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(-) Description

Title :  BACILLUS SUBTILIS MANGANESE TRANSPORT REGULATOR (MNTR) BOUND TO MANGANESE, AC CONFORMATION, PH 6.5
 
Authors :  J. I. Kliegman, S. L. Griner, J. D. Helmann, R. G. Brennan, A. Glasfeld
Date :  25 Nov 05  (Deposition) - 07 Mar 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Helix-Turn-Helix, Dna-Binding Protein, Metalloregulatory Protein, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. I. Kliegman, S. L. Griner, J. D. Helmann, R. G. Brennan, A. Glasfeld
Structural Basis For The Metal-Selective Activation Of The Manganese Transport Regulator Of Bacillus Subtilis.
Biochemistry V. 45 3493 2006
PubMed-ID: 16533030  |  Reference-DOI: 10.1021/BI0524215
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TRANSCRIPTIONAL REGULATOR MNTR
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PHB7506
    Expression System Strain: BL21(DE3)-RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: MNTR
    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  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1MN4Ligand/IonMANGANESE (II) ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:11 , HIS A:77 , GLU A:99 , GLU A:102 , HOH A:1177BINDING SITE FOR RESIDUE MN A 1150
2AC2SOFTWAREASP A:8 , GLU A:99 , GLU A:102 , HIS A:103 , HOH A:1168 , HOH A:1177BINDING SITE FOR RESIDUE MN A 1151
3AC3SOFTWAREGLU B:11 , HIS B:77 , GLU B:99 , GLU B:102 , HOH B:2180BINDING SITE FOR RESIDUE MN B 2150
4AC4SOFTWAREASP B:8 , GLU B:99 , GLU B:102 , HIS B:103 , HOH B:2171BINDING SITE FOR RESIDUE MN B 2151

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2F5D)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2F5D)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2F5D)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2F5D)

(-) Exons   (0, 0)

(no "Exon" information available for 2F5D)

(-) 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:130
 aligned with MNTR_BACSU | P54512 from UniProtKB/Swiss-Prot  Length:142

    Alignment length:134
                                    12        22        32        42        52        62        72        82        92       102       112       122       132    
           MNTR_BACSU     3 TPSMEDYIEQIYMLIEEKGYARVSDIAEALAVHPSSVTKMVQKLDKDEYLIYEKYRGLVLTSKGKKIGKRLVYRHELLEQFLRIIGVDEEKIYNDVEGIEHHLSWNSIDRIGDLVQYFEEDDARKKDLKSIQKK 136
               SCOP domains d2f5da1 A:3-62 Manganese transport regulator MntR           d2f5da2 A:63-136 Manganese transport regulator MntR                        SCOP domains
               CATH domains 2f5dA01 A:3-73 'winged helix' repressor DNA binding     domain         2f5dA02 A:74-136 Diphtheria Toxin Repressor, domain 2           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhh..hhhhhhhhh..hhhhhhhhhhhhhhh..ee.----..eehhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2f5d A   3 TPSMEDYIEQIYMLIEEKGYARVSDIAEALAVHPSSVTKMVQKLDKDEYLIY----GLVLTSKGKKIGKRLVYRHELLEQFLRIIGVDEEKIYNDVEGIEHHLSWNSIDRIGDLVQYFEEDDARKKDLKSIQKK 136
                                    12        22        32        42        52 |    | 62        72        82        92       102       112       122       132    
                                                                              54   59                                                                             


Chain B from PDB  Type:PROTEIN  Length:131
 aligned with MNTR_BACSU | P54512 from UniProtKB/Swiss-Prot  Length:142

    Alignment length:135
                                    11        21        31        41        51        61        71        81        91       101       111       121       131     
           MNTR_BACSU     2 TTPSMEDYIEQIYMLIEEKGYARVSDIAEALAVHPSSVTKMVQKLDKDEYLIYEKYRGLVLTSKGKKIGKRLVYRHELLEQFLRIIGVDEEKIYNDVEGIEHHLSWNSIDRIGDLVQYFEEDDARKKDLKSIQKK 136
               SCOP domains d2f5db1 B:2-62 Manganese transport regulator MntR            d2f5db2 B:63-136 Manganese transport regulator MntR                        SCOP domains
               CATH domains 2f5dB01 B:2-73 'winged helix' repressor DNA binding d    omain          2f5dB02 B:74-136 Diphtheria Toxin Repressor, domain 2           CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhhhhh..ee.----..eehhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2f5d B   2 TTPSMEDYIEQIYMLIEEKGYARVSDIAEALAVHPSSVTKMVQKLDKDEYLIY----GLVLTSKGKKIGKRLVYRHELLEQFLRIIGVDEEKIYNDVEGIEHHLSWNSIDRIGDLVQYFEEDDARKKDLKSIQKK 136
                                    11        21        31        41        51  |    |61        71        81        91       101       111       121       131     
                                                                               54   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  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2F5D)

(-) 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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        MNTR_BACSU | P54512: 1on1 1on2 2ev0 2ev5 2ev6 2f5c 2f5e 2f5f 2hyf 2hyg 3r60 3r61 4hv5 4hv6 4hx4 4hx7 4hx8

(-) Related Entries Specified in the PDB File

1on1 MNTR BOUND TO MANGANESE, AB CONFORMATION
2f5c MNTR BOUND TO MANGANESE, HEXAGONAL CRYSTAL FORM
2f5e MNTR BOUND TO MANGANESE, AB CONFORMATION, PH 6.5
2f5f MNTR BOUND TO MANGANESE, AC CONFORMATION, PH 8.5