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(-) Description

Title :  CRYSTAL STRUCTURE OF MARR
 
Authors :  V. Saridakis, D. Shahinas, X. Xu, D. Christendat
Date :  19 Dec 07  (Deposition) - 20 May 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Marr, Transcription Factor, Winged Helix Motif, Dna Binding, Dna-Binding, Transcription Regulation, Transcription Regulator (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. Saridakis, D. Shahinas, X. Xu, D. Christendat
Structural Insight On The Mechanism Of Regulation Of The Marr Family Of Proteins: High-Resolution Crystal Structure Of A Transcriptional Repressor From Methanobacterium Thermoautotrophicum.
J. Mol. Biol. V. 377 655 2008
PubMed-ID: 18272181  |  Reference-DOI: 10.1016/J.JMB.2008.01.001
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TRANSCRIPTIONAL REGULATOR
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Vector: PET15B
    Expression System Vector Type: PLASMID
    Gene: MT313
    Organism Scientific: METHANOBACTERIUM THERMOAUTOTROPHICUM

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric/Biological Unit (2, 8)
No.NameCountTypeFull Name
1NA6Ligand/IonSODIUM ION
2SAL2Ligand/Ion2-HYDROXYBENZOIC ACID

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:32 , GLN A:35BINDING SITE FOR RESIDUE NA A 146
2AC2SOFTWAREILE A:42 , PRO A:46 , HOH A:264BINDING SITE FOR RESIDUE NA A 147
3AC3SOFTWAREHIS A:28 , THR A:94 , ARG A:95 , HOH A:326BINDING SITE FOR RESIDUE NA A 148
4AC4SOFTWAREGLN A:50 , ASP A:51 , ARG A:88 , TYR A:89 , HOH A:306BINDING SITE FOR RESIDUE NA A 149
5AC5SOFTWAREGLU A:108 , TRP A:111 , GLU A:112 , PRO B:6 , LEU B:7 , LYS B:8BINDING SITE FOR RESIDUE NA B 146
6AC6SOFTWARETHR B:32 , GLN B:35 , HOH B:312 , HOH B:365BINDING SITE FOR RESIDUE NA B 147
7AC7SOFTWARESER A:12 , ARG A:16 , ALA B:34 , CYS B:38 , ILE B:64 , THR B:67BINDING SITE FOR RESIDUE SAL A 257
8AC8SOFTWAREALA A:37 , LEU A:40 , ARG A:44 , PHE A:57 , HOH A:323 , ILE B:5 , LYS B:8 , SER B:12 , ARG B:16BINDING SITE FOR RESIDUE SAL B 258

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3BPX)

(-) 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:147
 aligned with O26413_METTH | O26413 from UniProtKB/TrEMBL  Length:146

    Alignment length:147
                              1                                                                                                                                                
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       
         O26413_METTH     - --MDRDIPLKGLLSIILRSHRVFIGRELGHLNLTDAQVACLLRIHREPGIKQDELATFFHVDKGTIARTLRRLEESGFIEREQDPENRRRYILEVTRRGEEIIPLILKVEERWEDLLFRDFTEDERKLFRKMCRRLAEEAVRMRGEW 145
               SCOP domains d3bpxa_ A: automated matches                                                                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh....hhhhhhhhhh.hhhhhhhhhhhhhhh..eeeeee..eeeeeeeeehhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bpx A  -1 SHMDRDIPLKGLLSIILRSHRVFIGRELGHLNLTDAQVACLLRIHREPGIKQDELATFFHVDKGTIARTLRRLEESGFIEREQDPENRRRYILEVTRRGEEIIPLILKVEERWEDLLFRDFTEDERKLFRKMCRRLAEEAVRMRGEW 145
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       


Chain B from PDB  Type:PROTEIN  Length:138
 aligned with O26413_METTH | O26413 from UniProtKB/TrEMBL  Length:146

    Alignment length:138
                                    13        23        33        43        53        63        73        83        93       103       113       123       133        
         O26413_METTH     4 DIPLKGLLSIILRSHRVFIGRELGHLNLTDAQVACLLRIHREPGIKQDELATFFHVDKGTIARTLRRLEESGFIEREQDPENRRRYILEVTRRGEEIIPLILKVEERWEDLLFRDFTEDERKLFRKMCRRLAEEAVRM 141
               SCOP domains d3bpxb_ B: automated matches                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh...hhhhhhhhhh.hhhhhhhhhhhhhhh..eeeeee..eeeeeeeeehhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3bpx B   4 DIPLKGLLSIILRSHRVFIGRELGHLNLTDAQVACLLRIHREPGIKQDELATFFHVDKGTIARTLRRLEESGFIEREQDPENRRRYILEVTRRGEEIIPLILKVEERWEDLLFRDFTEDERKLFRKMCRRLAEEAVRM 141
                                    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 3BPX)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (O26413_METTH | O26413)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic 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: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.

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 Related Entries

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

UniProtKB/TrEMBL
        O26413_METTH | O26413: 3bpv

(-) Related Entries Specified in the PDB File

3bpv CRYSTAL STRUCTURE OF MARR