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(-) Description

Title :  CRYSTAL STRUCTURE OF THE ETHIDIUM-BOUND FORM OF THE MULTI-DRUG BINDING TRANSCRIPTIONAL REPRESSOR CGMR
 
Authors :  H. Itou, Y. Shirakihara, I. Tanaka
Date :  20 Jun 08  (Deposition) - 08 Jul 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A (1x),B (1x)
Keywords :  Helix Turn Helix, Dna-Binding, Transcription, Transcription Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Itou, N. Watanabe, M. Yao, Y. Shirakihara, I. Tanaka
Crystal Structures Of The Multidrug Binding Repressor Corynebacteriumglutamicum Cgmr In Complex With Inducers And With An Operator
J. Mol. Biol. V. 403 174 2010
PubMed-ID: 20691702  |  Reference-DOI: 10.1016/J.JMB.2010.07.042

(-) Compounds

Molecule 1 - TRANSCRIPTIONAL REGULATOR
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET26B
    Expression System Strain: BL21STAR(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 1-175
    Gene: CGL2612
    Organism Common: CORYNEBACTERIUM GLUTAMICUM
    Organism Scientific: CORYNEBACTERIUM GLUTAMICUM
    Organism Taxid: 196627
    Strain: ATCC13032
    Synonym: BACTERIAL REGULATORY PROTEIN, TETR FAMILY, CGMR

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (1x): A (1x)B (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 10)

Asymmetric Unit (3, 10)
No.NameCountTypeFull Name
1ET1Ligand/IonETHIDIUM
2GOL6Ligand/IonGLYCEROL
3SO43Ligand/IonSULFATE ION
Biological Unit 1 (2, 9)
No.NameCountTypeFull Name
1ET-1Ligand/IonETHIDIUM
2GOL6Ligand/IonGLYCEROL
3SO43Ligand/IonSULFATE ION
Biological Unit 2 (2, 5)
No.NameCountTypeFull Name
1ET-1Ligand/IonETHIDIUM
2GOL4Ligand/IonGLYCEROL
3SO41Ligand/IonSULFATE ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREILE A:152 , HIS A:153 , LEU B:59 , TRP B:63 , THR B:87 , LEU B:88 , LEU B:100 , TRP B:113 , GLN B:140 , ASP B:144 , PHE B:147BINDING SITE FOR RESIDUE ET B 184
02AC2SOFTWARESER B:47 , ARG B:48 , HIS B:49 , HIS B:180 , HIS B:181BINDING SITE FOR RESIDUE SO4 B 185
03AC3SOFTWARESER A:37 , LYS A:38 , SER A:39 , ASP B:154BINDING SITE FOR RESIDUE SO4 B 186
04AC4SOFTWARESER A:26 , TYR A:27 , ASP A:28 , LYS A:38 , SER B:158 , LYS B:159BINDING SITE FOR RESIDUE SO4 A 184
05AC5SOFTWARETYR A:16 , TYR A:20 , THR A:24 , SER A:29 , GLU A:32 , GLU B:23BINDING SITE FOR RESIDUE GOL A 185
06AC6SOFTWAREGLU A:23 , TYR B:16 , TYR B:20 , THR B:24 , SER B:29 , GLU B:32BINDING SITE FOR RESIDUE GOL B 187
07AC7SOFTWARETYR A:20 , SER A:21 , LEU B:22 , LEU B:98BINDING SITE FOR RESIDUE GOL B 188
08AC8SOFTWAREARG A:48 , LYS B:159BINDING SITE FOR RESIDUE GOL A 186
09AC9SOFTWARETYR A:27 , ILE A:42 , PRO A:46 , ASN B:91 , SER B:158 , LYS B:159BINDING SITE FOR RESIDUE GOL A 187
10BC1SOFTWARETRP A:63 , GLU A:96 , LEU A:100 , PHE A:147BINDING SITE FOR RESIDUE GOL A 188

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2ZOZ)

(-) 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:172
 aligned with Q8NMG3_CORGL | Q8NMG3 from UniProtKB/TrEMBL  Length:177

    Alignment length:172
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172  
         Q8NMG3_CORGL     3 TSKKEMILRTAIDYIGEYSLETLSYDSLAEATGLSKSGLIYHFPSRHALLLGMHELLADDWDKELRDITRDPEDPLERLRAVVVTLAENVSRPELLLLIDAPSHPDFLNAWRTVNHQWIPDTDDLENDAHKRAVYLVQLAADGLFVHDYIHDDVLSKSKRQAMLETILELIP 174
               SCOP domains d2zoza1 A:3-73 Transcriptional regulator Cgl2612                       d2zoza2 A:74-174 Transcriptional regulator Cgl2612                                                    SCOP domains
               CATH domains 2zozA00 A:3-174 Tetracycline Repressor, domain 2                                                                                                                             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh.....hhhhhhhhhh.hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh...hhhhhhhhhhh..hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zoz A   3 TSKKEMILRTAIDYIGEYSLETLSYDSLAEATGLSKSGLIYHFPSRHALLLGMHELLADDWDKELRDITRDPEDPLERLRAVVVTLAENVSRPELLLLIDAPSHPDFLNAWRTVNHQWIPDTDDLENDAHKRAVYLVQLAADGLFVHDYIHDDVLSKSKRQAMLETILELIP 174
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172  


Chain B from PDB  Type:PROTEIN  Length:181
 aligned with Q8NMG3_CORGL | Q8NMG3 from UniProtKB/TrEMBL  Length:177

    Alignment length:181
                                                                                                                                                                                                          177    
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170      |  - 
         Q8NMG3_CORGL     1 MRTSKKEMILRTAIDYIGEYSLETLSYDSLAEATGLSKSGLIYHFPSRHALLLGMHELLADDWDKELRDITRDPEDPLERLRAVVVTLAENVSRPELLLLIDAPSHPDFLNAWRTVNHQWIPDTDDLENDAHKRAVYLVQLAADGLFVHDYIHDDVLSKSKRQAMLETILELIPSQT----   -
               SCOP domains d2zozb1 B:1-73 Transcriptional regulator Cgl2612                         d2zozb2 B:74-181 Transcriptional regulator Cgl2612                                                           SCOP domains
               CATH domains 2zozB00 B:1-181 Tetracycline Repressor, domain 2                                                                                                                                      CATH domains
           Pfam domains (1) --------TetR_N-2zozB01 B:9-55                          ------------------------------------------------------------------------------------------------------------------------------ Pfam domains (1)
           Pfam domains (2) --------TetR_N-2zozB02 B:9-55                          ------------------------------------------------------------------------------------------------------------------------------ Pfam domains (2)
         Sec.struct. author ....hhhhhhhhhhhhhhhh.....hhhhhhhhhh.hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zoz B   1 MRTSKKEMILRTAIDYIGEYSLETLSYDSLAEATGLSKSGLIYHFPSRHALLLGMHELLADDWDKELRDITRDPEDPLERLRAVVVTLAENVSRPELLLLIDAPSHPDFLNAWRTVNHQWIPDTDDLENDAHKRAVYLVQLAADGLFVHDYIHDDVLSKSKRQAMLETILELIPSELHHHH 181
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180
   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 Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: HTH (544)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q8NMG3_CORGL | Q8NMG3)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
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

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

UniProtKB/TrEMBL
        Q8NMG3_CORGL | Q8NMG3: 2yve 2yvh 2zoy

(-) Related Entries Specified in the PDB File

2yve METHYLENE BLUE-COMPLEX OF CGMR
2yvh OPERATOR-COMPLEX OF CGMR
2zoy LIGAND FREE FORM OF CGMR