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(-) Description

Title :  CRYSTAL STRUCTURE OF RV3378C
 
Authors :  E. Layre, H. J. Lee, D. C. Young, A. J. Martinot, J. Buter, A. J. Minnaard, J. W. Annand, S. M. Fortune, B. B. Snider, I. Matsunaga, E. J. Rubin, T. A D. B. Moody
Date :  18 Jan 14  (Deposition) - 19 Feb 14  (Release) - 12 Mar 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.31
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Hydrolase, Nuclear Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Layre, H. J. Lee, D. C. Young, A. Jezek Martinot, J. Buter, A. J. Minnaard, J. W. Annand, S. M. Fortune, B. B. Snider, I. Matsunaga, E. J. Rubin, T. Alber, D. B. Moody
Molecular Profiling Of Mycobacterium Tuberculosis Identifies Tuberculosinyl Nucleoside Products Of The Virulence-Associated Enzyme Rv3378C.
Proc. Natl. Acad. Sci. Usa V. 111 2978 2014
PubMed-ID: 24516143  |  Reference-DOI: 10.1073/PNAS.1315883111

(-) Compounds

Molecule 1 - DITERPENE SYNTHASE
    Chains: A, B
    EC Number: 3.1.7.9, 3.1.7.8
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 83332
    Strain: H37RV
    Synonym: ISOTUBERCULOSINOL SYNTHASE, NOSYBERKOL SYNTHASE, TUBERCULOSINOL SYNTHASE, RV3378C

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 15)

Asymmetric/Biological Unit (2, 15)
No.NameCountTypeFull Name
1CIT3Ligand/IonCITRIC ACID
2HG12Ligand/IonMERCURY (II) ION

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:157 , HOH A:2100BINDING SITE FOR RESIDUE HG A1296
02AC2SOFTWARECYS B:157BINDING SITE FOR RESIDUE HG B1295
03AC3SOFTWAREHIS B:117 , GLU B:196BINDING SITE FOR RESIDUE HG B1296
04AC4SOFTWAREPHE B:67 , HIS B:154BINDING SITE FOR RESIDUE HG B1297
05AC5SOFTWARETYR A:90 , HIS B:41BINDING SITE FOR RESIDUE HG B1298
06AC6SOFTWAREHIS A:41 , TYR B:90BINDING SITE FOR RESIDUE HG A1297
07AC7SOFTWAREPHE A:67 , GLU A:153 , HIS A:154 , HOH A:2008 , HOH A:2063 , HOH A:2064 , HOH A:2147BINDING SITE FOR RESIDUE HG A1298
08AC8SOFTWARETRP A:176 , HIS A:180 , ARG A:275 , GLU B:43BINDING SITE FOR RESIDUE HG A1299
09AC9SOFTWAREHIS A:117 , GLU A:196 , HOH A:2066BINDING SITE FOR RESIDUE HG A1300
10BC1SOFTWAREHIS A:117 , THR A:145 , SER A:149BINDING SITE FOR RESIDUE HG A1301
11BC2SOFTWAREPHE A:293BINDING SITE FOR RESIDUE HG A1302
12BC3SOFTWAREPHE B:293BINDING SITE FOR RESIDUE HG B1299
13BC4SOFTWAREGLY A:35 , THR A:36 , ARG A:37 , ARG A:38 , PHE A:207 , ARG A:209 , HOH A:2022 , HOH A:2027 , HOH A:2106 , HOH A:2149 , PRO B:257 , TYR B:259BINDING SITE FOR RESIDUE CIT A1303
14BC5SOFTWAREPRO A:257 , TYR A:259 , HOH A:2134 , GLY B:35 , THR B:36 , ARG B:37 , ARG B:38 , PHE B:207 , ARG B:209 , HOH B:2016 , HOH B:2080 , HOH B:2097BINDING SITE FOR RESIDUE CIT B1300
15BC6SOFTWAREALA A:165 , LEU A:217 , HOH A:2082 , HOH A:2150 , HOH A:2151 , ALA B:165 , ALA B:166 , PRO B:216 , LEU B:217BINDING SITE FOR RESIDUE CIT A1304

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:23 -B:23

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Gly A:25 -Pro A:26
2Arg A:254 -Pro A:255
3Gly B:25 -Pro B:26
4Arg B:254 -Pro B:255
5Gln B:277 -Pro B:278

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4CMV)

(-) 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:285
 aligned with TUBOL_MYCTO | P9WJ60 from UniProtKB/Swiss-Prot  Length:296

