1B01,2CA9,2RBF,2RBF,5X3T,6IYA,2HZV


Conserved Protein Domain Family
RHH_CopG_NikR-like

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cd21631: RHH_CopG_NikR-like 
ribbon-helix-helix domains of transcription repressor CopG, nickel responsive transcription factor NikR, and similar proteins
This family includes the ribbon-helix-helix (RHH) domains of transcriptional repressor CopG, nickel-responsive transcription factor NikR, several antitoxins such as Shewanella oneidensis CopA(SO), Burkholderia pseudomallei HicB, and Caulobacter crescentus ParD, and similar proteins. CopG, a homodimeric RHH protein of around 45 residues, constitutes one of the smallest natural transcriptional repressors characterized and is the prototype of a series of repressor proteins encoded by plasmids that exhibit a similar genetic structure at their leading strand initiation and control regions. It is involved in the control of plasmid copy number. NikR, which consists of the N-terminal DNA-binding RHH domain and the C-terminal metal-binding domain (MBD) with four nickel ions, regulates several genes; in Helicobacter pylori, NikR regulates the urease enzyme under extreme acidic conditions, and is involved in the intracellular physiology of nickel. Protein HicB is part of the HicAB toxin-antitoxin (TA) system, where the toxins are RNases, found in many bacteria. In Burkholderia pseudomallei, the HicAB system may play a role in disease by regulating the frequency of persister cells, while in Yersinia pestis HicB acts as an autoregulatory protein that inhibits HicA, which acts as an mRNase. In Escherichia coli, an excess of HicA has been shown to de-repress a HicB-DNA complex and restore transcription of HicB. The CopG family RHH domain, represented by this model, forms a homodimer and binds DNA.
Statistics
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PSSM-Id: 409020
Aligned: 21 rows
Threshold Bit Score: 30.1691
Created: 23-Dec-2019
Updated: 17-Oct-2022
Structure
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Program:
Drawing:
Aligned Rows:
 
dimer interfaceDNA binding
Conserved site includes 24 residues -Click on image for an interactive view with Cn3D
Feature 1:dimer interface [polypeptide binding site]
Evidence:
  • Comment:the ribbon-helix-helix (RHH) type DNA-binding motif dimerizes as two antiparallel beta-strands which compose a ribbon; the beta-strands are involved both in dimer formation and in specific interactions with the DNA by fitting snugly into the major groove
  • Structure:1B01: Streptococcus agalactiae transcriptional repressor CopG forms a homodimer; contacts at 4.0A
  • Citation:PMID 9857196
  • Structure:6IYA: Shewanella oneidensis CopA(SO) forms a homodimer; contacts at 4.0A
  • Structure:2RBF: Escherichia coli proline utilization A (PutA) ribbon-helix-helix domain (PutA52) forms a homodimer; contacts at 4.0A

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1        #######   ## ##  #  #     ##  ## ######  # 
1B01_A         3 KRLTITLSeSVLENLEKMAREMg-LSKSAMISVALENYKKGQE 44  Streptococcus agalactiae
2CA9_A        11 IRFSVSLQqNLLDELDNRIIKNgySSRSELVRDMIREKLVEDN 53  Helicobacter pylori 26695
5X3T_A         2 DKTTVYLPdELKAAVKRAARQRg-VSEAQVIRESIRAAVGGAK 43  Mycobacterium tuberculosis H37Rv
2HZV_A         2 QRVTITLDdDLLETLDSLSQRRgyNNRSEAIRDILRSALAQEA 44  Escherichia coli
P9WLZ1         2 KRTNIYLDeEQTASLDKLAAQEg-VSRAELIRLLLNRALTTAG 43  Mycobacterium tuberculosis H37Rv
P9WJ45         2 KRLQIYIDeDVDRALAVEARRRr-TSKAALIREYVAEHLRQPG 43  Mycobacterium tuberculosis H37Rv
PZS05878       2 SRTQIYLPpDLSADLDRLARKRg-VSRADLIRLAARRLLEHED 43  Chloroflexi bacterium
RLI74322       5 IRTTIAFDeETAKIFEELKHEG--VSQSEIIRRALRFYYSFKD 45  Archaeoglobales archaeon
WP_130135970   2 KRTNIYLDeEQTASLDKLAAQEg-VSRAELIRLLLNRAHETLM 43  Staphylococcus condimenti
OIO98157       4 NRITIRLEdDLSRRLDRLSKASg-VSRSLLIRKAVAQYCANQV 45  Armatimonadetes bacterium CG2_30_59_28

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