3GDX,2EWR,1VJ7,1FA0,1KNY,1V4A,1OU5,1NO5,1NO5,1R8C


Conserved Protein Domain Family
NT_Pol-beta-like

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cd05397: NT_Pol-beta-like 
Click on image for an interactive view with Cn3D
Nucleotidyltransferase (NT) domain of DNA polymerase beta and similar proteins.
This superfamily includes the NT domains of DNA polymerase beta and other family X DNA polymerases, as well as the NT domains of Class I and Class II CCA-adding enzymes, RelA- and SpoT-like ppGpp synthetases and hydrolases, 2'5'-oligoadenylate (2-5A)synthetases, Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), poly (A) polymerases, terminal uridylyl transferases, and Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins. The Escherichia coli CCA-adding enzyme belongs to this superfamily but is not included as this enzyme lacks the N-terminal helix conserved in the remainder of the superfamily. In the majority of the Pol beta-like superfamily NTs, two carboxylates, Dx[D/E], together with a third more distal carboxylate coordinate two divalent metal cations that are essential for catalysis. These divalent metal ions are involved in a two-metal ion mechanism of nucleotide addition. Two of the three catalytic carboxylates are found in Rel-Spo enzymes, with the second carboxylate of the DXD motif missing. Evidence supports a single-cation synthetase mechanism for Rel-Spo enzymes.
Statistics
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PSSM-Id: 143387
Aligned: 10 rows
Threshold Bit Score: 33.8353
Created: 1-Nov-2000
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
 
metal binding
Conserved site includes 3 residues -Click on image for an interactive view with Cn3D
Feature 1:metal binding triad [ion binding site]
Evidence:
  • Comment:Metal binding residues conserved in the majority of the Pol beta-like superfamily nucleotidyltransferases.
  • Structure:1NO5_B, Haemophilus influenzae HI0073 monomer, bound with two metal ions, contacts determined at 4A.
  • Structure:1FA0_A,Yeast PAP bound with two manganese ions, contacts determined at 4A.
  • Structure:1R8C_A, Archaeoglobus fulgidus CCA-adding enzyme bound with two Mn ions, contacts determined at 3.5A.
  • Structure:3GDX_A, Human Pol beta bound with 2 Mg ions, contacts determined at 4A.

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1                                                                  #  #               
3GDX_A    147 LQMQDIVLNEVKkvd----------------seYIATVCGSFRRgae-----------ssGD-MDVLLThpsftsestkq 198 human
2EWR_A     19 LRVLRKIYDRLKne------------------kVNWVVTGSLSFalqgv-------pvevHD-IDIQTDeegayeierif 72  Thermotoga maritima
1VJ7_A    215 EALVDDIVTKIKsytte------------qglfGDVYGRPKHIYsiyrkmrdkkkrfdqiFDlIAIRCVmetqsdvyamv 282 Streptococcus dysg...
1FA0_A     49 VQVLKILQELAQrfvyevskkknmsdgmardagGKIFTYGSYRLgvh----------gpgSD-IDTLVVvpkhvtredff 117 baker's yeast
1KNY_A     13 MKIVHEIKERILdkyg--------------ddvKAIGVYGSLGRqtd----------gpySD-IEMMCVmsteeaefs-- 65  Staphylococcus aureus
1V4A_A    124 ETLIVAARDWLYdaccrewgtp--cnaqgeaqpLLILGXGKLGGgel----------nfsSD-IDLIFAwpehgctqggr 190 Escherichia coli
1OU5_A     56 TEGLKSLTELFVke------------------nHELRIAGGAVRdlln--------gvkpQD-IDFATTatptqmkemfq 108 human
1NO5_B     11 SEELAIVKTILQqlv----------------pdYTVWAFGSRVKgka----------kkySD-LDLAIIseepldflard 63  Haemophilus influe...
1NO5_A     11 SEELAIVKTILQqlv----------------pdYTVWAFGSRVKgka----------kkySD-LDLAIIseepldflard 63  Haemophilus influe...
1R8C_A     25 REAEEELRRRLDel------------------gVEYVFVGSYARntwl---------kgsLE-IDVFLLfpeefskeelr 76  Archaeoglobus fulg...
Feature 1                                                     #     
3GDX_A    199 pkllhqvveqlqkvhfitdtlskgetkfmgvcqlpskndekeyphrRIDIR-LI 251 human
2EWR_A     73 sefvskkvr------------------fsstekicshfgeliidgiKVEIX-GD 107 Thermotoga maritima
1VJ7_A    283 gyihelwrpmpgrf--------kdyiaapkangyqsihttvygpkgPIEIQ-IR 327 Streptococcus dysgalactiae subsp. equisimilis
1FA0_A    118 tvfdsllrerke------------ldeiapvpdafvpiikikfsgiSIDLI-CA 158 baker's yeast
1KNY_A     66 --------------------------------------hewttgewKVEVN-FY 80  Staphylococcus aureus
1V4A_A    191 reldnaqfft----------------rxgqrlikvldqptqdgfvyRVDXRlRP 228 Escherichia coli
1OU5_A    109 sagirmi----------------------nnrgekhgtitarlheeNFEIT-TL 139 human
1NO5_B     64 r---------------------------------lkeafsesdlpwRVDLL-DW 83  Haemophilus influenzae
1NO5_A     64 r---------------------------------lkeafsesdlpwRVDLL-DW 83  Haemophilus influenzae
1R8C_A     77 ergleigkav---------------ldsyeiryaehpyvhgvvkgvEVDVV-PC 114 Archaeoglobus fulgidus

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