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(-) Description

Title :  STRUCTURE OF TRMBL2, AN ARCHAEAL CHROMATIN PROTEIN, SHOWS A NOVEL MODE OF DNA BINDING.
 
Authors :  M. U. Ahmad, K. Diederichs, W. Welte
Date :  28 May 15  (Deposition) - 02 Sep 15  (Release) - 07 Oct 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.20
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Chromatin Binding Protein, Archaea, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. U. Ahmad, I. Waege, W. Hausner, M. Thomm, W. Boos, K. Diederichs, W. Welte
Structural Insights Into Nonspecific Binding Of Dna By Trmbl2, An Archaeal Chromatin Protein.
J. Mol. Biol. V. 427 3216 2015
PubMed-ID: 26299937  |  Reference-DOI: 10.1016/J.JMB.2015.08.012

(-) Compounds

Molecule 1 - TRMBL2
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET24D
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: TRMBL2, PF0496
    Organism Scientific: PYROCOCCUS FURIOSUS
    Organism Taxid: 2261
 
Molecule 2 - DNA (5'- D(P*TP*AP*TP*AP*TP*CP*AP*TP*CP*GP*AP*TP*AP*GP*TP*GP*AP*TP*AP*TP*A)- 3')
    Chains: E
    Engineered: YES
    Organism Scientific: PYROCOCCUS FURIOSUS
    Organism Taxid: 2261
    Other Details: TGM SEQUENCE
    Synthetic: YES
 
Molecule 3 - DNA (5'- D(P*TP*AP*TP*AP*TP*CP*AP*CP*TP*AP*TP*CP*GP*AP*TP*GP*AP*TP*AP*TP*A)- 3')
    Chains: F
    Engineered: YES
    Organism Scientific: PYROCOCCUS FURIOSUS
    Organism Taxid: 2261
    Other Details: TGM SEQUENCE
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:83 , ASN C:134binding site for residue GOL A 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5BPI)

(-) Cis Peptide Bonds  (7, 7)

Asymmetric/Biological Unit
No.Residues
1Pro B:119 -Lys B:120
2Gly B:122 -Val B:123
3Gly C:67 -Lys C:68
4Lys D:68 -Thr D:69
5Thr D:69 -Asn D:70
6Glu D:124 -Arg D:125
7Cys D:217 -Asp D:218

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5BPI)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5BPI)

(-) Exons   (0, 0)

(no "Exon" information available for 5BPI)

(-) 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:263
                                                                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh..hhhhhhhhhhhhhhh..hhhhhhhh...hhhhhhhhhhhhhhhh.eeee.....eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..............eeee.hhhhhhhhhhhhhh....eeeeee.......hhhhhhhhhh...eeeeeee..hhhhhh...hhhhhhh...eeeee......eeee..eeeee..hhhhhhh....eeeeehhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5bpi A   2 SKDRMVELLQEHFELNLYEARAYVALVAFGVLTPAELASVSEVPAPRTYDVLRSLEKKGFAMTQPGKTNKYRPVHPANVLEKFIQDWQERVKEELEAKKKAKEELLELMAPLIETEVPKYGVERVWVVRGIKNSTLKTKEMLEEAQNEILLADDGFIAVNLEDDIIKAVDRGVKTKILLTKNLLPRLKASKIIDYAKEGKLELRALDKFDLPMLICDEEVFFALEDLAARYFNYETQVWIKDHRVVALFKEKFNEYWEKAEKV 264
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261   


