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(-) Description

Title :  CRYSTAL STRUCTURE OF PERR-ZN-MN
 
Authors :  D. A. K. Traore, J. -L. Ferrer, L. Jacquamet, V. Duarte, J. -M. Latour
Date :  13 Nov 08  (Deposition) - 16 Jun 09  (Release) - 30 Jun 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.15
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Dna Binding Protein, Helix-Turn-Helix, Cytoplasm, Dna- Binding, Manganese, Oxidation, Repressor, Transcription, Transcription Regulation, Zinc (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Jacquamet, D. A. K. Traore, J. -L. Ferrer, O. Proux, D. Testemale, J. -L. Hazemann, E. Nazarenko, A. El Ghazouani, C. Caux-Thang, V. Duarte, J. -M. Latour
Structural Characterization Of The Active Form Of Perr: Insights Into The Metal-Induced Activation Of Perr And Fur Proteins For Dna Binding
Mol. Microbiol. V. 73 20 2009
PubMed-ID: 19508285  |  Reference-DOI: 10.1111/J.1365-2958.2009.06753.X
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PEROXIDE OPERON REGULATOR
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-30C(NOVAGEN)
    Expression System Taxid: 562
    Expression System Vector: PLASMID
    Gene: PERR
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
    Synonym: PERR

 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
1MN2Ligand/IonMANGANESE (II) ION
2ZN2Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:37 , ASP A:85 , HIS A:91 , HIS A:93 , ASP A:104 , HOH A:301BINDING SITE FOR RESIDUE MN A 201
2AC2SOFTWARECYS A:96 , CYS A:99 , CYS A:136 , CYS A:139BINDING SITE FOR RESIDUE ZN A 202
3AC3SOFTWAREHIS B:37 , ASP B:85 , HIS B:91 , HIS B:93 , ASP B:104BINDING SITE FOR RESIDUE MN B 203
4AC4SOFTWARECYS B:96 , CYS B:99 , CYS B:136 , CYS B:139BINDING SITE FOR RESIDUE ZN B 204

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3F8N)

(-) Cis Peptide Bonds  (18, 18)

Asymmetric/Biological Unit
No.Residues
1Gly A:49 -Lys A:50
2Tyr A:77 -Gly A:78
3Ser A:89 -Asp A:90
4Asp A:90 -His A:91
5Pro A:108 -Gly A:109
6Gly A:109 -Leu A:110
7Leu A:110 -Asp A:111
8Asp A:111 -Glu A:112
9Val A:113 -Glu A:114
10Gly B:49 -Lys B:50
11Tyr B:77 -Gly B:78
12Ser B:89 -Asp B:90
13Asp B:90 -His B:91
14Pro B:108 -Gly B:109
15Gly B:109 -Leu B:110
16Asp B:111 -Glu B:112
17Val B:113 -Glu B:114
18Glu B:138 -Cys B:139

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3F8N)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3F8N)

(-) Exons   (0, 0)

(no "Exon" information available for 3F8N)

(-) 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:137
 aligned with PERR_BACSU | P71086 from UniProtKB/Swiss-Prot  Length:145

    Alignment length:137
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       
           PERR_BACSU     4 HELKEALETLKETGVRITPQRHAILEYLVNSMAHPTADDIYKALEGKFPNMSVATVYNNLRVFRESGLVKELTYGDASSRFDFVTSDHYHAICENCGKIVDFHYPGLDEVEQLAAHVTGFKVSHHRLEIYGVCQECS 140
               SCOP domains d3f8na_ A: automated matches                                                                                                              SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh...hhhhhhhhhhhhhh....hhhhhhhhhh......hhhhhhhhhhhhhhh..eeee.......eeee......eeee.................hhhhhhhhh....eeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3f8n A   4 HELKEALETLKETGVRITPQRHAILEYLVNSMAHPTADDIYKALEGKFPNMSVATVYNNLRVFRESGLVKELTYGDASSRFDFVTSDHYHAICENCGKIVDFHYPGLDEVEQLAAHVTGFKVSHHRLEIYGVCQECS 140
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       


Chain B from PDB  Type:PROTEIN  Length:136
 aligned with PERR_BACSU | P71086 from UniProtKB/Swiss-Prot  Length:145

    Alignment length:136
                                    13        23        33        43        53        63        73        83        93       103       113       123       133      
           PERR_BACSU     4 HELKEALETLKETGVRITPQRHAILEYLVNSMAHPTADDIYKALEGKFPNMSVATVYNNLRVFRESGLVKELTYGDASSRFDFVTSDHYHAICENCGKIVDFHYPGLDEVEQLAAHVTGFKVSHHRLEIYGVCQEC 139
               SCOP domains d3f8nb_ B: automated matches                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh...hhhhhhhhhhhhhh....hhhhhhhhhh......hhhhhhhhhhhhhhh....ee.......ee........eeee.................hhhhhhhhh.eeeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3f8n B   4 HELKEALETLKETGVRITPQRHAILEYLVNSMAHPTADDIYKALEGKFPNMSVATVYNNLRVFRESGLVKELTYGDASSRFDFVTSDHYHAICENCGKIVDFHYPGLDEVEQLAAHVTGFKVSHHRLEIYGVCQEC 139
                                    13        23        33        43        53        63        73        83        93       103       113       123       133
   Legend:   → Mismatch (orange background)
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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  (1, 2)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3F8N)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3F8N)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (PERR_BACSU | P71086)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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: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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  3f8n
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  PERR_BACSU | P71086
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 Related Entries

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

UniProtKB/Swiss-Prot
        PERR_BACSU | P71086: 2fe3 2rgv

(-) Related Entries Specified in the PDB File

2fe3 INACTIVE APO FORM OF PERR
2rgv INACTIVE OXIDIZED FORM PERR