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(-) Description

Title :  CRYSTAL STRUCUTRE OF THE TRANSCRIPTIONAL FACTOR FROM C.GLUTAMICUM AT 2.2 ANGSTROM RESOLUTION
 
Authors :  Y. G. Gao, M. Yao, I. Tanaka
Date :  22 Mar 07  (Deposition) - 18 Sep 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  A,B  (2x)
Biol. Unit 4:  C,D  (2x)
Keywords :  Helix-Turn-Helix, Interwined Alpha Helices, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. G. Gao, M. Yao, H. Itou, Y. Zhou, I. Tanaka
The Structures Of Transcription Factor Cgl2947 From Corynebacterium Glutamicum In Two Crystal Forms: A Novel Homodimer Assembling And The Implication For Effector-Binding Mode
Protein Sci. V. 16 1878 2007
PubMed-ID: 17766384  |  Reference-DOI: 10.1110/PS.072976907

(-) Compounds

Molecule 1 - PREDICTED TRANSCRIPTIONAL REGULATORS
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET26(B)
    Expression System Strain: B834(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: CGL2947
    Organism Scientific: CORYNEBACTERIUM GLUTAMICUM ATCC 13032
    Organism Taxid: 196627
    Strain: ATCC13032
    Synonym: TRANSCRIPTION FACTOR, BACTERIAL REGULATORY PROTEIN, GNTR FAMILY

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD
Biological Unit 3 (2x): AB  
Biological Unit 4 (2x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1MSE2Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1MSE2Mod. Amino AcidSELENOMETHIONINE
Biological Unit 3 (1, 4)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE
Biological Unit 4 (1, 4)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 2EK5)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2EK5)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2EK5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2EK5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2EK5)

(-) Exons   (0, 0)

(no "Exon" information available for 2EK5)

(-) 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:115
 aligned with Q8NLJ5_CORGL | Q8NLJ5 from UniProtKB/TrEMBL  Length:121

    Alignment length:115
                                    12        22        32        42        52        62        72        82        92       102       112     
         Q8NLJ5_CORGL     3 VPLYKQIASLIEDSIVDGTLSIDQRVPSTNELAAFHRINPATARNGLTLLVEAGILYKKRGIGMFVSAQAPALIRERRDAAFAATYVAPLIDESIHLGFTRARIHALLDQVAESR 117
               SCOP domains ------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh..........hhhhhhhhh..hhhhhhhhhhhhhh...eeee...eeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 2ek5 A   3 VPLYKQIASLIEDSIVDGTLSIDQRVPSTNELAAFHRINPATARNGLTLLVEAGILYKKRGIGmFVSAQAPALIRERRDAAFAATYVAPLIDESIHLGFTRARIHALLDQVAESR 117
                                    12        22        32        42        52        62   |    72        82        92       102       112     
                                                                                          66-MSE                                               


Chain B from PDB  Type:PROTEIN  Length:109
 aligned with Q8NLJ5_CORGL | Q8NLJ5 from UniProtKB/TrEMBL  Length:121

    Alignment length:109
                                    19        29        39        49        59        69        79        89        99       109         
         Q8NLJ5_CORGL    10 ASLIEDSIVDGTLSIDQRVPSTNELAAFHRINPATARNGLTLLVEAGILYKKRGIGMFVSAQAPALIRERRDAAFAATYVAPLIDESIHLGFTRARIHALLDQVAESRG 118
               SCOP domains ------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhh..........hhhhhhhhhh.hhhhhhhhhhhhhhh..eeee...eeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------- Transcript
                 2ek5 B  10 ASLIEDSIVDGTLSIDQRVPSTNELAAFHRINPATARNGLTLLVEAGILYKKRGIGmFVSAQAPALIRERRDAAFAATYVAPLIDESIHLGFTRARIHALLDQVAESRG 118
                                    19        29        39        49        59      | 69        79        89        99       109         
                                                                                   66-MSE                                                


Chain C from PDB  Type:PROTEIN  Length:118
 aligned with Q8NLJ5_CORGL | Q8NLJ5 from UniProtKB/TrEMBL  Length:121

    Alignment length:118
                                    12        22        32        42        52        62        72        82        92       102       112        
         Q8NLJ5_CORGL     3 VPLYKQIASLIEDSIVDGTLSIDQRVPSTNELAAFHRINPATARNGLTLLVEAGILYKKRGIGMFVSAQAPALIRERRDAAFAATYVAPLIDESIHLGFTRARIHALLDQVAESRGLY 120
               SCOP domains ---------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh..........hhhhhhhhhh.hhhhhhhhhhhhhhh..eeee...eeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 2ek5 C   3 VPLYKQIASLIEDSIVDGTLSIDQRVPSTNELAAFHRINPATARNGLTLLVEAGILYKKRGIGmFVSAQAPALIRERRDAAFAATYVAPLIDESIHLGFTRARIHALLDQVAESRGLY 120
                                    12        22        32        42        52        62   |    72        82        92       102       112        
                                                                                          66-MSE                                                  


Chain D from PDB  Type:PROTEIN  Length:115
 aligned with Q8NLJ5_CORGL | Q8NLJ5 from UniProtKB/TrEMBL  Length:121

    Alignment length:115
                                    12        22        32        42        52        62        72        82        92       102       112     
         Q8NLJ5_CORGL     3 VPLYKQIASLIEDSIVDGTLSIDQRVPSTNELAAFHRINPATARNGLTLLVEAGILYKKRGIGMFVSAQAPALIRERRDAAFAATYVAPLIDESIHLGFTRARIHALLDQVAESR 117
               SCOP domains ------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh..........hhhhhhhhhh.hhhhhhhhhhhhhhh..eeee...eeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 2ek5 D   3 VPLYKQIASLIEDSIVDGTLSIDQRVPSTNELAAFHRINPATARNGLTLLVEAGILYKKRGIGmFVSAQAPALIRERRDAAFAATYVAPLIDESIHLGFTRARIHALLDQVAESR 117
                                    12        22        32        42        52        62   |    72        82        92       102       112     
                                                                                          66-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  (0, 0)

(no "SCOP Domain" information available for 2EK5)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2EK5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2EK5)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q8NLJ5_CORGL | Q8NLJ5)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    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: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

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UniProtKB/TrEMBL
        Q8NLJ5_CORGL | Q8NLJ5: 2du9

(-) Related Entries Specified in the PDB File

2du9 THE SAME PROTEIN COMPLEXED WITH MPD