Chain B from PDB  Type:PROTEIN  Length:263
                                                                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh..hhhhhhhhhhhhhhh..hhhhhhhh...hhhhhhhhhhhhhhhh.eeee.....eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..............eeee.hhhhhhhhhhhhhh....eeeeee.......hhhhhhhhhh...eeeeeee..hhhhhh...hhhhhhh...eeeee......eeee..eeeee..hhhhhhh....eeeeehhhhhhhhhhhhhhhhh..ee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5bpi B   2 SKDRMVELLQEHFELNLYEARAYVALVAFGVLTPAELASVSEVPAPRTYDVLRSLEKKGFAMTQPGKTNKYRPVHPANVLEKFIQDWQERVKEELEAKKKAKEELLELMAPLIETEVPKYGVERVWVVRGIKNSTLKTKEMLEEAQNEILLADDGFIAVNLEDDIIKAVDRGVKTKILLTKNLLPRLKASKIIDYAKEGKLELRALDKFDLPMLICDEEVFFALEDLAARYFNYETQVWIKDHRVVALFKEKFNEYWEKAEKV 264
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261   


Chain C from PDB  Type:PROTEIN  Length:258
                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhh..hhhhhhhhhhhhhhh..hhhhhhhhh..hhhhhhhhhhhhhh...eee.......eee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........eeeee.hhhhhhhhhhhhhh...eeeeee.......hhhhhhhhhhh..eeeeeee.hhhhhhh.hhhhhhhh....eeeee......eeee..eeeee..hhhhhhh...eeeeeehhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5bpi C   2 SKDRMVELLQEHFELNLYEARAYVALVAFGVLTPAELASVSEVPAPRTYDVLRSLEKKGFAMTQPGKTNKYRPVHPANVLEKFIQDWQERVKEELEAKKKAKEELLELMAPLIETEVERVWVVRGIKNSTLKTKEMLEEAQNEILLADDGFIAVNLEDDIIKAVDRGVKTKILLTKNLLPRLKASKIIDYAKEGKLELRALDKFDLPMLICDEEVFFALEDLAARYFNYETQVWIKDHRVVALFKEKFNEYWEKAEKV 264
                                    11        21        31        41        51        61        71        81        91       101       111     ||126       136       146       156       166       176       186       196       206       216       226       236       246       256        
                                                                                                                                             117|                                                                                                                                             
                                                                                                                                              123                                                                                                                                             


Chain D from PDB  Type:PROTEIN  Length:255
                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh..hhhhhhhhhhhhhhh..hhhhhhhhh..hhhhhhhhhhhhhhh..eee.......eee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......eeeee.hhhhhhhhhhhhhh...eeeeee.......hhhhhhhhhh...eeeeeee.hhhhhhh.hhhhhhhh....eeeee......eee...eeeee..hhhhhhh...eeeeeehhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5bpi D   2 SKDRMVELLQEHFELNLYEARAYVALVAFGVLTPAELASVSEVPAPRTYDVLRSLEKKGFAMTQPGKTNKYRPVHPANVLEKFIQDWQERVKEELEAKKKAKEELLELMAPLIEERVWVVRGIKNSTLKTKEMLEEAQNEILLADDGFIAVNLEDDIIKAVDRGVKTKILLTKNLLPRLKASKIIDYAKEGKLELRALDKFDLPMLICDEEVFFALEDLAARYFNYETQVWIKDHRVVALFKEKFNEYWEKAEKV 264
                                    11        21        31        41        51        61        71        81        91       101       111   ||  129       139       149       159       169       179       189       199       209       219       229       239       249       259     
                                                                                                                                           115|                                                                                                                                            
                                                                                                                                            124                                                                                                                                            


Chain E from PDB  Type:DNA  Length:21
                                                     
                 5bpi E   1 TATATCATCGATAGTGATATA  21
                                    10        20 


Chain F from PDB  Type:DNA  Length:21
                                                     
                 5bpi F   1 TATATCACTATCGATGATATA  21
                                    10        20
   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 5BPI)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5BPI)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5BPI)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
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    Gly B:122 - Val B:123   [ RasMol ]  
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  5bpi
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  TMBL2_PYRFU | Q8U3H1
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 Related Entries

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UniProtKB/Swiss-Prot
        TMBL2_PYRFU | Q8U3H1: 5box 5bpd 5bqt

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