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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 :  2.40
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
    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
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2IMD2Ligand/IonIMIDAZOLE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:37binding site for residue GOL A 301
2AC2SOFTWAREGLY C:131 , ILE C:132 , LYS C:133 , ASN C:234 , TYR C:235 , GLU C:236binding site for residue GOL C 301
3AC3SOFTWARESER C:2 , ARG C:22 , SER C:42 , GLU C:43 , PHE D:233binding site for residue IMD C 302
4AC4SOFTWAREGLU C:219 , HIS C:244 , HOH C:417binding site for residue IMD C 303

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Lys A:189 -Ala A:190
2Ser A:191 -Lys A:192
3Ala B:190 -Ser B:191
4Gly C:67 -Lys C:68

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5BPD)

(-) 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...hhhhhhhhhhhhhhh..eeee.....eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..............eeee.hhhhhhhhhhhhhhhh..eeeeee.......hhhhhhhhhhh..eeeeeee.hhhhhh...hhhhhhhh...eeeee......eeee..eeeee..hhhhhhh....eeeeehhhhhhhhhhhhhhhhh..ee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5bpd 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:262
                                                                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh..hhhhhhhhhhhhhhh..hhhhhhhhh..hhhhhhhhhhhhhhh..eeee.....eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..............eeee.hhhhhhhhhhhhhhhh..eeeeee.......hhhhhhhhhhh..eeeeeee.hhhhhh....hhhhhhh...eeeee......eeee..eeeee..hhhhhhh....eeeeehhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5bpd B   2 SKDRMVELLQEHFELNLYEARAYVALVAFGVLTPAELASVSEVPAPRTYDVLRSLEKKGFAMTQPGKTNKYRPVHPANVLEKFIQDWQERVKEELEAKKKAKEELLELMAPLIETEVPKYGVERVWVVRGIKNSTLKTKEMLEEAQNEILLADDGFIAVNLEDDIIKAVDRGVKTKILLTKNLLPRLKASKIIDYAKEGKLELRALDKFDLPMLICDEEVFFALEDLAARYFNYETQVWIKDHRVVALFKEKFNEYWEKAEK 263
                                    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:260
                                                                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh..hhhhhhhhhhhhhhh..hhhhhhhhh..hhhhhhhhhhhhhhh..eee.......eee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........eeeee.hhhhhhhhhhhhhhh..eeeeee.......hhhhhhhhhhh..eeeeeee.hhhhhhh.hhhhhhhhh...eeeee......eeee..eeeee..hhhhhhh...eeeeeehhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5bpd C   2 SKDRMVELLQEHFELNLYEARAYVALVAFGVLTPAELASVSEVPAPRTYDVLRSLEKKGFAMTQPGKTNKYRPVHPANVLEKFIQDWQERVKEELEAKKKAKEELLELMAPLIETEVPVERVWVVRGIKNSTLKTKEMLEEAQNEILLADDGFIAVNLEDDIIKAVDRGVKTKILLTKNLLPRLKASKIIDYAKEGKLELRALDKFDLPMLICDEEVFFALEDLAARYFNYETQVWIKDHRVVALFKEKFNEYWEKAEKV 264
                                    11        21        31        41        51        61        71        81        91       101       111       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264
                                                                                                                                               119|                                                                                                                                             
                                                                                                                                                123                                                                                                                                             


Chain D from PDB  Type:PROTEIN  Length:260
                                                                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh..hhhhhhhhhhhhhhh..hhhhhhhhh..hhhhhhhhhhhhhhh..eee.......eee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............eeeee.hhhhhhhhhhhhhhh..eeeeee.......hhhhhhhhhhh..eeeeeee.hhhhhhh.hhhhhhhhh...eeeee......eeee..eeeee..hhhhhhh...eeeeeehhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5bpd D   1 MSKDRMVELLQEHFELNLYEARAYVALVAFGVLTPAELASVSEVPAPRTYDVLRSLEKKGFAMTQPGKTNKYRPVHPANVLEKFIQDWQERVKEELEAKKKAKEELLELMAPLIETEKYGVERVWVVRGIKNSTLKTKEMLEEAQNEILLADDGFIAVNLEDDIIKAVDRGVKTKILLTKNLLPRLKASKIIDYAKEGKLELRALDKFDLPMLICDEEVFFALEDLAARYFNYETQVWIKDHRVVALFKEKFNEYWEKAE 262
                                    10        20        30        40        50        60        70        80        90       100       110      |122       132       142       152       162       172       182       192       202       212       222       232       242       252       262
                                                                                                                                              117|                                                                                                                                              
                                                                                                                                               120                                                                                                                                              


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


Chain F from PDB  Type:DNA  Length:21
                                                     
                 5bpd 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 5BPD)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)

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

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