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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 :  2.21
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  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1CIT1Ligand/IonCITRIC ACID
2EDO3Ligand/Ion1,2-ETHANEDIOL
3PEG2Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:119 , PHE A:120 , TYR A:124 , THR A:145 , TYR A:194 , GLY A:195 , HOH A:2075 , HOH A:2159BINDING SITE FOR RESIDUE EDO A1297
2AC2SOFTWAREGLY A:221 , SER A:224 , ARG A:251 , HIS A:252 , HOH A:2132 , ARG B:209 , SER B:211BINDING SITE FOR RESIDUE EDO A1298
3AC3SOFTWAREARG A:38 , PHE A:207 , GLY A:208 , ARG A:209 , TRP A:292 , CIT A:1300 , HOH A:2134BINDING SITE FOR RESIDUE PEG A1299
4AC4SOFTWARESER A:220 , GLY A:221 , HOH A:2116 , SER B:80 , ASN B:163 , PHE B:213 , ASP B:214 , HOH B:2134 , HOH B:2152BINDING SITE FOR RESIDUE EDO B1297
5AC5SOFTWARETHR A:212 , PHE A:215 , SER A:219 , HOH A:2124 , HOH A:2125 , ASP B:214 , PHE B:215 , PRO B:216 , SER B:219 , HOH B:2135BINDING SITE FOR RESIDUE PEG B1298
6AC6SOFTWAREGLY A:35 , THR A:36 , ARG A:37 , ARG A:38 , PEG A:1299 , LYS B:256 , PRO B:257 , TYR B:259BINDING SITE FOR RESIDUE CIT A1300

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4CMW)

(-) 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:288
 aligned with TUBOL_MYCTO | P9WJ60 from UniProtKB/Swiss-Prot  Length:296

    Alignment length:295
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291     
          TUBOL_MYCTO     2 NLVSEKEFLDLPLVSVAEIVRCRGPKVSVFPFDGTRRWFHLECNPQYDDYQQAALRQSIRILKMLFEHGIETVISPIFSDDLLDRGDRYIVQALEGMALLANDEEILSFYKEHEVHVLFYGDYKKRLPSTAQGAAVVKSFDDLTISTSSNTEHRLCFGVFGNDAAESVAQFSISWNETHGKPPTRREIIEGYYGEYVDKADMFIGFGRFSTFDFPLLSSGKTSLYFTVAPSYYMTETTLRRILYDHIYLRHFRPKPDYSAMSADQLNVLRNRYRAQPDRVFGVGCVHDGIWFAEG 296
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhh..eee....hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh...eeeeeee....-------....hhhhhhhhhhhhhhhhhhhh.eeeeee.hhhhhh..hhhhhhhhhhhhhhhhhh.....eeeeeee....hhhhhhhhhhhhhhhhh...hhhhhhhhhhh.......eeeee................eeeee..hhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh...ee..eeee..eeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4cmw A   2 NLVSEKEFLDLPLVSVAEIVRCRGPKVSVFPFDGTRRWFHLECNPQYDDYQQAALRQSIRILKMLFEHGIETVISPIFSDDL-------IVQALEGMALLANDEEILSFYKEHEVHVLFYGDYKKRLPSTAQGAAVVKSFDDLTISTSSNTEHRLCFGVFGNDAAESVAQFSISWNETHGKPPTRREIIEGYYGEYVDKADMFIGFGRFSTFDFPLLSSGKTSLYFTVAPSYYMTETTLRRILYDHIYLRHFRPKPDYSAMSADQLNVLRNRYRAQPDRVFGVGCVHDGIWFAEG 296
                                    11        21        31        41        51        61        71        81 |      91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291     
                                                                                                            83      91                                                                                                                                                                                                             


Chain A from PDB  Type:PROTEIN  Length:288
 aligned with TUBOL_MYCTU | P9WJ61 from UniProtKB/Swiss-Prot  Length:296

    Alignment length:295
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291     
          TUBOL_MYCTU     2 NLVSEKEFLDLPLVSVAEIVRCRGPKVSVFPFDGTRRWFHLECNPQYDDYQQAALRQSIRILKMLFEHGIETVISPIFSDDLLDRGDRYIVQALEGMALLANDEEILSFYKEHEVHVLFYGDYKKRLPSTAQGAAVVKSFDDLTISTSSNTEHRLCFGVFGNDAAESVAQFSISWNETHGKPPTRREIIEGYYGEYVDKADMFIGFGRFSTFDFPLLSSGKTSLYFTVAPSYYMTETTLRRILYDHIYLRHFRPKPDYSAMSADQLNVLRNRYRAQPDRVFGVGCVHDGIWFAEG 296
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhh..eee....hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh...eeeeeee....-------....hhhhhhhhhhhhhhhhhhhh.eeeeee.hhhhhh..hhhhhhhhhhhhhhhhhh.....eeeeeee....hhhhhhhhhhhhhhhhh...hhhhhhhhhhh.......eeeee................eeeee..hhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh...ee..eeee..eeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4cmw A   2 NLVSEKEFLDLPLVSVAEIVRCRGPKVSVFPFDGTRRWFHLECNPQYDDYQQAALRQSIRILKMLFEHGIETVISPIFSDDL-------IVQALEGMALLANDEEILSFYKEHEVHVLFYGDYKKRLPSTAQGAAVVKSFDDLTISTSSNTEHRLCFGVFGNDAAESVAQFSISWNETHGKPPTRREIIEGYYGEYVDKADMFIGFGRFSTFDFPLLSSGKTSLYFTVAPSYYMTETTLRRILYDHIYLRHFRPKPDYSAMSADQLNVLRNRYRAQPDRVFGVGCVHDGIWFAEG 296
                                    11        21        31        41        51        61        71        81 |      91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291     
                                                                                                            83      91                                                                                                                                                                                                             


