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 
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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
View PSSM: cd05397
Aligned: 10 rows
Threshold Bit Score: 29.5981
Threshold Setting Gi: 48425924
Created: 1-Nov-2000
Updated: 17-Jan-2013
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.
    View structure with Cn3D
  • Structure:1FA0_A,Yeast PAP bound with two manganese ions, contacts determined at 4A.
    View structure with Cn3D
  • Structure:1R8C_A, Archaeoglobus fulgidus CCA-adding enzyme bound with two Mn ions, contacts determined at 3.5A.
    View structure with Cn3D
  • Structure:3GDX_A, Human Pol beta bound with 2 Mg ions, contacts determined at 4A.
    View structure with Cn3D

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
                      10        20        30        40        50        60        70        80
              ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                                  #  #               
3GDX_A    147 LQMQDIVLNEVKkvd----------------seYIATVCGSFRRgae-----------ssGD-MDVLLThpsftsestkq 198
2EWR_A     19 LRVLRKIYDRLKne------------------kVNWVVTGSLSFalqgv-------pvevHD-IDIQTDeegayeierif 72
1VJ7_A    215 EALVDDIVTKIKsytte------------qglfGDVYGRPKHIYsiyrkmrdkkkrfdqiFDlIAIRCVmetqsdvyamv 282
1FA0_A     49 VQVLKILQELAQrfvyevskkknmsdgmardagGKIFTYGSYRLgvh----------gpgSD-IDTLVVvpkhvtredff 117
1KNY_A     13 MKIVHEIKERILdkyg--------------ddvKAIGVYGSLGRqtd----------gpySD-IEMMCVmsteeaefs-- 65
1V4A_A    124 ETLIVAARDWLYdaccrewgtp--cnaqgeaqpLLILGXGKLGGgel----------nfsSD-IDLIFAwpehgctqggr 190
1OU5_A     56 TEGLKSLTELFVke------------------nHELRIAGGAVRdlln--------gvkpQD-IDFATTatptqmkemfq 108
1NO5_B     11 SEELAIVKTILQqlv----------------pdYTVWAFGSRVKgka----------kkySD-LDLAIIseepldflard 63
1NO5_A     11 SEELAIVKTILQqlv----------------pdYTVWAFGSRVKgka----------kkySD-LDLAIIseepldflard 63
1R8C_A     25 REAEEELRRRLDel------------------gVEYVFVGSYARntwl---------kgsLE-IDVFLLfpeefskeelr 76
                      90       100       110       120       130
              ....*....|....*....|....*....|....*....|....*....|....
Feature 1                                                     #     
3GDX_A    199 pkllhqvveqlqkvhfitdtlskgetkfmgvcqlpskndekeyphrRIDIR-LI 251
2EWR_A     73 sefvskkvr------------------fsstekicshfgeliidgiKVEIX-GD 107
1VJ7_A    283 gyihelwrpmpgrf--------kdyiaapkangyqsihttvygpkgPIEIQ-IR 327
1FA0_A    118 tvfdsllrerke------------ldeiapvpdafvpiikikfsgiSIDLI-CA 158
1KNY_A     66 --------------------------------------hewttgewKVEVN-FY 80
1V4A_A    191 reldnaqfft----------------rxgqrlikvldqptqdgfvyRVDXRlRP 228
1OU5_A    109 sagirmi----------------------nnrgekhgtitarlheeNFEIT-TL 139
1NO5_B     64 r---------------------------------lkeafsesdlpwRVDLL-DW 83
1NO5_A     64 r---------------------------------lkeafsesdlpwRVDLL-DW 83
1R8C_A     77 ergleigkav---------------ldsyeiryaehpyvhgvvkgvEVDVV-PC 114

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