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(-) Description

Title :  STRUCTURE OF E. COLI TRANSCRIPTIONAL REGULATOR RUTR WITH BOUND URACIL
 
Authors :  D. R. Cooper, A. A. Knapik, J. J. Petkowski, P. J. Porebski, T. Osinski, S W. Minor, New York Structural Genomics Research Consortium (N
Date :  29 Mar 13  (Deposition) - 14 Aug 13  (Release) - 14 Aug 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Psi-Biology, New York Structural Genomics Research Consortium, Nysgrc, Helix-Turn-Helix, Transcriptional Regulator, Transcription Regulator (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. R. Cooper, A. A. Knapik, J. J. Petkowski, P. J. Porebski, T. Osinski, S. C. Almo, W. Minor, New York Structural Genomics Research Consortium (Nysgrc)
Structure Of E. Coli Transcriptional Regulator Rutr With Bound Uracil
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - HTH-TYPE TRANSCRIPTIONAL REGULATOR RUTR
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: B1013, JW0998, RUTR, YCDC
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12
    Synonym: RUT OPERON REPRESSOR

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 9)

Asymmetric/Biological Unit (2, 9)
No.NameCountTypeFull Name
1SO47Ligand/IonSULFATE ION
2URA2Ligand/IonURACIL

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:85 , GLU A:86 , ASP A:87 , LYS B:19 , ASN B:54 , TYR B:58BINDING SITE FOR RESIDUE SO4 A 301
2AC2SOFTWAREALA A:89 , PRO A:90 , LEU A:91 , ALA A:92 , HOH A:431BINDING SITE FOR RESIDUE SO4 A 302
3AC3SOFTWARELYS A:95 , ARG A:99 , GLN A:202 , HOH A:446 , HOH A:448BINDING SITE FOR RESIDUE SO4 A 303
4AC4SOFTWAREARG A:12 , SER A:13 , VAL A:16 , HOH A:470BINDING SITE FOR RESIDUE SO4 A 304
5AC5SOFTWARELEU A:74 , TRP A:77 , LYS A:101 , PHE A:115 , TRP A:167 , GLN A:171 , HOH A:404 , PHE B:176 , GLN B:179BINDING SITE FOR RESIDUE URA A 305
6AC6SOFTWAREARG B:40 , LEU B:41 , GLU B:42 , LYS B:52 , HOH B:537BINDING SITE FOR RESIDUE SO4 B 301
7AC7SOFTWAREARG A:85 , SER B:51 , ASN B:54BINDING SITE FOR RESIDUE SO4 B 302
8AC8SOFTWARELYS B:95 , ARG B:99 , GLN B:202 , HOH B:420BINDING SITE FOR RESIDUE SO4 B 303
9AC9SOFTWAREPHE A:176 , GLN A:179 , LEU B:74 , TRP B:77 , LYS B:101 , PHE B:115 , TRP B:167 , GLN B:171 , HOH B:408BINDING SITE FOR RESIDUE URA B 304

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4JYK)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4JYK)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4JYK)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4JYK)

(-) Exons   (0, 0)

(no "Exon" information available for 4JYK)

(-) 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:201
                                                                                                                                                                                                                                         
               SCOP domains d4jyka1 A:12-86 Hypothetical transcriptional regulator YcdC                d4jyka2 A:87-212 Hypothetical transcriptional regulator YcdC                                                                   SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhh.hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jyk A  12 RSRAVSAKKKAILSAALDTFSQFGFHGTRLEQIAELAGVSKTNLLYYFPSKEALYIAVLRQILDIWLAPLKAFREDFAPLAAIKEYIRLKLEVSRDYPQASRLFCMEMLAGAPLLMDELTGDLKALIDEKSALIAGWVKSGKLAPIDPQHLIFMIWASTQHYADFAPQVEAVTGATLRDEVFFNQTVENVQRIIIEGIRPR 212
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211 


Chain B from PDB  Type:PROTEIN  Length:196
                                                                                                                                                                                                                                    
               SCOP domains d4jykb1 B:17-86 Hypothetical transcriptional regulator YcdC           d4jykb2 B:87-212 Hypothetical transcriptional regulator YcdC                                                                   SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jyk B  17 SAKKKAILSAALDTFSQFGFHGTRLEQIAELAGVSKTNLLYYFPSKEALYIAVLRQILDIWLAPLKAFREDFAPLAAIKEYIRLKLEVSRDYPQASRLFCMEMLAGAPLLMDELTGDLKALIDEKSALIAGWVKSGKLAPIDPQHLIFMIWASTQHYADFAPQVEAVTGATLRDEVFFNQTVENVQRIIIEGIRPR 212
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206
   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  (2, 4)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4JYK)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4JYK)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)

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  4jyk
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  RUTR_ECOLI | P0ACU2
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 Related Entries

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

UniProtKB/Swiss-Prot
        RUTR_ECOLI | P0ACU2: 3loc 4x1e 4xk4

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