Chain B from PDB  Type:PROTEIN  Length:286
 aligned with TUBOL_MYCTO | P9WJ60 from UniProtKB/Swiss-Prot  Length:296

    Alignment length:294
                                    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 LVSEKEFLDLPLVSVAEIVRCRGPKVSVFPFDGTRRWFHLECNPQYDDYQQAALRQSIRILKMLFEHGIETVISPIFSDDLLDRGDRYIVQALEGMALLANDEEILSFYKEHEVHVLFYGDYKKRLPSTAQGAAVVKSFDDLTISTSSNTEHRLCFGVFGNDAAESVAQFSISWNETHGKPPTRREIIEGYYGEYVDKADMFIGFGRFSTFDFPLLSSGKTSLYFTVAPSYYMTETTLRRILYDHIYLRHFRPKPDYSAMSADQLNVLRNRYRAQPDRVFGVGCVHDGIWFAEG 296
               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.......hhhhhhhhhhhhhhhhhhh--..ee..eeee..eeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4cmw B   3 LVSEKEFLDLPLVSVAEIVRCRGPKVSVFPFDGTRRWFHLECNPQYDDYQQAALRQSIRILKMLFEHGIETVISPIFS------GDRYIVQALEGMALLANDEEILSFYKEHEVHVLFYGDYKKRLPSTAQGAAVVKSFDDLTISTSSNTEHRLCFGVFGNDAAESVAQFSISWNETHGKPPTRREIIEGYYGEYVDKADMFIGFGRFSTFDFPLLSSGKTSLYFTVAPSYYMTETTLRRILYDHIYLRHFRPKPDYSAMSADQLNVLRNRYRA--DRVFGVGCVHDGIWFAEG 296
                                    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    
                                                                                                        80     87                                                                                                                                                                                          276  |                 
                                                                                                                                                                                                                                                                                                              279                 


Chain B from PDB  Type:PROTEIN  Length:286
 aligned with TUBOL_MYCTU | P9WJ61 from UniProtKB/Swiss-Prot  Length:296

    Alignment length:294
                                    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 LVSEKEFLDLPLVSVAEIVRCRGPKVSVFPFDGTRRWFHLECNPQYDDYQQAALRQSIRILKMLFEHGIETVISPIFSDDLLDRGDRYIVQALEGMALLANDEEILSFYKEHEVHVLFYGDYKKRLPSTAQGAAVVKSFDDLTISTSSNTEHRLCFGVFGNDAAESVAQFSISWNETHGKPPTRREIIEGYYGEYVDKADMFIGFGRFSTFDFPLLSSGKTSLYFTVAPSYYMTETTLRRILYDHIYLRHFRPKPDYSAMSADQLNVLRNRYRAQPDRVFGVGCVHDGIWFAEG 296
               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.......hhhhhhhhhhhhhhhhhhh--..ee..eeee..eeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4cmw B   3 LVSEKEFLDLPLVSVAEIVRCRGPKVSVFPFDGTRRWFHLECNPQYDDYQQAALRQSIRILKMLFEHGIETVISPIFS------GDRYIVQALEGMALLANDEEILSFYKEHEVHVLFYGDYKKRLPSTAQGAAVVKSFDDLTISTSSNTEHRLCFGVFGNDAAESVAQFSISWNETHGKPPTRREIIEGYYGEYVDKADMFIGFGRFSTFDFPLLSSGKTSLYFTVAPSYYMTETTLRRILYDHIYLRHFRPKPDYSAMSADQLNVLRNRYRA--DRVFGVGCVHDGIWFAEG 296
                                    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    
                                                                                                        80     87                                                                                                                                                                                          276  |                 
                                                                                                                                                                                                                                                                                                              279
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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 4CMW)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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 4cmv 4cmx 4kt8
        TUBOL_MYCTU | P9WJ61: 3wqk 3wql 3wqm 3wqn 4cmv 4cmx 4kt8

(-) Related Entries Specified in the PDB File

4cmv CRYSTAL STRUCTURE OF RV3378C
4cmx CRYSTAL STRUCTURE OF RV3378C