1J5N,1HME,1HSM,1CKT,1L8Z,1QRV,1K99


Conserved Protein Domain Family
HMGB-UBF_HMG-box

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cd01390: HMGB-UBF_HMG-box 
Click on image for an interactive view with Cn3D
HMGB-UBF_HMG-box, class II and III members of the HMG-box superfamily of DNA-binding proteins. These proteins bind the minor groove of DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal proteins, HMG1 and HMG2, which bind to bent or distorted DNA such as four-way DNA junctions, synthetic DNA cruciforms, kinked cisplatin-modified DNA, DNA bulges, cross-overs in supercoiled DNA, and can cause looping of linear DNA. Class III members include nucleolar and mitochondrial transcription factors, UBF and mtTF1, which bind four-way DNA junctions.
Statistics
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PSSM-Id: 238686
View PSSM: cd01390
Aligned: 120 rows
Threshold Bit Score: 39.5334
Threshold Setting Gi: 21465996
Created: 10-Jan-2006
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
 
DNA binding
Conserved site includes 13 residues -Click on image for an interactive view with Cn3D
Feature 1:DNA binding site [nucleic acid binding site]
Evidence:
  • Comment:aromatic residues interact directly with the DNA backbone
  • Structure:1J5N_A, non-sequence-specific HMGB (Nhp6a) binds SRY DNA
    View structure with Cn3D

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1       # ## ##  ##  #   #                       #  #  #                  #        
1J5N_A     21 PKRALSAYMFFANENRDIVRSenpd-----------itfgQVGKKLGEKWKALTpeEKQPYEAKAQADKKRYESEKE 86  Saccharomyces cerevisiae
AAN31640  100 PKRPPTAYFLFLADYRIRMANkgi-------------ehkELLKMAGEEWRSLSneDKKPYEKKALEESKKYESAMT 163 bloodfluke planorb
NP_010459 106 PKKPLTVFFAYSAYVRQELREdrqkagl------pplsstEITQEISKKWKELSdnEKEKWKQAYNVELENYQREKS 176 baker's yeast
XP_330562 114 PKRPLTPYFLYMQTARPIIANdlgee----------apkgAVQEEGQRRWSVMGaaEKQGWNNAYQYNLRLYNARVH 180 Neurospora crassa
EAA42500   11 PVKPLTAFFIYFKEQSVGMTEks---------------tiEKGRILGQKWKELSdkEKQHYYDIYEKNMKAYSTDIA 72  Giardia lamblia ATCC ...
EAA46437   10 PTKPFTPYFAFMHDHLDEYRDvv---------------pkERTKVLGRRWKELDekTRKQYTDSYEEQTRLYKEAMK 71  Giardia lamblia ATCC ...
NP_585883  44 PKKPMSGYFIFGQEQRKKNEElsrl------------pvaDQGRAISEMWKKLSdeEREEYNKISNRERELYQARIE 108 Encephalitozoon cuniculi
CAD48137  153 LKKPLTAYMLFNNHRRPTLRNehpckikylirhtielqitDVSKMIGQEWTKLSedQKRVWNDKAKEERLAYDLKRY 229 Sterkiella nova
AAL13284   17 PKKPKTAYFLFCDEHREEAKKkageg----------ksasEVSKILGEMWGKLTeeQKKPYNDRYKIEMEKHKKVMD 83  Naegleria fowleri
AAC35540  327 PKKPTSSYFLFCKDARKSVLEehpg-----------innsTVTAHISLKWMELGeeEKQVYNSKAAELMEAYKKEVE 392 thale cress

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