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(-) Description

Title :  CRYSTAL STRUCTURE OF A TRUNCATED FORM OF THERMUS THERMOPHILUS CARH BOUND TO ADENOSYLCOBALAMIN (DARK STATE)
 
Authors :  M. Jost, C. L. Drennan
Date :  25 Jun 15  (Deposition) - 30 Sep 15  (Release) - 04 Nov 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Transcription Factor, Light Sensor, Adenosylcobalamin-Binding, Dna- Binding, Transcription, Transcriptional Regulator (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Jost, J. Fernandez-Zapata, M. C. Polanco, J. M. Ortiz-Guerrero, P. Y. Chen, G. Kang, S. Padmanabhan, M. Elias-Arnanz, C. L. Drennan
Structural Basis For Gene Regulation By A B12-Dependent Photoreceptor.
Nature V. 526 536 2015
PubMed-ID: 26416754  |  Reference-DOI: 10.1038/NATURE14950

(-) Compounds

Molecule 1 - LIGHT-DEPENDENT TRANSCRIPTIONAL REGULATOR CARH
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: BL21 STAR PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TT_P0056
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 262724
    Strain: HB27 / ATCC BAA-163 / DSM 7039

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 9)

Asymmetric/Biological Unit (3, 9)
No.NameCountTypeFull Name
15AD4Ligand/Ion5'-DEOXYADENOSINE
2B124Ligand/IonCOBALAMIN
3GOL1Ligand/IonGLYCEROL

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:121 , LEU A:124 , ARG A:125 , GLY A:128 , GLU A:129 , TRP A:131 , HIS A:132 , GLU A:141 , HIS A:142 , SER A:145 , GLY A:174 , GLU A:175 , ARG A:176 , HIS A:177 , GLU A:178 , ILE A:179 , GLY A:180 , SER A:222 , VAL A:224 , LEU A:225 , GLY A:247 , GLY A:248 , GLN A:249 , MET A:264 , ASP A:266 , LEU A:267 , 5AD A:301 , HOH A:401 , HOH A:403 , HOH A:406 , HOH A:408 , HOH A:437 , HOH A:442binding site for residue B12 A 300
2AC2SOFTWARETRP A:131 , VAL A:138 , GLU A:141 , HIS A:142 , B12 A:300 , ASP B:201 , HOH B:424binding site for residue 5AD A 301
3AC3SOFTWARELEU B:121 , LEU B:124 , ARG B:125 , GLY B:128 , TRP B:131 , HIS B:132 , GLU B:141 , HIS B:142 , SER B:145 , ARG B:149 , GLY B:174 , GLU B:175 , ARG B:176 , HIS B:177 , GLU B:178 , ILE B:179 , GLY B:180 , VAL B:220 , LEU B:221 , SER B:222 , VAL B:224 , LEU B:225 , GLY B:247 , GLY B:248 , GLN B:249 , MET B:264 , LEU B:267 , 5AD B:302 , HOH B:401 , HOH B:402 , HOH B:415 , HOH B:418 , HOH B:434 , ARG D:230binding site for residue B12 B 301
4AC4SOFTWAREASP A:201 , PRO A:203 , TRP B:131 , VAL B:138 , GLU B:141 , HIS B:142 , B12 B:301binding site for residue 5AD B 302
5AC5SOFTWARELYS B:238 , ALA B:241 , PRO B:242 , ARG B:243 , VAL B:244 , GLY B:260 , GLU B:262binding site for residue GOL B 303
6AC6SOFTWARELEU C:121 , LEU C:124 , ARG C:125 , GLY C:128 , GLU C:129 , TRP C:131 , GLU C:141 , HIS C:142 , SER C:145 , GLY C:174 , GLU C:175 , ARG C:176 , HIS C:177 , GLU C:178 , ILE C:179 , GLY C:180 , VAL C:220 , LEU C:221 , SER C:222 , VAL C:224 , LEU C:225 , GLY C:247 , GLY C:248 , GLN C:249 , MET C:264 , ASP C:266 , LEU C:267 , 5AD C:301 , HOH C:408 , HOH C:409 , HOH C:414 , HOH C:433 , HOH C:447 , HOH C:452binding site for residue B12 C 300
7AC7SOFTWARETRP C:131 , VAL C:138 , GLU C:141 , HIS C:142 , B12 C:300 , HOH C:404 , HOH C:442 , HOH C:445 , ASP D:201binding site for residue 5AD C 301
8AC8SOFTWAREALA B:231 , HOH B:416 , HOH B:431 , LEU D:121 , LEU D:124 , ARG D:125 , GLY D:128 , TRP D:131 , HIS D:132 , GLU D:141 , HIS D:142 , SER D:145 , ARG D:149 , GLY D:174 , GLU D:175 , ARG D:176 , HIS D:177 , GLU D:178 , ILE D:179 , GLY D:180 , LEU D:221 , SER D:222 , VAL D:224 , LEU D:225 , GLY D:247 , GLY D:248 , GLN D:249 , MET D:264 , ASP D:266 , LEU D:267 , 5AD D:301 , HOH D:402 , HOH D:407 , HOH D:413 , HOH D:427 , HOH D:429 , HOH D:447binding site for residue B12 D 300
9AC9SOFTWAREASP C:201 , PRO C:203 , TRP D:131 , VAL D:138 , GLU D:141 , HIS D:142 , B12 D:300 , HOH D:401 , HOH D:452binding site for residue 5AD D 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5C8A)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5C8A)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5C8A)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5C8A)

