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

(-) Description

Title :  STRUCTURE OF THE MNTR CO2+ COMPLEX
 
Authors :  A. Glasfeld, M. B. Brophy, J. I. Kliegman, S. L. Griner, J. C. Nix
Date :  20 Mar 11  (Deposition) - 11 Apr 12  (Release) - 06 Feb 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Winged Helix-Turn-Helix, Transcription Regulator (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. M. Mcguire, B. J. Cuthbert, Z. Ma, K. D. Grauer-Gray, M. Brunjes Brophy, K. A. Spear, S. Soonsanga, J. I. Kliegman, S. L. Griner, J. D. Helmann, A. Glasfeld
Roles Of The A And C Sites In The Manganese-Specific Activation Of Mntr.
Biochemistry V. 52 701 2013
PubMed-ID: 23298157  |  Reference-DOI: 10.1021/BI301550T

(-) Compounds

Molecule 1 - TRANSCRIPTIONAL REGULATOR MNTR
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PHB7506
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: BACILLUS SUBTILIS, BSU24520, MNTR, YQHN
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
    Synonym: MANGANESE TRANSPORT REGULATOR

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1CO2Ligand/IonCOBALT (II) ION
2EPE2Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:11 , HIS A:77 , GLU A:99 , GLU A:102 , HOH A:143BINDING SITE FOR RESIDUE CO A 1
2AC2SOFTWAREGLU B:11 , HIS B:77 , GLU B:99 , GLU B:102 , HOH B:144BINDING SITE FOR RESIDUE CO B 143
3AC3SOFTWARESER A:106 , TRP A:107 , GLU B:18 , LYS B:93 , HOH B:188BINDING SITE FOR RESIDUE EPE B 301
4AC4SOFTWAREILE A:17 , GLU A:18 , GLU A:19 , LYS A:20 , GLY A:21 , LYS A:93 , HOH A:176 , HOH A:187 , SER B:106 , TRP B:107BINDING SITE FOR RESIDUE EPE A 302

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3R61)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3R61)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3R61)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3R61)

(-) Exons   (0, 0)

(no "Exon" information available for 3R61)

(-) 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:128
 aligned with MNTR_BACSU | P54512 from UniProtKB/Swiss-Prot  Length:142

    Alignment length:133
                                    13        23        33        43        53        63        73        83        93       103       113       123       133   
           MNTR_BACSU     4 PSMEDYIEQIYMLIEEKGYARVSDIAEALAVHPSSVTKMVQKLDKDEYLIYEKYRGLVLTSKGKKIGKRLVYRHELLEQFLRIIGVDEEKIYNDVEGIEHHLSWNSIDRIGDLVQYFEEDDARKKDLKSIQKK 136
               SCOP domains d3r61a1 A:4-62 automated matches                           d3r61a2 A:63-136 automated matches                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhhhhh..ee-----..eehhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3r61 A   4 PSMEDYIEQIYMLIEEKGYARVSDIAEALAVHPSSVTKMVQKLDKDEYLI-----GLVLTSKGKKIGKRLVYRHELLEQFLRIIGVDEEKIYNDVEGIEHHLSWNSIDRIGDLVQYFEEDDARKKDLKSIQKK 136
                                    13        23        33        43        53     |  63        73        83        93       103       113       123       133   
                                                                            53    59                                                                             


Chain B from PDB  Type:PROTEIN  Length:128
 aligned with MNTR_BACSU | P54512 from UniProtKB/Swiss-Prot  Length:142

    Alignment length:133
                                    13        23        33        43        53        63        73        83        93       103       113       123       133   
           MNTR_BACSU     4 PSMEDYIEQIYMLIEEKGYARVSDIAEALAVHPSSVTKMVQKLDKDEYLIYEKYRGLVLTSKGKKIGKRLVYRHELLEQFLRIIGVDEEKIYNDVEGIEHHLSWNSIDRIGDLVQYFEEDDARKKDLKSIQKK 136
               SCOP domains d3r61b1 B:4-62 automated matches                           d3r61b2 B:63-136 automated matches                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh..hhhhhhhhh..hhhhhhhhhhhhhhh..ee-----..eehhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3r61 B   4 PSMEDYIEQIYMLIEEKGYARVSDIAEALAVHPSSVTKMVQKLDKDEYLI-----GLVLTSKGKKIGKRLVYRHELLEQFLRIIGVDEEKIYNDVEGIEHHLSWNSIDRIGDLVQYFEEDDARKKDLKSIQKK 136
                                    13        23        33        43        53     |  63        73        83        93       103       113       123       133   
                                                                            53    59
   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  (2, 4)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3R61)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3R61)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (MNTR_BACSU | P54512)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0030145    manganese ion binding    Interacting selectively and non-covalently with manganese (Mn) ions.
    GO:0046983    protein dimerization activity    The formation of a protein dimer, a macromolecular structure consists of two noncovalently associated identical or nonidentical subunits.
    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.
    GO:0046914    transition metal ion binding    Interacting selectively and non-covalently with a transition metal ions; a transition metal is an element whose atom has an incomplete d-subshell of extranuclear electrons, or which gives rise to a cation or cations with an incomplete d-subshell. Transition metals often have more than one valency state. Biologically relevant transition metals include vanadium, manganese, iron, copper, cobalt, nickel, molybdenum and silver.
biological process
    GO:0030026    cellular manganese ion homeostasis    Any process involved in the maintenance of an internal steady state of manganese ions at the level of a cell.
    GO:0045893    positive regulation of transcription, DNA-templated    Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
    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/Biological 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
    CO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    EPE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3r61)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites 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
  3r61
    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
  MNTR_BACSU | P54512
    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
  MNTR_BACSU | P54512
    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
        MNTR_BACSU | P54512: 1on1 1on2 2ev0 2ev5 2ev6 2f5c 2f5d 2f5e 2f5f 2hyf 2hyg 3r60 4hv5 4hv6 4hx4 4hx7 4hx8

(-) Related Entries Specified in the PDB File

2ev6 MNTR ZN2+
2f5d MNTR MN2+
3r60 MNTR FE2+