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(-) Description

Title :  CRYSTAL STRUCTURE OF PUTATIVE TRANSCRIPTIONAL REGULATOR YCDC
 
Authors :  Y. V. Patskovsky, A. A. Knapik, V. Mennella, S. K. Burley, W. Minor, S. C. York Sgx Research Center For Structural Genomics (Nysgxrc)
Date :  03 Feb 10  (Deposition) - 16 Mar 10  (Release) - 16 Jun 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Helix-Turn-Helix, Putative Transcriptional Regulator, Dimer, Uracil, Structural Genomics, Psi, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc, Dna-Binding, Repressor, Transcription, Transcription Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. V. Patskovsky, V. Mennella, S. C. Almo
Crystal Structure Of Hypothetical Transcriptional Regulator Ycdc From Escherichia Coli
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - HTH-TYPE TRANSCRIPTIONAL REGULATOR RUTR
    ChainsA, B, C, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidT7 TOPO-CT
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneB1013, JW0998, RUTR, YCDC
    Organism ScientificESCHERICHIA COLI
    Organism Taxid83333
    StrainK12
    SynonymRUT OPERON REPRESSOR

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)AB  
Biological Unit 2 (1x)  CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 20)

Asymmetric Unit (2, 20)
No.NameCountTypeFull Name
1MSE16Mod. Amino AcidSELENOMETHIONINE
2URA4Ligand/IonURACIL
Biological Unit 1 (2, 10)
No.NameCountTypeFull Name
1MSE8Mod. Amino AcidSELENOMETHIONINE
2URA2Ligand/IonURACIL
Biological Unit 2 (2, 10)
No.NameCountTypeFull Name
1MSE8Mod. Amino AcidSELENOMETHIONINE
2URA2Ligand/IonURACIL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:76 , LYS A:100 , PHE A:114 , TRP A:166 , GLN A:170 , GLN B:178BINDING SITE FOR RESIDUE URA A 212
2AC2SOFTWAREPHE A:175 , GLN A:178 , LEU B:73 , TRP B:76 , LYS B:100 , TRP B:166 , GLN B:170 , HOH B:224BINDING SITE FOR RESIDUE URA B 212
3AC3SOFTWARELEU C:73 , TRP C:76 , LYS C:100 , PHE C:114 , TRP C:166 , GLN C:170 , GLN D:178BINDING SITE FOR RESIDUE URA C 212
4AC4SOFTWAREPHE C:175 , GLN C:178 , LEU D:73 , TRP D:76 , LYS D:100 , PHE D:114 , TRP D:166 , GLN D:170BINDING SITE FOR RESIDUE URA D 212

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3LOC)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3LOC)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3LOC)

(-) PROSITE Motifs  (1, 4)

Asymmetric Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HTH_TETR_2PS50977 TetR-type HTH domain profile.RUTR_ECOLI17-77
 
 
 
  4A:16-76
B:16-76
C:16-76
D:16-76
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HTH_TETR_2PS50977 TetR-type HTH domain profile.RUTR_ECOLI17-77
 
 
 
  2A:16-76
B:16-76
-
-
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HTH_TETR_2PS50977 TetR-type HTH domain profile.RUTR_ECOLI17-77
 
 
 
  2-
-
C:16-76
D:16-76

(-) Exons   (0, 0)

(no "Exon" information available for 3LOC)

(-) Sequences/Alignments

Asymmetric 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
 aligned with RUTR_ECOLI | P0ACU2 from UniProtKB/Swiss-Prot  Length:212

    Alignment length:201
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211 
           RUTR_ECOLI    12 RSRAVSAKKKAILSAALDTFSQFGFHGTRLEQIAELAGVSKTNLLYYFPSKEALYIAVLRQILDIWLAPLKAFREDFAPLAAIKEYIRLKLEVSRDYPQASRLFCMEMLAGAPLLMDELTGDLKALIDEKSALIAGWVKSGKLAPIDPQHLIFMIWASTQHYADFAPQVEAVTGATLRDEVFFNQTVENVQRIIIEGIRPR 212
               SCOP domains d3loca1 A:11-85 Hypothetical transcriptional regulator YcdC                d3loca2 A:86-211 Hypothetical transcriptional regulator YcdC                                                                   SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----HTH_TETR_2  PDB: A:16-76 UniProt: 17-77                      --------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3loc A  11 RSRAVSAKKKAILSAALDTFSQFGFHGTRLEQIAELAGVSKTNLLYYFPSKEALYIAVLRQILDIWLAPLKAFREDFAPLAAIKEYIRLKLEVSRDYPQASRLFCmEmLAGAPLLmDELTGDLKALIDEKSALIAGWVKSGKLAPIDPQHLIFmIWASTQHYADFAPQVEAVTGATLRDEVFFNQTVENVQRIIIEGIRPR 211
                                    20        30        40        50        60        70        80        90       100       110     | 120     | 130       140       150       160   |   170       180       190       200       210 
                                                                                                                                   116-MSE   126-MSE                               164-MSE                                           
                                                                                                                                     118-MSE                                                                                         

Chain B from PDB  Type:PROTEIN  Length:201
 aligned with RUTR_ECOLI | P0ACU2 from UniProtKB/Swiss-Prot  Length:212

