Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Biol.Unit 1 - manually
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Biol.Unit 1 - manually
Biol.Unit 1 - manually  (Jmol Viewer)
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF THE ARGININE REPRESSOR PROTEIN FROM MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH THE DNA OPERATOR
 
Authors :  L. T. Cherney, M. M. Cherney, C. R. Garen, G. J. Lu, M. N. James, Tb Struct Genomics Consortium (Tbsgc)
Date :  01 Oct 08  (Deposition) - 14 Oct 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B,D
Biol. Unit 1:  A,B,D  (2x)
Biol. Unit 2:  A,B,D  (1x)
Keywords :  Mycobacterium Tuberculosis, Arginine Repressor Protein, Dna Binding, Argr-Operator Complex, Structural Genomics, Tb Structural Genomics, Tb Structural Genomics Consortium, Tbsgc, Amino-Acid Biosynthesis, Arginine Biosynthesis, Dna-Binding, Transcription, Transcription Regulation, Dna Binding Protein-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. T. Cherney, M. M. Cherney, C. R. Garen, G. J. Lu, M. N. James
Crystal Structure Of The Arginine Repressor Protein In Complex With The Dna Operator From Mycobacterium Tuberculosis.
J. Mol. Biol. V. 384 1330 2008
PubMed-ID: 18952097  |  Reference-DOI: 10.1016/J.JMB.2008.10.015

(-) Compounds

Molecule 1 - ARGININE REPRESSOR
    Atcc: 25618
    Chains: D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGST-1657
    Expression System Strain: BL21(DE3)PLYSS
    Expression System Vector Type: PLASMID
    Gene: ARGR, AHRC, RV1657, MT1695, MTCY06H11.22
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 83332
    Strain: H37RV
 
Molecule 2 - 5'-D(*DTP*DTP*DGP*DCP*DAP*DTP*DAP*DAP*DCP*DGP*DAP*DTP*DGP*D CP*DAP*DA)-3'
    Chains: A
    Engineered: YES
    Other Details: ARGR BOX DNA SEGMENT, STRAND A
    Other Details - Source: DNA STRAND A
    Synthetic: YES
 
Molecule 3 - 5'-D(*DTP*DTP*DGP*DCP*DAP*DTP*DCP*DGP*DTP*DTP*DAP*DTP*DGP*D CP*DAP*DA)-3'
    Chains: B
    Engineered: YES
    Other Details: ARGR BOX DNA SEGMENT, STRAND B
    Other Details - Source: DNA STRAND B
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABD
Biological Unit 1 (2x): ABD
Biological Unit 2 (1x): ABD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
1SO43Ligand/IonSULFATE ION
Biological Unit 1 (1, 6)
No.NameCountTypeFull Name
1SO46Ligand/IonSULFATE ION
Biological Unit 2 (1, 3)
No.NameCountTypeFull Name
1SO43Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS D:125 , ASP D:132 , THR D:142 , ALA D:144 , ASP D:146 , ASP D:147 , THR D:148 , HOH D:208BINDING SITE FOR RESIDUE SO4 D 171
2AC2SOFTWAREGLY D:89 , VAL D:90 , SER D:91 , GLY D:93 , THR D:94 , ASP D:95 , ARG D:96 , ARG D:133 , HOH D:177BINDING SITE FOR RESIDUE SO4 D 172
3AC3SOFTWAREARG D:170BINDING SITE FOR RESIDUE SO4 D 173

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3ERE)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ser D:85 -Pro D:86
2Glu D:155 -Pro D:156

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3ERE)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3ERE)

(-) Exons   (0, 0)

(no "Exon" information available for 3ERE)

(-) 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:DNA  Length:16
                                                
                 3ere A   1 TTGCATAACGATGCAA  16
                                    10      


Chain B from PDB  Type:DNA  Length:16
                                                
                 3ere B   1 TTGCATCGTTATGCAA  16
                                    10      


Chain D from PDB  Type:PROTEIN  Length:156
 aligned with ARGR_MYCTO | P9WPY8 from UniProtKB/Swiss-Prot  Length:201

