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(-) Description

Title :  CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS DECAPRENYL DIPHOSPHATE SYNTHASE IN COMPLEX WITH BPH-640
 
Authors :  X. Feng, H. C. Chan, T. P. Ko
Date :  28 Jan 14  (Deposition) - 02 Apr 14  (Release) - 02 Apr 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.83
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Polyprenyl Transferase, Decaprenyl Diphosphate Synthase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. C. Chan, X. Feng, T. P. Ko, C. H. Huang, Y. Hu, Y. Zheng, S. Bogue, C. Nakano, T. Hoshino, L. Zhang, P. Lv, W. Liu, D. C. Crick, P. H. Liang, A. H. Wang, E. Oldfield, R. T. Guo
Structure And Inhibition Of Tuberculosinol Synthase And Decaprenyl Diphosphate Synthase From Mycobacterium Tuberculosis
J. Am. Chem. Soc. V. 136 2892 2014
PubMed-ID: 24475925  |  Reference-DOI: 10.1021/JA413127V

(-) Compounds

Molecule 1 - DECAPRENYL DIPHOSPHATE SYNTHASE
    Chains: A, B
    EC Number: 2.5.1.86, 2.5.1.87
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 13-296
    Gene: RV2361C
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 1773
    Synonym: DECAPP, DECAPRENYL PYROPHOSPHATE SYNTHASE, LONG-CHAIN ISOPRENYL DIPHOSPHATE SYNTHASE, TRANS,POLYCIS-DECAPRENYL DIPHOSPHATE SYNTHASE

 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
140B2Ligand/Ion[HYDROXY(1,1':3',1''-TERPHENYL-3-YL)METHANEDIYL]BIS(PHOSPHONIC ACID)

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:77 , GLY A:79 , ARG A:80 , THR A:83 , ARG A:89 , ARG A:127 , HOH A:679 , HOH A:809 , ARG B:144 , ASN B:172 , GLU B:173 , VAL B:176 , ARG B:292 , PHE B:293BINDING SITE FOR RESIDUE 40B A 500
2AC2SOFTWAREGLY B:77 , ASN B:78 , GLY B:79 , ARG B:80 , ARG B:89 , ASN B:124 , ARG B:127 , HOH B:722 , HOH B:781 , HOH B:804 , HOH B:810BINDING SITE FOR RESIDUE 40B B 500

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Phe A:26 -Pro A:27
2Trp A:32 -Pro A:33
3Phe B:26 -Pro B:27
4Trp B:32 -Pro B:33
5Ala B:42 -Pro B:43

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4ONC)

(-) 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:277
                                                                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............ee......................ee.........hhhhh..eeeee..hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheeeeee......hhhhhhhhhhhhhhhh....eeeeeeeeehhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh.........eeee..................eeee...hhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4onc A  13 FPQLPPAPDDYPTFPDTSTWPVVFPELPAAGPCRPPQHTSKAAAPRIPADRLPNHVAIVMDGNGRWATQRGLARTEGHKMGEAVVIDIACGAIELGIKWLSLYAFSTENWKRSPEEVRFLMGFNRDVVRRRRDTLKKLGVRIRWVGSRPRLWRSVINELAVAEEMTKSNDVITINYCVNYGGRTEITEATREIAREVAAGRLNPERITESTIARHLQRPDIPDVDLFLRTSGEQRSSNFMLWQAAYAEYIFQDKLWPDYDRRDLWAACEEYASRTRR 292
                                    22        32        42|       55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       
                                                        42|                                                                                                                                                                                                                                                      
                                                         46                                                                                                                                                                                                                                                      


Chain B from PDB  Type:PROTEIN  Length:282
                                                                                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ............ee.......................ee.........hhhhh..eeeee..hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee......hhhhhhhhhhhhhhhh....eeeeeeeeehhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh.........eeee..................eeee...hhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4onc B  13 FPQLPPAPDDYPTFPDTSTWPVVFPELPAAPGPCRPPQHTSKAAAPRIPADRLPNHVAIVMDGNGRWATQRGLARTEGHKMGEAVVIDIACGAIELGIKWLSLYAFSTENWKRSPEEVRFLMGFNRDVVRRRRDTLKKLGVRIRWVGSRPRLWRSVINELAVAEEMTKSNDVITINYCVNYGGRTEITEATREIAREVAAGRLNPERITESTIARHLQRPDIPDVDLFLRTSGEQRSSNFMLWQAAYAEYIFQDKLWPDYDRRDLWAACEEYASRTRRFGSA 296
                                    22        32        42||      54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294  
                                                         43|                                                                                                                                                                                                                                                          
                                                          46
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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 4ONC)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (14, 21)

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
        DPDS_MYCTO | P9WFF6: 2vg2 2vg3 2vg4
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(-) Related Entries Specified in the PDB File

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