1MDY,1AM9,1HLO,1AN4


Conserved Protein Domain Family
HLH

?
cd00083: HLH 
Click on image for an interactive view with Cn3D
Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and have a PAS domain which allows the dimerization between PAS proteins, the binding of small molecules (e.g., dioxin), and interactions with non-PAS proteins.
Statistics
?
PSSM-Id: 238036
View PSSM: cd00083
Aligned: 145 rows
Threshold Bit Score: 34.8823
Threshold Setting Gi: 15226839
Created: 1-Nov-2000
Updated: 17-Jan-2013
Structure
?
Program:
Drawing:
Aligned Rows:
 
Conserved site includes 8 residues -Click on image for an interactive view with Cn3D
Feature 1:DNA binding region [nucleic acid binding site]
Evidence:

Sequence Alignment
?
Format: Row Display: Color Bits: Type Selection:
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
Feature 1           ##     ### #                        #  #                   
1MDY_B         3 NADRRKAATMRERRRLSKVNEAFETLKRSTSsnp---nqRLPKVEILRNAIRYIEGLQALLR 61
gi 5921794    32 DKAKRVSRNKSEKKRRDQFNVLIKELGSMLPgn----arKMDKSTVLQKSIDFLRKHKETTA 89
gi 3914285    12 SELRKEKSRDAARCRRSKETEVFYELAHELPlphs-vssHLDKASIMRLAISFLRTHKLLSS 72
gi 13124810   84 LELRKEKSRDAARSRRGKENYEFYELAKMLPlpaa-itsQLDKASIIRLTISYLKLRDFSGH 144
gi 3914159    43 QAQRKEKSRNAARWRRGKENLEFFELAKLLPlpga-issQLDKASIVRLSVTYLRLRRFAAL 103
gi 17737314   34 PANGREARNLAEKQRRDKLNASIQELATMVPhaae-ssrRLDKTAVLRFATHGLRLQYVFGK 94
gi 7939531   160 SCSKPGTKACREKLRREKLNDKFMDLSSVLEpgr---tpKTDKSAILDDAIRVVNQLRGEAH 218
gi 13124829   70 NEKRKEKSRDAARCRRSKETEIFMELSAALPlktd-dvnQLDKASVMRITIAFLKIREMLQF 130
gi 17560694  113 MERRRETSRHAARDRRSKESDIFDDLKMCVPiveegtvtHLDRIALLRVAATICRLRKTAGN 174
gi 7511825    13 SFLCRKSRNLSEKKRRDQFNSLVDDLSALIStss--rkmDKSTVLKSTIAFLKNHNEATDRS 72

| Disclaimer | Privacy statement | Accessibility |
NCBI Home NCBI Search NCBI SiteMap