(-) Exons   (0, 0)

(no "Exon" information available for 5C8A)

(-) 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:194
                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh.......eeee.......hhhhhhhhhhhhh....eee.....hhhhhhhhhhhh...eeeee...hhhhhh...........eeeee....hhhhhhhhh.ee...hhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5c8a A  81 EDLGTGLLEALLRGDLAGAEALFRRGLRFWGPEGVLEHLLLPVLREVGEAWHRGEIGVAEEHLASTFLRARLQELLDLAGFPPGPPVLVTTPPGERHEIGAMLAAYHLRRKGVPALYLGPDTPLPDLRALARRLGAGAVVLSAVLSEPLRALPDGALKDLAPRVFLGGQGAGPEEARRLGAEYMEDLKGLAEAL 274
                                    90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270    


Chain B from PDB  Type:PROTEIN  Length:194
                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh.......eeee.......hhhhhhhhhhhhhh...eee.....hhhhhhhhhhhh...eeeee...hhhhhh...........eeeee....hhhhhhhhh.ee.....hhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5c8a B  83 LGTGLLEALLRGDLAGAEALFRRGLRFWGPEGVLEHLLLPVLREVGEAWHRGEIGVAEEHLASTFLRARLQELLDLAGFPPGPPVLVTTPPGERHEIGAMLAAYHLRRKGVPALYLGPDTPLPDLRALARRLGAGAVVLSAVLSEPLRALPDGALKDLAPRVFLGGQGAGPEEARRLGAEYMEDLKGLAEALWL 276
                                    92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272    


Chain C from PDB  Type:PROTEIN  Length:195
                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh.......eeee.......hhhhhhhhhhhhh....eee.....hhhhhhhhhhhh...eeeee...hhhhhh...........eeeee....hhhhhhhhh.ee..hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5c8a C  80 PEDLGTGLLEALLRGDLAGAEALFRRGLRFWGPEGVLEHLLLPVLREVGEAWHRGEIGVAEEHLASTFLRARLQELLDLAGFPPGPPVLVTTPPGERHEIGAMLAAYHLRRKGVPALYLGPDTPLPDLRALARRLGAGAVVLSAVLSEPLRALPDGALKDLAPRVFLGGQGAGPEEARRLGAEYMEDLKGLAEAL 274
                                    89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269     


Chain D from PDB  Type:PROTEIN  Length:194
                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh......eeee.......hhhhhhhhhhhhhh...eee.....hhhhhhhhhhhhh..eeeee...hhhhhh...........eeeee....hhhhhhhhh.ee..hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5c8a D  81 EDLGTGLLEALLRGDLAGAEALFRRGLRFWGPEGVLEHLLLPVLREVGEAWHRGEIGVAEEHLASTFLRARLQELLDLAGFPPGPPVLVTTPPGERHEIGAMLAAYHLRRKGVPALYLGPDTPLPDLRALARRLGAGAVVLSAVLSEPLRALPDGALKDLAPRVFLGGQGAGPEEARRLGAEYMEDLKGLAEAL 274
                                    90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270
   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 5C8A)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5C8A)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5C8A)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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        Q746J7_THET2 | Q746J7: 3whp 5c8d 5c8e 5c8f

(-) Related Entries Specified in the PDB File

5c8d 5c8e 5c8f