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(-) Description

Title :  CRYSTAL STRUCTURE OF B. LICHENIFORMIS CDPS YVMC-BLIC IN COMPLEX WITH CAPSO
 
Authors :  L. Bonnefond, T. Arai, T. Suzuki, R. Ishitani, O. Nureki
Date :  03 Sep 10  (Deposition) - 23 Feb 11  (Release) - 08 Jun 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Trna, Rossmann Fold, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Bonnefond, T. Arai, Y. Sakaguchi, T. Suzuki, R. Ishitani, O. Nureki
Structural Basis For Nonribosomal Peptide Synthesis By An Aminoacyl-Trna Synthetase Paralog.
Proc. Natl. Acad. Sci. Usa V. 108 3912 2011
PubMed-ID: 21325056  |  Reference-DOI: 10.1073/PNAS.1019480108

(-) Compounds

Molecule 1 - PUTATIVE UNCHARACTERIZED PROTEIN YVMC
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET22B
    Expression System Strain: BL21(DE3) ROSETTA2
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: BL00817, BLI03566, YVMC
    Organism Scientific: BACILLUS LICHENIFORMIS
    Organism Taxid: 279010
    Strain: ATCC 14580
    Synonym: YVMC

 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  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
13CX2Ligand/Ion(2S)-3-(CYCLOHEXYLAMINO)-2-HYDROXYPROPANE-1-SULFONICACID
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
13CX1Ligand/Ion(2S)-3-(CYCLOHEXYLAMINO)-2-HYDROXYPROPANE-1-SULFONICACID
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
13CX1Ligand/Ion(2S)-3-(CYCLOHEXYLAMINO)-2-HYDROXYPROPANE-1-SULFONICACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:35 , MET A:150 , TYR A:180 , GLU A:184 , TYR A:204 , ARG A:206 , HOH A:260 , HOH A:284BINDING SITE FOR RESIDUE 3CX A 258
2AC2SOFTWAREILE B:36 , ALA B:153 , ALA B:154 , TYR B:180 , GLU B:184 , TYR B:204 , ARG B:206 , HOH B:263 , HOH B:268 , HOH B:279 , HOH B:289BINDING SITE FOR RESIDUE 3CX B 258

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3OQJ)

(-) 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:213
 aligned with CDLS_BACLD | Q65EX3 from UniProtKB/Swiss-Prot  Length:249

    Alignment length:222
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232  
           CDLS_BACLD    13 FKTETLTQNCNEILKRRRHVLVGISPFNSRFSEDYIHRLIAWAVREFQSVSVLLAGKEAANLLEALGTPHGKAERKVRKEVSRNRRFAEKALEAHGGNPEDIHTFSDFANQTAYRNLRMEVEAAFFDQTHFRNACLEMSHAAILGRARGTRMDVVEVSADMLELAVEYVIAELPFFIAAPDILGVEETLLAYHRPWKLGEQISRNEFAVKMRPNQGYLMVSE 234
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeee.hhhhhhhhhhh.eeeeee.......hhhhhhhhhhhhhhhh.eeeeee...hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.---------...hhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee...hhhhhhhhh..........eeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3oqj A  13 FKTETLTQNCNEILKRRRHVLVGISPFNSRFSEDYIHRLIAWAVREFQSVSVLLAGKEAANLLEALGTPHGKAERKVRKEVSRNRRFAEKALEAHGGNPEDIHTFSDFANQTAYRNLRMEVEAAFFDQTHFRNACLEMSHAAILG---------VEVSADMLELAVEYVIAELPFFIAAPDILGVEETLLAYHRPWKLGEQISRNEFAVKMRPNQGYLMVSE 234
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152    |    -    |  172       182       192       202       212       222       232  
                                                                                                                                                                          157       167                                                                   


Chain B from PDB  Type:PROTEIN  Length:220
 aligned with CDLS_BACLD | Q65EX3 from UniProtKB/Swiss-Prot  Length:249

    Alignment length:222
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232  
           CDLS_BACLD    13 FKTETLTQNCNEILKRRRHVLVGISPFNSRFSEDYIHRLIAWAVREFQSVSVLLAGKEAANLLEALGTPHGKAERKVRKEVSRNRRFAEKALEAHGGNPEDIHTFSDFANQTAYRNLRMEVEAAFFDQTHFRNACLEMSHAAILGRARGTRMDVVEVSADMLELAVEYVIAELPFFIAAPDILGVEETLLAYHRPWKLGEQISRNEFAVKMRPNQGYLMVSE 234
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeee.hhhhhhhhhhh.eeeeee.......hhhhhhhhhhhhhhhh.eeeeee...hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.--.........hhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee...hhhhhhhhh..........eeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3oqj B  13 FKTETLTQNCNEILKRRRHVLVGISPFNSRFSEDYIHRLIAWAVREFQSVSVLLAGKEAANLLEALGTPHGKAERKVRKEVSRNRRFAEKALEAHGGNPEDIHTFSDFANQTAYRNLRMEVEAAFFDQTHFRNACLEMSHAAILGR--GTRMDVVEVSADMLELAVEYVIAELPFFIAAPDILGVEETLLAYHRPWKLGEQISRNEFAVKMRPNQGYLMVSE 234
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152     | 162       172       182       192       202       212       222       232  
                                                                                                                                                                           158  |                                                                         
                                                                                                                                                                              161
   Legend:   → Mismatch (orange background)
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  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 3OQJ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (CDLS_BACLD | Q65EX3)
molecular function
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0016755    transferase activity, transferring amino-acyl groups    Catalysis of the transfer of an amino-acyl group from one compound (donor) to another (acceptor).
biological process
    GO:0046148    pigment biosynthetic process    The chemical reactions and pathways resulting in the formation of a pigment, any general or particular coloring matter in living organisms, e.g. melanin.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CDLS_BACLD | Q65EX3: 3oqh 3oqi 3s7t

(-) Related Entries Specified in the PDB File

3oqh 3oqi