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(-) Description

Title :  CRYSTAL STRUCTURE OF BRADYRHIZOBIUM JAPONICUM GLYCINE:[CARRIER PROTEIN] LIGASE COMPLEXED WITH COGNATE CARRIER PROTEIN AND AN ANALOGUE OF GLYCYL ADENYLATE
 
Authors :  M. Luic, I. Weygand-Durasevic, N. Ivic, M. Mocibob
Date :  13 Sep 12  (Deposition) - 06 Mar 13  (Release) - 19 Jun 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.44
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
    Glycine: [ACYL-CARRIER-PROTEIN] LIGASE 1
    Organism Scientific: BRADYRHIZOBIUM JAPONICUM
    Organism Taxid: 224911
    Strain: USDA 110
 
Molecule 2 - AMINOACYL CARRIER PROTEIN 1
    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: BSR0959
    Organism Scientific: BRADYRHIZOBIUM JAPONICUM
    Organism Taxid: 224911
    Strain: USDA 110

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 8)

Asymmetric/Biological Unit (4, 8)
No.NameCountTypeFull Name
1G5A2Ligand/Ion5'-O-(GLYCYLSULFAMOYL)ADENOSINE
2PNS2Ligand/Ion4'-PHOSPHOPANTETHEINE
3SO42Ligand/IonSULFATE ION
4ZN2Ligand/IonZINC ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:131 , GLU A:176 , CYS A:279 , G5A A:1001BINDING SITE FOR RESIDUE ZN A 1000
2AC2SOFTWAREALA A:129 , CYS A:131 , ARG 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 , ASN A:255 , CYS A:279 , ALA A:281 , GLY A:283 , ARG A:286 , ZN A:1000 , HOH A:1116 , HOH A:1155 , PNS C:1000BINDING SITE FOR RESIDUE G5A A 1001
3AC3SOFTWARECYS B:131 , GLU B:176 , CYS B:279 , G5A B:402BINDING SITE FOR RESIDUE ZN B 401
4AC4SOFTWARECYS B:131 , ARG B:159 , GLU B:161 , LEU B:169 , PHE B:172 , MET B:174 , GLU B:176 , LYS B:235 , ALA B:250 , CYS B:251 , MET B:252 , SER B:253 , ASN B:255 , CYS B:279 , GLY B:283 , ARG B:286 , ZN B:401 , HOH B:520 , HOH B:540 , PNS D:1000BINDING SITE FOR RESIDUE G5A B 402
5AC5SOFTWAREPRO A:303 , SER B:118 , HOH B:503 , HOH B:504 , HOH B:561 , HOH B:563 , HOH B:593BINDING SITE FOR RESIDUE SO4 B 403
6AC6SOFTWAREARG B:66 , HOH B:542BINDING SITE FOR RESIDUE SO4 B 404
7AC7SOFTWARETYR A:132 , ASP A:215 , PHE A:217 , GLN A:229 , HIS A:257 , HIS A:260 , G5A A:1001 , THR C:41 , SER C:42BINDING SITE FOR RESIDUE PNS C 1000
8AC8SOFTWARETYR B:132 , ASP B:215 , PHE B:217 , GLN B:229 , GLN B:232 , HIS B:257 , ARG B:258 , HIS B:260 , G5A B:402 , HOH B:595 , SER D:42BINDING SITE FOR RESIDUE PNS D 1000

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4H2T)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4H2T)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4H2T)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4H2T)

(-) Exons   (0, 0)

(no "Exon" information available for 4H2T)

(-) 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 ..hhhhhhhheeeeee..eeeeehhhhhhhhhhhhhhhhh....eeeee...eeehhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhh..hhhhhheeeeeee......hhhhhhhh........eeeeeeeeee............eeeeeeeeeeehhhhhhhhhhhhhhhhhhhhhhh....eeee.....hhhhhhhhhhhhhhh..eeeeee........eeeeeeee..hhhhhhhh.........eeeeeeeehhhhhhhhhhhhh.hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4h2t A  18 DPLDHLADKLFHSMGSDGVYARTALYESIVERLAALITSHREAGTEALRFPPVMSRAQLEKSGYLKSFPNLLGCVCGLHGTEREINAAVSRFDAGGDWTTSLSPADLVLSPAACYPVYPIAASRGPLPKGGLRFDVAADCFRREPSKHLDRLQSFRMREYVCIGTPDDVSDFRERWMVRAQAIARDLGLTFRVDYASDPFFGRVGQMKAVSQKQQQLKFELLIPLRSEEQPTACMSFNYHREHFGTTWGIQDANGEPAHTGCVAFGMDRLAVAMFHTHGTDLSAWPAKVRDILGL 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.....eeee...eeehhhhhhhhhhhhh....eeeeee..hhhhhhhhhhhhhh..hhhh.eeeeeeee......hhhhhhhh........eeeeeeeeee............eeeeeeeeeeehhhhhhhhhhhhhhhhhhhhhhh....eeee.....hhhhhhhhhhhhhhhh.eeeeee........eeeeeeee..hhhhhhhh.........eeeeeeeehhhhhhhhhhhhh.hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4h2t B  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 C from PDB  Type:PROTEIN  Length:22
                                                      
               SCOP domains ---------------------- SCOP domains
               CATH domains ---------------------- CATH domains
               Pfam domains ---------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------- SAPs(SNPs)
                    PROSITE ---------------------- PROSITE
                 Transcript ---------------------- Transcript
                 4h2t C  35 LVDVGLTSMDMVNLMLGVEAEF  56
                                    44        54  


Chain D from PDB  Type:PROTEIN  Length:77
                                                                                                             
               SCOP domains ----------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh...........hhhhhh.hhhhhhhhhhhhhhhh.........hhhhhh....hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------- Transcript
                 4h2t D   7 DVRNRIIKLVKGILEQNALAADVTPQAKLVDVGLTSMDMVNLMLGVEAEFDFTIPQSEITPENFQSVETLERMVMTQ  83
                                    16        26        36        46        56        66        76
   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  (0, 0)

(no "SCOP Domain" information available for 4H2T)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4H2T)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4H2T)

(-) Gene Ontology  (7, 7)

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 4h2u 4h2v 4h2w 4h2x 4h2y
        AACP1_BRADU | Q89VT6: 4h2s 4h2u 4h2v

(-) Related Entries Specified in the PDB File

3mf2 THE SAME ENZYME BUT NOT COMPLEXED WITH COGNATE CARRIER PROTEIN
4h2s
4h2u
4h2v
4h2w
4h2x
4h2y