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(-) Description

Title :  MYCOBACTERIUM TUBERCULOSIS ADENYLYL CYCLASE RV1900C CHD, IN COMPLEX WITH A SUBSTRATE ANALOG.
 
Authors :  S. C. Sinha, M. Wetterer, S. R. Sprang, J. E. Schultz, J. U. Linder
Date :  21 Dec 04  (Deposition) - 15 Feb 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Cyclase Homology Domain, Chd, Rv1900C, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. C. Sinha, M. Wetterer, S. R. Sprang, J. E. Schultz, J. U. Linder
Origin Of Asymmetry In Adenylyl Cyclases: Structures Of Mycobacterium Tuberculosis Rv1900C.
Embo J. V. 24 663 2005
PubMed-ID: 15678099  |  Reference-DOI: 10.1038/SJ.EMBOJ.7600573

(-) Compounds

Molecule 1 - LIPJ
    Chains: A, B, C, D
    EC Number: 4.6.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE30
    Expression System Strain: B834(DE3)[PREP4]
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RV1900C CHD
    Gene: RV1900C
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 83332
    Strain: H37RV

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1APC2Ligand/IonDIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
2MN2Ligand/IonMANGANESE (II) ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1APC1Ligand/IonDIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
2MN-1Ligand/IonMANGANESE (II) ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1APC1Ligand/IonDIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
2MN-1Ligand/IonMANGANESE (II) ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:3 , ASP A:302 , ILE A:303 , SER A:306 , ASP A:346 , APC A:601BINDING SITE FOR RESIDUE MN A 501
2AC2SOFTWAREASP D:302 , ILE D:303 , SER D:306 , ASP D:346 , APC D:602BINDING SITE FOR RESIDUE MN D 502
3AC3SOFTWAREHOH A:3 , HOH A:12 , HOH A:95 , HOH A:223 , ASP A:302 , GLY A:305 , SER A:306 , GLN A:308 , GLY A:345 , ASP A:346 , ARG A:377 , MN A:501 , HOH B:73 , LYS B:442BINDING SITE FOR RESIDUE APC A 601
4AC4SOFTWARELYS C:442 , HOH D:186 , HOH D:224 , ASP D:302 , GLY D:305 , SER D:306 , GLN D:308 , GLY D:345 , ASP D:346 , ARG D:377 , MN D:502BINDING SITE FOR RESIDUE APC D 602

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1YBU)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1YBU)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1YBU)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1YBU)

(-) Exons   (0, 0)

(no "Exon" information available for 1YBU)

(-) 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:166
 aligned with O07732_MYCTU | O07732 from UniProtKB/TrEMBL  Length:462

    Alignment length:166
                                   300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450      
         O07732_MYCTU   291 AERMLATIMFTDIVGSTQHAAALGDDRWRDLLDNHDTIVCHEIQRFGGREVNTAGDGFVATFTSPSAAIACADDIVDAVAALGIEVRIGIHAGEVEVRDASHGTDVAGVAVHIGARVCALAGPSEVLVSSTVRDIVAGSRHRFAERGEQELKGVPGRWRLCVLMRD 456
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee........eeee.hhhhhhhhhhhhhhhhhh....eeeeeeeeeeeee......eeehhhhhhhhhhhhhh....eeeehhhhhh.......eeeeee..........eeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ybu A 291 AERMLATIMFTDIVGSTQHAAALGDDRWRDLLDNHDTIVCHEIQRFGGREVNTAGDGFVATFTSPSAAIACADDIVDAVAALGIEVRIGIHAGEVEVRDASHGTDVAGVAVHIGARVCALAGPSEVLVSSTVRDIVAGSRHRFAERGEQELKGVPGRWRLCVLMRD 456
                                   300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450      


Chain B from PDB  Type:PROTEIN  Length:163
 aligned with O07732_MYCTU | O07732 from UniProtKB/TrEMBL  Length:462

    Alignment length:166
                                   300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450      
         O07732_MYCTU   291 AERMLATIMFTDIVGSTQHAAALGDDRWRDLLDNHDTIVCHEIQRFGGREVNTAGDGFVATFTSPSAAIACADDIVDAVAALGIEVRIGIHAGEVEVRDASHGTDVAGVAVHIGARVCALAGPSEVLVSSTVRDIVAGSRHRFAERGEQELKGVPGRWRLCVLMRD 456
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee....eeeee.hhhhhhhhhhhhhhhhhh....eeeeeeeeeeeee..---.eeehhhhhhhhhhhh......eeeehhhhhhhh.....eeeeeee........eeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ybu B 291 AERMLATIMFTDIVGSTQHAAALGDDRWRDLLDNHDTIVCHEIQRFGGREVNTAGDGFVATFTSPSAAIACADDIVDAVAALGIEVRIGIHAGEVEVRDA---TDVAGVAVHIGARVCALAGPSEVLVSSTVRDIVAGSRHRFAERGEQELKGVPGRWRLCVLMRD 456
                                   300       310       320       330       340       350       360       370       380       390   |   400       410       420       430       440       450      
                                                                                                                             390 394                                                              