    Alignment length:156
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164      
           ARGR_MYCTO    15 AANRAGRQARIVAILSSAQVRSQNELAALLAAEGIEVTQATLSRDLEELGAVKLRGADGGTGIYVVPEDGSPVRGVSGGTDRMARLLGELLVSTDDSGNLAVLRTPPGAAHYLASAIDRAALPQVVGTIAGDDTILVVAREPTTGAQLAGMFENFG 170
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhh....hhhhhhhhhhhh....hhhhhhhhhhh...eeee.....eeeee.............hhhhhhhhhhhhh.eeeee..eeeee....hhhhhhhhhhhh....eeeeee...eeeeee....hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ere D  15 AANRAGRQARIVAILSSAQVRSQNELAALLAAEGIEVTQATLSRDLEELGAVKLRGADGGTGIYVVPEDGSPVRGVSGGTDRMARLLGELLVSTDDSGNLAVLRTPPGAAHYLASAIDRAALPQVVGTIAGDDTILVVAREPTTGAQLAGMFENLR 170
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164      


Chain D from PDB  Type:PROTEIN  Length:156
 aligned with ARGR_MYCTU | P9WPY9 from UniProtKB/Swiss-Prot  Length:170

    Alignment length:156
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164      
           ARGR_MYCTU    15 AANRAGRQARIVAILSSAQVRSQNELAALLAAEGIEVTQATLSRDLEELGAVKLRGADGGTGIYVVPEDGSPVRGVSGGTDRMARLLGELLVSTDDSGNLAVLRTPPGAAHYLASAIDRAALPQVVGTIAGDDTILVVAREPTTGAQLAGMFENLR 170
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhh....hhhhhhhhhhhh....hhhhhhhhhhh...eeee.....eeeee.............hhhhhhhhhhhhh.eeeee..eeeee....hhhhhhhhhhhh....eeeeee...eeeeee....hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ere D  15 AANRAGRQARIVAILSSAQVRSQNELAALLAAEGIEVTQATLSRDLEELGAVKLRGADGGTGIYVVPEDGSPVRGVSGGTDRMARLLGELLVSTDDSGNLAVLRTPPGAAHYLASAIDRAALPQVVGTIAGDDTILVVAREPTTGAQLAGMFENLR 170
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164
   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 3ERE)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3ERE)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3ERE)

(-) Gene Ontology  (10, 20)

Asymmetric Unit(hide GO term definitions)
Chain D   (ARGR_MYCTO | P9WPY8)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0034618    arginine binding    Interacting selectively and non-covalently with 2-amino-5-(carbamimidamido)pentanoic acid.
    GO:0003700    transcription factor activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
biological process
    GO:0006526    arginine biosynthetic process    The chemical reactions and pathways resulting in the formation of arginine, 2-amino-5-(carbamimidamido)pentanoic acid.
    GO:0006525    arginine metabolic process    The chemical reactions and pathways involving arginine, 2-amino-5-(carbamimidamido)pentanoic acid.
    GO:0008652    cellular amino acid biosynthetic process    The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
    GO:0051259    protein oligomerization    The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of component monomers; protein oligomers may be composed of different or identical monomers. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Chain D   (ARGR_MYCTU | P9WPY9)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0034618    arginine binding    Interacting selectively and non-covalently with 2-amino-5-(carbamimidamido)pentanoic acid.
    GO:0003700    transcription factor activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
biological process
    GO:0006526    arginine biosynthetic process    The chemical reactions and pathways resulting in the formation of arginine, 2-amino-5-(carbamimidamido)pentanoic acid.
    GO:0006525    arginine metabolic process    The chemical reactions and pathways involving arginine, 2-amino-5-(carbamimidamido)pentanoic acid.
    GO:0008652    cellular amino acid biosynthetic process    The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
    GO:0051259    protein oligomerization    The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of component monomers; protein oligomers may be composed of different or identical monomers. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Glu D:155 - Pro D:156   [ RasMol ]  
    Ser D:85 - Pro D:86   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3ere
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  ARGR_MYCTO | P9WPY8
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  ARGR_MYCTU | P9WPY9
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  ARGR_MYCTO | P9WPY8
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  ARGR_MYCTU | P9WPY9
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        ARGR_MYCTO | P9WPY8: 2zfz 3bue 3cag 3fhz 3laj 3lap
        ARGR_MYCTU | P9WPY9: 2zfz 3bue 3cag 3fhz 3laj 3lap

(-) Related Entries Specified in the PDB File

2zfz CRYSTAL STRUCTURE OF THE C-TERMINAL DOMAIN HEXAMER OF ARGR FROM MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH ARGININE
3bue CRYSTAL STRUCTURE OF THE C-TERMINAL DOMAIN HEXAMER OF ARGR FROM MYCOBACTERIUM TUBERCULOSIS
3cag CRYSTAL STRUCTURE OF THE OLIGOMERIZATION DOMAIN HEXAMER OF THE ARGININE REPRESSOR PROTEIN FROM MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH 9 ARGININES.