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(-) Description

Title :  CRYSTAL STRUCTURE OF SEMET B. LICHENIFORMIS CDPS YVMC-BLIC
 
Authors :  L. Bonnefond, R. Ishitani, O. Nureki
Date :  26 May 11  (Deposition) - 22 Jun 11  (Release) - 22 Jun 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.81
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Rossmann Fold, Ligase, Trna, Cyclodipeptide (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, 11)

Asymmetric Unit (1, 11)
No.NameCountTypeFull Name
1MSE11Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 5)
No.NameCountTypeFull Name
1MSE5Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 6)
No.NameCountTypeFull Name
1MSE6Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 3S7T)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3S7T)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3S7T)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3S7T)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3S7T)

(-) Exons   (0, 0)

(no "Exon" information available for 3S7T)

(-) 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:214
 aligned with CDLS_BACLD | Q65EX3 from UniProtKB/Swiss-Prot  Length:249

    Alignment length:224
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231    
           CDLS_BACLD    12 LFKTETLTQNCNEILKRRRHVLVGISPFNSRFSEDYIHRLIAWAVREFQSVSVLLAGKEAANLLEALGTPHGKAERKVRKEVSRNRRFAEKALEAHGGNPEDIHTFSDFANQTAYRNLRMEVEAAFFDQTHFRNACLEMSHAAILGRARGTRMDVVEVSADMLELAVEYVIAELPFFIAAPDILGVEETLLAYHRPWKLGEQISRNEFAVKMRPNQGYLMVSEA 235
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.hhhhhhhhhhh.eeeee........hhhhhhhhhhhhhhhh.eeeeee...hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh----------...hhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee...hhhhhhhhh..........eeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3s7t A  12 LFKTETLTQNCNEILKRRRHVLVGISPFNSRFSEDYIHRLIAWAVREFQSVSVLLAGKEAANLLEALGTPHGKAERKVRKEVSRNRRFAEKALEAHGGNPEDIHTFSDFANQTAYRNLRmEVEAAFFDQTHFRNACLEmSHAAIL----------VEVSADmLELAVEYVIAELPFFIAAPDILGVEETLLAYHRPWKLGEQISRNEFAVKmRPNQGYLmVSEA 235
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151    |    -     | 171 |     181       191       201       211       221 |     231    
                                                                                                                                                 131-MSE            150-MSE56        167     |                                               223-MSE 231-MSE
                                                                                                                                                                                           173-MSE                                                          


Chain B from PDB  Type:PROTEIN  Length:223
 aligned with CDLS_BACLD | Q65EX3 from UniProtKB/Swiss-Prot  Length:249

    Alignment length:223
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231   
           CDLS_BACLD    12 LFKTETLTQNCNEILKRRRHVLVGISPFNSRFSEDYIHRLIAWAVREFQSVSVLLAGKEAANLLEALGTPHGKAERKVRKEVSRNRRFAEKALEAHGGNPEDIHTFSDFANQTAYRNLRMEVEAAFFDQTHFRNACLEMSHAAILGRARGTRMDVVEVSADMLELAVEYVIAELPFFIAAPDILGVEETLLAYHRPWKLGEQISRNEFAVKMRPNQGYLMVSE 234
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee.hhhhhhhhhhh.eeeee........hhhhhhhhhhhhhhhh.eeeeee...hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhh.eee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee...hhhhhhhhh..........eeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3s7t B  12 LFKTETLTQNCNEILKRRRHVLVGISPFNSRFSEDYIHRLIAWAVREFQSVSVLLAGKEAANLLEALGTPHGKAERKVRKEVSRNRRFAEKALEAHGGNPEDIHTFSDFANQTAYRNLRmEVEAAFFDQTHFRNACLEmSHAAILGRARGTRmDVVEVSADmLELAVEYVIAELPFFIAAPDILGVEETLLAYHRPWKLGEQISRNEFAVKmRPNQGYLmVSE 234
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161  |    171 |     181       191       201       211       221 |     231   
                                                                                                                                                 131-MSE            150-MSE       164-MSE  173-MSE                                           223-MSE 231-MSE
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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 3S7T)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3S7T)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3S7T)

(-) 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 3oqj

(-) Related Entries Specified in the PDB File

3oqh THE SAME PROTEIN STRUCTURE SOLVED BY MOLECULAR REPLACEMENT.
3oqi THE SAME PROTEIN COMPLEXED WITH CHES.
3oqj THE SAME PROTEIN COMPLEXED WITH CAPSO.