:255 , HIS A:257 , ZN A:401 , HOH A:590 , HOH A:626 , HOH A:648 , SER D:35 , PHE D:36BINDING SITE FOR RESIDUE PNS D 101

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4H2Y)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4H2Y)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4H2Y)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4H2Y)

(-) Exons   (0, 0)

(no "Exon" information available for 4H2Y)

(-) 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:295
                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhheee......eeeehhhhhhhhhhhhhhhhh....eeeee...eeehhhhhhhhhhhhhhhhheeeee...hhhhhhhhhhhhhhh.hhhhhheeeeeee......hhhhhhhh........eeeeeeeeee............eeeeeeeeeeehhhhhhhhhhhhhhhhhhhhhhh....eeee.....hhhhhhhhhhhhhhh..eeeeee........eeeeeeee..hhhhhhhh.........eeeeeeeehhhhhhhhhhhhh.hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4h2y A  18 DPLDHLADKLFHSMGSDGVYARTALYESIVERLAALITSHREAGTEALRFPPVMSRAQLEKSGYLKSFPNLLGCVCGLHGTEREINAAVSRFDAGGDWTTSLSPADLVLSPAACYPVYPIAASRGPLPKGGLRFDVAADCFRREPSKHLDRLQSFRMREYVCIGTPDDVSDFRERWMVRAQAIARDLGLTFRVDYASDPFFGRAGKMLANNQRDQQLKFELLIPLRSEEQPTACMSFNYHREHFGTTWGIQDANGEPAHTGCVAFGMDRLAVAMFHTHGTDLSAWPAKVRDILGL 312
                                    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:296
                                                                                                                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhheee......eeeehhhhhhhhhhhhhhhhh....eeeee...eeehhhhhhhhhhhhh.....eeee...hhhhhhhhhhhhhh..hhhhhheeeeeee......hhhhhhhh........eeeeeeeeee............eeeeeeeeeeehhhhhhhhhhhhhhhhhhhhhhh....eeee.....hhhhhhhhhhhhhhh..eeeeee........eeeeeeee..hhhhhhhh.........eeeeeeeehhhhhhhhhhhhh.hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4h2y B  17 ADPLDHLADKLFHSMGSDGVYARTALYESIVERLAALITSHREAGTEALRFPPVMSRAQLEKSGYLKSFPNLLGCVCGLHGTEREINAAVSRFDAGGDWTTSLSPADLVLSPAACYPVYPIAASRGPLPKGGLRFDVAADCFRREPSKHLDRLQSFRMREYVCIGTPDDVSDFRERWMVRAQAIARDLGLTFRVDYASDPFFGRAGKMLANNQRDQQLKFELLIPLRSEEQPTACMSFNYHREHFGTTWGIQDANGEPAHTGCVAFGMDRLAVAMFHTHGTDLSAWPAKVRDILGL 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 C from PDB  Type:PROTEIN  Length:77
                                                                                                             
               SCOP domains d4h2yc_ C: automated matches                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh.....hhhhh.....hhhhh.hhhhhhhhhhhhhhhh....hhhhh.hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------- Transcript
                 4h2y C   0 HMNATIREILAKFGQLPTPVDTIADEADLYAAGLSSFASVQLMLGIEEAFDIEFPDNLLNRKSFASIKAIEDTVKLI  76
                                     9        19        29        39        49        59        69       


Chain D from PDB  Type:PROTEIN  Length:63
                                                                                               
               SCOP domains d4h2yd_ D: automated matches                                    SCOP domains
               CATH domains --------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhh.........hhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------- Transcript
                 4h2y D   2 NATIREILAKFGQLPLYAAGLSSFASVQLMLGIEEAFDIEFPDNLLNRKSFASIKAIEDTVKL  75
                                    11    ||  32        42        52        62        72   
                                         16|                                               
                                          28
   Legend:   → Mismatch (orange background)
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    → 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  (1, 2)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4H2Y)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4H2Y)

(-) Gene Ontology  (7, 12)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        AACL1_BRADU | Q89VT8: 3mey 3mf1 3mf2 3pzc 4h2s 4h2t 4h2u 4h2v 4h2w 4h2x
        AACL_AGRFC | Q7CWR3: 4h2w 4h2x
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(-) Related Entries Specified in the PDB File

3mf2 THE SAME ENZYME BUT NOT COMPLEXED WITH COGNATE CARRIER PROTEIN
4h2s
4h2t
4h2u
4h2v
4h2w
4h2x