    Alignment length:201
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211 
           RUTR_ECOLI    12 RSRAVSAKKKAILSAALDTFSQFGFHGTRLEQIAELAGVSKTNLLYYFPSKEALYIAVLRQILDIWLAPLKAFREDFAPLAAIKEYIRLKLEVSRDYPQASRLFCMEMLAGAPLLMDELTGDLKALIDEKSALIAGWVKSGKLAPIDPQHLIFMIWASTQHYADFAPQVEAVTGATLRDEVFFNQTVENVQRIIIEGIRPR 212
               SCOP domains d3locb1 B:11-85 Hypothetical transcriptional regulator YcdC                d3locb2 B:86-211 Hypothetical transcriptional regulator YcdC                                                                   SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----HTH_TETR_2  PDB: B:16-76 UniProt: 17-77                      --------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3loc B  11 RSRAVSAKKKAILSAALDTFSQFGFHGTRLEQIAELAGVSKTNLLYYFPSKEALYIAVLRQILDIWLAPLKAFREDFAPLAAIKEYIRLKLEVSRDYPQASRLFCmEmLAGAPLLmDELTGDLKALIDEKSALIAGWVKSGKLAPIDPQHLIFmIWASTQHYADFAPQVEAVTGATLRDEVFFNQTVENVQRIIIEGIRPR 211
                                    20        30        40        50        60        70        80        90       100       110     | 120     | 130       140       150       160   |   170       180       190       200       210 
                                                                                                                                   116-MSE   126-MSE                               164-MSE                                           
                                                                                                                                     118-MSE                                                                                         

Chain C from PDB  Type:PROTEIN  Length:200
 aligned with RUTR_ECOLI | P0ACU2 from UniProtKB/Swiss-Prot  Length:212

    Alignment length:200
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212
           RUTR_ECOLI    13 SRAVSAKKKAILSAALDTFSQFGFHGTRLEQIAELAGVSKTNLLYYFPSKEALYIAVLRQILDIWLAPLKAFREDFAPLAAIKEYIRLKLEVSRDYPQASRLFCMEMLAGAPLLMDELTGDLKALIDEKSALIAGWVKSGKLAPIDPQHLIFMIWASTQHYADFAPQVEAVTGATLRDEVFFNQTVENVQRIIIEGIRPR 212
               SCOP domains d3locc1 C:12-85 Hypothetical transcriptional regulator YcdC               d3locc2 C:86-211 Hypothetical transcriptional regulator YcdC                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----HTH_TETR_2  PDB: C:16-76 UniProt: 17-77                      --------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3loc C  12 SRAVSAKKKAILSAALDTFSQFGFHGTRLEQIAELAGVSKTNLLYYFPSKEALYIAVLRQILDIWLAPLKAFREDFAPLAAIKEYIRLKLEVSRDYPQASRLFCmEmLAGAPLLmDELTGDLKALIDEKSALIAGWVKSGKLAPIDPQHLIFmIWASTQHYADFAPQVEAVTGATLRDEVFFNQTVENVQRIIIEGIRPR 211
                                    21        31        41        51        61        71        81        91       101       111    | |121    |  131       141       151       161  |    171       181       191       201       211
                                                                                                                                  116-MSE   126-MSE                               164-MSE                                           
                                                                                                                                    118-MSE                                                                                         

Chain D from PDB  Type:PROTEIN  Length:201
 aligned with RUTR_ECOLI | P0ACU2 from UniProtKB/Swiss-Prot  Length:212

    Alignment length:201
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211 
           RUTR_ECOLI    12 RSRAVSAKKKAILSAALDTFSQFGFHGTRLEQIAELAGVSKTNLLYYFPSKEALYIAVLRQILDIWLAPLKAFREDFAPLAAIKEYIRLKLEVSRDYPQASRLFCMEMLAGAPLLMDELTGDLKALIDEKSALIAGWVKSGKLAPIDPQHLIFMIWASTQHYADFAPQVEAVTGATLRDEVFFNQTVENVQRIIIEGIRPR 212
               SCOP domains d3locd1 D:11-85 Hypothetical transcriptional regulator YcdC                d3locd2 D:86-211 Hypothetical transcriptional regulator YcdC                                                                   SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhh.hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----HTH_TETR_2  PDB: D:16-76 UniProt: 17-77                      --------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3loc D  11 RSRAVSAKKKAILSAALDTFSQFGFHGTRLEQIAELAGVSKTNLLYYFPSKEALYIAVLRQILDIWLAPLKAFREDFAPLAAIKEYIRLKLEVSRDYPQASRLFCmEmLAGAPLLmDELTGDLKALIDEKSALIAGWVKSGKLAPIDPQHLIFmIWASTQHYADFAPQVEAVTGATLRDEVFFNQTVENVQRIIIEGIRPR 211
                                    20        30        40        50        60        70        80        90       100       110     | 120     | 130       140       150       160   |   170       180       190       200       210 
                                                                                                                                   116-MSE   126-MSE                               164-MSE                                           
                                                                                                                                     118-MSE                                                                                         

   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  (2, 8)

Asymmetric Unit

(-) CATH Domains  (0, 0 ; only for superseded entry 1PB6: 2,8)

(no "CATH Domain" information available for 3LOC, only for superseded entry 1PB6 replaced by 3LOC)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3LOC)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (RUTR_ECOLI | P0ACU2)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0003700    transcription factor activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
biological process
    GO:0045892    negative regulation of transcription, DNA-templated    Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0045893    positive regulation of transcription, DNA-templated    Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.

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 Related Entries

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

UniProtKB/Swiss-Prot
        RUTR_ECOLI | P0ACU24jyk 4x1e 4xk4

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