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(-) Description

Title :  CRYSTAL STRUCTURE OF NTDA FROM BACILLUS SUBTILIS IN COMPLEX WITH THE INTERNAL ALDIMINE
 
Authors :  K. E. Van Straaten, D. R. J. Palmer, D. A. R. Sanders
Date :  08 Apr 13  (Deposition) - 16 Oct 13  (Release) - 01 Jan 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.31
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Sugar Aminotransferase, Aspertate Aminotransferase Fold, Homo-Dimer, Additional N-Terninal Domain, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. E. Van Straaten, J. B. Ko, R. Jagdhane, S. Anjum, D. R. Palmer, D. A. Sanders
The Structure Of Ntda, A Sugar Aminotransferase Involved In The Kanosamine Biosynthetic Pathway In Bacillus Subtilis, Reveals A New Subclass Of Aminotransferases.
J. Biol. Chem. V. 288 34121 2013
PubMed-ID: 24097983  |  Reference-DOI: 10.1074/JBC.M113.500637

(-) Compounds

Molecule 1 - NTD BIOSYNTHESIS OPERON PROTEIN NTDA
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28B
    Expression System Strain: BL21-GOLD (DE3)
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: 939788, BSU10550, NP_388936.1, NTDA, YHJL
    Organism Scientific: BACILLUS SUBTILIS SUBSP. SUBTILIS
    Organism Taxid: 224308
    Strain: 168

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1LLP2Mod. Amino Acid2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)

(-) Sites  (0, 0)

(no "Site" information available for 4K2B)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4K2B)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Tyr A:378 -Tyr A:379
2Tyr B:378 -Tyr B:379

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4K2B)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4K2B)

(-) Exons   (0, 0)

(no "Exon" information available for 4K2B)

(-) 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:437
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..hhhhhhhhhhhhh......eeee..hhhhhhhhhh.....hhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhh......eeee.....hhhhhhhhhh..eeee..........hhhhhhhhh...eeee...hhhhh..hhhhhhhhhhhhh.eeeee...............eeeee.............eeeee.hhhhhhhhhhhhh..ee..eeeee..........hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh................eeee.hhhhhhhhhhhhhhhhh.........hhhhh.hhhhhhhh....hhhhhhhhhheeee......hhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4k2b A   3 KQVKISGKSKENMSLLKHLKGDVQGKELVIEDSIVNERWKQVLKEKIDIEHDLFNYQKNREISKVPFLPVDRLITNDEVEDILNTLTEVLPTGKFTSGPYLEQFEKVLSTYLHKRYVIATSSGTDAIMIGLLALGLNPGDEVIMPANSFSATENAVLASGGVPIYVDINPQTFCIDPDKIEEAITPYTKFILPVHLYGKHSDMQHIRQIANRYKLKVIEDACQGIGLTDLGKYADITTLSFNPYkNFGVCGKAGAIATDNEELAKKCIQFSYHGFEVNVKNKKVINFGFNSKMDNLQAAIGLERMKYLSLNNFKRLFLADRYITQLAELQNKGYIELPELSEDHVWHLFPIKVRTEDRADIMTKLNEDFGVQTDVYYPILSHMQKTPLVQDKYAGLQLVHTEKAHSQVLHLPLYPSFTLEEQDRVMEGLFHVIKQEI 439
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242    |  252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       
                                                                                                                                                                                                                                                                              247-LLP                                                                                                                                                                                            


Chain B from PDB  Type:PROTEIN  Length:439
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee..hhhhhhhhhhhh........eee..hhhhhhhhhhh....hhhhhh...............hhhhh.hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhh......eeee.....hhhhhhhhhh..eeee..........hhhhhhhhh...eeee...hhhhh..hhhhhhhhhhhh..eeeee...............eeeee.............eeeee.hhhhhhhhhhhhh..ee..eeeee..........hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh................eeee....hhhhhhhhhhhhhh.........hhhhh.hhhhhhhh....hhhhhhhhhheeee......hhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4k2b B   1 MQKQVKISGKSKENMSLLKHLKGDVQGKELVIEDSIVNERWKQVLKEKIDIEHDLFNYQKNREISKVPFLPVDRLITNDEVEDILNTLTEVLPTGKFTSGPYLEQFEKVLSTYLHKRYVIATSSGTDAIMIGLLALGLNPGDEVIMPANSFSATENAVLASGGVPIYVDINPQTFCIDPDKIEEAITPYTKFILPVHLYGKHSDMQHIRQIANRYKLKVIEDACQGIGLTDLGKYADITTLSFNPYkNFGVCGKAGAIATDNEELAKKCIQFSYHGFEVNVKNKKVINFGFNSKMDNLQAAIGLERMKYLSLNNFKRLFLADRYITQLAELQNKGYIELPELSEDHVWHLFPIKVRTEDRADIMTKLNEDFGVQTDVYYPILSHMQKTPLVQDKYAGLQLVHTEKAHSQVLHLPLYPSFTLEEQDRVMEGLFHVIKQEI 439
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240      |250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430         
                                                                                                                                                                                                                                                                                247-LLP
   Legend:   → Mismatch (orange background)
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  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 4K2B)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4K2B)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4K2B)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Tyr A:378 - Tyr A:379   [ RasMol ]  
    Tyr B:378 - Tyr B:379   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        NTDA_BACSU | O07566: 4k2i 4k2m

(-) Related Entries Specified in the PDB File

4k2i 4k2m