Chain C from PDB  Type:PROTEIN  Length:163
 aligned with O07732_MYCTU | O07732 from UniProtKB/TrEMBL  Length:462

    Alignment length:166
                                   300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450      
         O07732_MYCTU   291 AERMLATIMFTDIVGSTQHAAALGDDRWRDLLDNHDTIVCHEIQRFGGREVNTAGDGFVATFTSPSAAIACADDIVDAVAALGIEVRIGIHAGEVEVRDASHGTDVAGVAVHIGARVCALAGPSEVLVSSTVRDIVAGSRHRFAERGEQELKGVPGRWRLCVLMRD 456
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee....eeeee.hhhhhhhhhhhhhhhhhh....eeeeeeeeeeee...---..eehhhhhhhhhhhh......eeeehhhhhhhh.....eeeeeee........eeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ybu C 291 AERMLATIMFTDIVGSTQHAAALGDDRWRDLLDNHDTIVCHEIQRFGGREVNTAGDGFVATFTSPSAAIACADDIVDAVAALGIEVRIGIHAGEVEVRDA---TDVAGVAVHIGARVCALAGPSEVLVSSTVRDIVAGSRHRFAERGEQELKGVPGRWRLCVLMRD 456
                                   300       310       320       330       340       350       360       370       380       390   |   400       410       420       430       440       450      
                                                                                                                             390 394                                                              


Chain D from PDB  Type:PROTEIN  Length:166
 aligned with O07732_MYCTU | O07732 from UniProtKB/TrEMBL  Length:462

    Alignment length:166
                                   300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450      
         O07732_MYCTU   291 AERMLATIMFTDIVGSTQHAAALGDDRWRDLLDNHDTIVCHEIQRFGGREVNTAGDGFVATFTSPSAAIACADDIVDAVAALGIEVRIGIHAGEVEVRDASHGTDVAGVAVHIGARVCALAGPSEVLVSSTVRDIVAGSRHRFAERGEQELKGVPGRWRLCVLMRD 456
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) Guanylate_cyc-1ybuD01 D:291-454                                                                                                                                     -- Pfam domains (1)
           Pfam domains (2) Guanylate_cyc-1ybuD02 D:291-454                                                                                                                                     -- Pfam domains (2)
           Pfam domains (3) Guanylate_cyc-1ybuD03 D:291-454                                                                                                                                     -- Pfam domains (3)
           Pfam domains (4) Guanylate_cyc-1ybuD04 D:291-454                                                                                                                                     -- Pfam domains (4)
         Sec.struct. author ..eeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee......eeeeee.hhhhhhhhhhhhhhhhhh....eeeeeeeeeeeee......eeehhhhhhhhhhhhhh....eeeehhhhhh.......eeeeee..........eeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ybu D 291 AERMLATIMFTDIVGSTQHAAALGDDRWRDLLDNHDTIVCHEIQRFGGREVNTAGDGFVATFTSPSAAIACADDIVDAVAALGIEVRIGIHAGEVEVRDASHGTDVAGVAVHIGARVCALAGPSEVLVSSTVRDIVAGSRHRFAERGEQELKGVPGRWRLCVLMRD 456
                                   300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450
   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 1YBU)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1YBU)

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: Nucleot_cyclase (14)

(-) Gene Ontology  (14, 14)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (O07732_MYCTU | O07732)
molecular function
    GO:0004016    adenylate cyclase activity    Catalysis of the reaction: ATP = 3',5'-cyclic AMP + diphosphate.
    GO:0004383    guanylate cyclase activity    Catalysis of the reaction: GTP = 3',5'-cyclic GMP + diphosphate.
    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:0030145    manganese ion binding    Interacting selectively and non-covalently with manganese (Mn) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004601    peroxidase activity    Catalysis of the reaction: donor + hydrogen peroxide = oxidized donor + 2 H2O.
    GO:0016849    phosphorus-oxygen lyase activity    Catalysis of the cleavage of a phosphorus-oxygen bond by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond.
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
biological process
    GO:0006171    cAMP biosynthetic process    The chemical reactions and pathways resulting in the formation of the nucleotide cAMP (cyclic AMP, adenosine 3',5'-cyclophosphate).
    GO:0006182    cGMP biosynthetic process    The chemical reactions and pathways resulting in the formation of cyclic GMP, guanosine 3',5'-phosphate.
    GO:0098869    cellular oxidant detoxification    Any process carried out at the cellular level that reduces or removes the toxicity superoxide radicals or hydrogen peroxide.
    GO:0009190    cyclic nucleotide biosynthetic process    The chemical reactions and pathways resulting in the formation of a cyclic nucleotide, a nucleotide in which the phosphate group is in diester linkage to two positions on the sugar residue.
    GO:0035556    intracellular signal transduction    The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell.
cellular component
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

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  1ybu
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  O07732_MYCTU | O07732
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  4.6.1.1
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 Related Entries

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

UniProtKB/TrEMBL
        O07732_MYCTU | O07732: 1ybt

(-) Related Entries Specified in the PDB File

1ybt SAME PROTEIN WITHOUT LIGAND