    Alignment length:292
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293  
          TUBOL_MYCTO     4 VSEKEFLDLPLVSVAEIVRCRGPKVSVFPFDGTRRWFHLECNPQYDDYQQAALRQSIRILKMLFEHGIETVISPIFSDDLLDRGDRYIVQALEGMALLANDEEILSFYKEHEVHVLFYGDYKKRLPSTAQGAAVVKSFDDLTISTSSNTEHRLCFGVFGNDAAESVAQFSISWNETHGKPPTRREIIEGYYGEYVDKADMFIGFGRFSTFDFPLLSSGKTSLYFTVAPSYYMTETTLRRILYDHIYLRHFRPKPDYSAMSADQLNVLRNRYRAQPDRVFGVGCVHDGIWFAE 295
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhh..eee....hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh...eeeeeee..-------.hhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee.hhhhhh..hhhhhhhhhhhhhhhhhh.....eeeeeee....hhhhhhhhhhhhhhhhh...hhhhhhhhhhh.......eeeee................eeeee..hhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh...ee..eeee..eeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4cmv A   4 VSEKEFLDLPLVSVAEIVRCRGPKVSVFPFDGTRRWFHLECNPQYDDYQQAALRQSIRILKMLFEHGIETVISPIFSD-------RYIVQALEGMALLANDEEILSFYKEHEVHVLFYGDYKKRLPSTAQGAAVVKSFDDLTISTSSNTEHRLCFGVFGNDAAESVAQFSISWNETHGKPPTRREIIEGYYGEYVDKADMFIGFGRFSTFDFPLLSSGKTSLYFTVAPSYYMTETTLRRILYDHIYLRHFRPKPDYSAMSADQLNVLRNRYRAQPDRVFGVGCVHDGIWFAE 295
                                    13        23        33        43        53        63        73       | -     |  93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293  
                                                                                                        81      89                                                                                                                                                                                                              


Chain A from PDB  Type:PROTEIN  Length:285
 aligned with TUBOL_MYCTU | P9WJ61 from UniProtKB/Swiss-Prot  Length:296

    Alignment length:292
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293  
          TUBOL_MYCTU     4 VSEKEFLDLPLVSVAEIVRCRGPKVSVFPFDGTRRWFHLECNPQYDDYQQAALRQSIRILKMLFEHGIETVISPIFSDDLLDRGDRYIVQALEGMALLANDEEILSFYKEHEVHVLFYGDYKKRLPSTAQGAAVVKSFDDLTISTSSNTEHRLCFGVFGNDAAESVAQFSISWNETHGKPPTRREIIEGYYGEYVDKADMFIGFGRFSTFDFPLLSSGKTSLYFTVAPSYYMTETTLRRILYDHIYLRHFRPKPDYSAMSADQLNVLRNRYRAQPDRVFGVGCVHDGIWFAE 295
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhh..eee....hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh...eeeeeee..-------.hhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee.hhhhhh..hhhhhhhhhhhhhhhhhh.....eeeeeee....hhhhhhhhhhhhhhhhh...hhhhhhhhhhh.......eeeee................eeeee..hhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh...ee..eeee..eeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4cmv A   4 VSEKEFLDLPLVSVAEIVRCRGPKVSVFPFDGTRRWFHLECNPQYDDYQQAALRQSIRILKMLFEHGIETVISPIFSD-------RYIVQALEGMALLANDEEILSFYKEHEVHVLFYGDYKKRLPSTAQGAAVVKSFDDLTISTSSNTEHRLCFGVFGNDAAESVAQFSISWNETHGKPPTRREIIEGYYGEYVDKADMFIGFGRFSTFDFPLLSSGKTSLYFTVAPSYYMTETTLRRILYDHIYLRHFRPKPDYSAMSADQLNVLRNRYRAQPDRVFGVGCVHDGIWFAE 295
                                    13        23        33        43        53        63        73       | -     |  93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293  
                                                                                                        81      89                                                                                                                                                                                                              


Chain B from PDB  Type:PROTEIN  Length:285
 aligned with TUBOL_MYCTO | P9WJ60 from UniProtKB/Swiss-Prot  Length:296

