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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 :  29 May 15  (Deposition) - 02 Sep 15  (Release) - 07 Oct 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym./Biol. Unit :  A,B,C,D
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 - PUTATIVE HTH-TYPE TRANSCRIPTIONAL REGULATOR TRMBL2
    Chains: A, B, C, D
    Organism Scientific: PYROCOCCUS FURIOSUS
    Organism Taxid: 2261

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN B:79 , LEU D:137 , GLU D:141binding site for residue CA B 301
2AC2SOFTWAREGLU D:144binding site for residue CA D 301
3AC3SOFTWARETYR C:50 , ASP C:51 , VAL C:52 , LEU C:53 , SER C:55 , LEU C:56 , GLU C:57 , LYS C:58 , SER C:191 , LYS C:192 , ILE C:193 , ILE C:194 , TYR C:196 , ALA C:197 , LYS C:198 , GLU C:199 , TYR D:50 , ASP D:51 , VAL D:52 , LEU D:53 , SER D:55 , LEU D:56 , GLU D:57 , LYS D:58 , LYS D:101 , GLU D:104 , LYS D:192 , ILE D:194 , TYR D:196 , ALA D:197 , LYS D:198 , GLU D:199binding site for Di-peptide ARG D 54 and ASP C 195

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (19, 19)

Asymmetric/Biological Unit
No.Residues
1Gly A:156 -Phe A:157
2Val A:160 -Asn A:161
3Glu A:199 -Gly A:200
4Asp A:227 -Leu A:228
5Phe A:233 -Asn A:234
6Ala A:261 -Glu A:262
7Gly B:156 -Phe B:157
8Val B:160 -Asn B:161
9Glu B:199 -Gly B:200
10Glu B:259 -Lys B:260
11Glu B:262 -Lys B:263
12Gly C:67 -Lys C:68
13Glu C:117 -Val C:118
14Val C:118 -Pro C:119
15Lys C:189 -Ala C:190
16Ala C:190 -Ser C:191
17Val D:118 -Pro D:119
18Ile D:194 -Asp D:195
19Leu D:228 -Ala D:229

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5BQT)

(-) 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:261
                                                                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh..hhhhhhhhhhhhhhh..hhhhhhhhh..hhhhhhhhhhhhhhh..eeee.....eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........eeeeehhhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhh..eeeeeee.hhhhhhh..hhhhhhhh..eeeeee......eeee...eeee............eeeee.hhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5bqt A   2 SKDRMVELLQEHFELNLYEARAYVALVAFGVLTPAELASVSEVPAPRTYDVLRSLEKKGFAMTQPGKTNKYRPVHPANVLEKFIQDWQERVKEELEAKKKAKEELLELMAPLIETEVPKYGVERVWVVRGIKNSTLKTKEMLEEAQNEILLADDGFIAVNLEDDIIKAVDRGVKTKILLTKNLLPRLKASKIIDYAKEGKLELRALDKFDLPMLICDEEVFFALEDLAARYFNYETQVWIKDHRVVALFKEKFNEYWEKAE 262
                                    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:253
                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh..hhhhhhhhhhhhhhh..hhhhhhhhh..hhhhhhhhhhhhhhh..eeee.....eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........eeeeehhhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhh..eeeeee.hhhhhhhh..hhhhhhhh...eeee.......eeee...eeee...eeeee.hhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5bqt B   2 SKDRMVELLQEHFELNLYEARAYVALVAFGVLTPAELASVSEVPAPRTYDVLRSLEKKGFAMTQPGKTNKYRPVHPANVLEKFIQDWQERVKEELEAKKKAKEELLELMAPLIETEVPKYGVERVWVVRGIKNSTLKTKEMLEEAQNEILLADDGFIAVNLEDDIIKAVDRGVKTKILLTKNLLPRLKASKIIDYAKEGKLELRALDKFDLPMLICDEEVFFALYETQVWIKDHRVVALFKEKFNEYWEKAEK 263
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221   ||  240       250       260   
                                                                                                                                                                                                                                                         225|                            
                                                                                                                                                                                                                                                          235                            


Chain C 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..eee.......eee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........eeeee.hhhhhhhhhhhhhhh..eeeeee.......hhhhhhhhhhh..eeeeeee.hhhhhh..hhhhhhhhh...eeeee......eeee...eeee.....hhhhh..eeeee.hhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5bqt C   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 D 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..eee.......eee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........eeeee.hhhhhhhhhhhhhhh..eeeeee.......hhhhhhhhhh...eeeeeee.hhh......hhhhhh.....eeeee......eeee..eeeee.....hhhhh..eeeee.hhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5bqt D   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
   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 5BQT)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Ala A:261 - Glu A:262   [ RasMol ]  
    Ala C:190 - Ser C:191   [ RasMol ]  
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    Gly A:156 - Phe A:157   [ RasMol ]  
    Gly B:156 - Phe B:157   [ RasMol ]  
    Gly C:67 - Lys C:68   [ RasMol ]  
    Ile D:194 - Asp D:195   [ RasMol ]  
    Leu D:228 - Ala D:229   [ RasMol ]  
    Lys C:189 - Ala C:190   [ RasMol ]  
    Phe A:233 - Asn A:234   [ RasMol ]  
    Val A:160 - Asn A:161   [ RasMol ]  
    Val B:160 - Asn B:161   [ RasMol ]  
    Val C:118 - Pro C:119   [ RasMol ]  
    Val D:118 - Pro D:119   [ RasMol ]  
 

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  5bqt
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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 5bpi

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