    Alignment length:292
                                    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  
          TUBOL_MYCTO     3 LVSEKEFLDLPLVSVAEIVRCRGPKVSVFPFDGTRRWFHLECNPQYDDYQQAALRQSIRILKMLFEHGIETVISPIFSDDLLDRGDRYIVQALEGMALLANDEEILSFYKEHEVHVLFYGDYKKRLPSTAQGAAVVKSFDDLTISTSSNTEHRLCFGVFGNDAAESVAQFSISWNETHGKPPTRREIIEGYYGEYVDKADMFIGFGRFSTFDFPLLSSGKTSLYFTVAPSYYMTETTLRRILYDHIYLRHFRPKPDYSAMSADQLNVLRNRYRAQPDRVFGVGCVHDGIWFA 294
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhh..eee....hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh...eeeeeee..-------.hhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee.hhhhhh..hhhhhhhhhhhhhhhhhh.....eeeeeee....hhhhhhhhhhhhhhhh....hhhhhhhhhhh.......eeeee................eeeee..hhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh....ee...eee..eee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4cmv B   3 LVSEKEFLDLPLVSVAEIVRCRGPKVSVFPFDGTRRWFHLECNPQYDDYQQAALRQSIRILKMLFEHGIETVISPIFSD-------RYIVQALEGMALLANDEEILSFYKEHEVHVLFYGDYKKRLPSTAQGAAVVKSFDDLTISTSSNTEHRLCFGVFGNDAAESVAQFSISWNETHGKPPTRREIIEGYYGEYVDKADMFIGFGRFSTFDFPLLSSGKTSLYFTVAPSYYMTETTLRRILYDHIYLRHFRPKPDYSAMSADQLNVLRNRYRAQPDRVFGVGCVHDGIWFA 294
                                    12        22        32        42        52        62        72        |-      | 92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292  
                                                                                                         81      89                                                                                                                                                                                                             


Chain B from PDB  Type:PROTEIN  Length:285
 aligned with TUBOL_MYCTU | P9WJ61 from UniProtKB/Swiss-Prot  Length:296

    Alignment length:292
                                    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  
          TUBOL_MYCTU     3 LVSEKEFLDLPLVSVAEIVRCRGPKVSVFPFDGTRRWFHLECNPQYDDYQQAALRQSIRILKMLFEHGIETVISPIFSDDLLDRGDRYIVQALEGMALLANDEEILSFYKEHEVHVLFYGDYKKRLPSTAQGAAVVKSFDDLTISTSSNTEHRLCFGVFGNDAAESVAQFSISWNETHGKPPTRREIIEGYYGEYVDKADMFIGFGRFSTFDFPLLSSGKTSLYFTVAPSYYMTETTLRRILYDHIYLRHFRPKPDYSAMSADQLNVLRNRYRAQPDRVFGVGCVHDGIWFA 294
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhh..eee....hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh...eeeeeee..-------.hhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee.hhhhhh..hhhhhhhhhhhhhhhhhh.....eeeeeee....hhhhhhhhhhhhhhhh....hhhhhhhhhhh.......eeeee................eeeee..hhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh....ee...eee..eee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4cmv B   3 LVSEKEFLDLPLVSVAEIVRCRGPKVSVFPFDGTRRWFHLECNPQYDDYQQAALRQSIRILKMLFEHGIETVISPIFSD-------RYIVQALEGMALLANDEEILSFYKEHEVHVLFYGDYKKRLPSTAQGAAVVKSFDDLTISTSSNTEHRLCFGVFGNDAAESVAQFSISWNETHGKPPTRREIIEGYYGEYVDKADMFIGFGRFSTFDFPLLSSGKTSLYFTVAPSYYMTETTLRRILYDHIYLRHFRPKPDYSAMSADQLNVLRNRYRAQPDRVFGVGCVHDGIWFA 294
                                    12        22        32        42        52        62        72        |-      | 92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292  
                                                                                                         81      89
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → 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 4CMV)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (TUBOL_MYCTO | P9WJ60)
molecular function
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0016765    transferase activity, transferring alkyl or aryl (other than methyl) groups    Catalysis of the transfer of an alkyl or aryl (but not methyl) group from one compound (donor) to another (acceptor).

Chain A,B   (TUBOL_MYCTU | P9WJ61)
molecular function
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0016791    phosphatase activity    Catalysis of the hydrolysis of phosphoric monoesters, releasing inorganic phosphate.
    GO:0016765    transferase activity, transferring alkyl or aryl (other than methyl) groups    Catalysis of the transfer of an alkyl or aryl (but not methyl) group from one compound (donor) to another (acceptor).
biological process
    GO:0016311    dephosphorylation    The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
    GO:0016102    diterpenoid biosynthetic process    The chemical reactions and pathways resulting in the formation of diterpenoid compounds, terpenoids with four isoprene units.
    GO:0052572    response to host immune response    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of detecting the immune response of the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction.

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 Related Entries

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

UniProtKB/Swiss-Prot
        TUBOL_MYCTO | P9WJ60: 3wqk 3wql 3wqm 3wqn 4cmw 4cmx 4kt8
        TUBOL_MYCTU | P9WJ61: 3wqk 3wql 3wqm 3wqn 4cmw 4cmx 4kt8

(-) Related Entries Specified in the PDB File

4cmw CRYSTAL STRUCTURE OF RV3378C
4cmx CRYSTAL STRUCTURE OF RV3378C