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InterPro: IPR012337 Polynucleotidyl transferase, ribonuclease H fold

Protein matchesHelp
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UniProtKB
Matches:
57130 proteins
AccessionHelp
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IPR012337 PolynucTfrase_RNaseH_fold
TypeHelp
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Domain
SignaturesHelp
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InterPro RelationshipsHelp
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Children IPR001352 Ribonuclease HII/HIII
IPR001584 Integrase, catalytic core
IPR002156 Ribonuclease H
IPR002176 Crossover junction endodeoxyribonuclease RuvC
IPR002562 3'-5' exonuclease
IPR003165 Stem cell self-renewal protein Piwi
IPR004189 Transposase, Bacteriophage Mu-type
IPR005227 Resolvase, holliday junction-type, YqgF-like
IPR006133 DNA-directed DNA polymerase, family B, exonuclease domain
IPR006932 Holliday junction resolvase, poxvirus
IPR006941 Ribonuclease CAF1
IPR009773 Lactococcus phage M3
IPR013520 Exonuclease, RNase T/DNA polymerase III
IPR015242 Mitochondrial resolvase Ydc2, catalytic
IPR015361 Taq polymerase, thermostable, exonuclease region
IPR019288 Predicted 3'-5' exonuclease, PolB-like
Found in IPR002297 DNA-directed DNA-polymerase, family A, mitochondria
IPR004578 DNA-directed DNA polymerase, family B, pol2
IPR006172 DNA-directed DNA polymerase, family B
IPR006292 Ribonuclease D
IPR006308 DNA polymerase III, alpha subunit, Gram-positive type
IPR006310 DnaQ exonuclease/DinG helicase
IPR014382 DNA-directed DNA polymerase, family B, adenovirus
IPR014636 RNase H, phosphoglycerate mutase domain-containing
IPR015833 DNA-directed DNA polymerase, family B, mitochondrial linear plasmid
IPR016265 DNA-directed DNA polymerase, family A, mitochondria, subgroup
IPR017067 Ribonuclease H1, eukaryote
IPR017290 Ribonuclease H, bacteria
IPR018320 DNA polymerase 1
Contains IPR001598 Transposase, IS30, conserved site
IPR003201 Transposase Tn5, dimerisation
IPR006641 Resolvase, RNase H-like fold
IPR013617 DNA-directed DNA polymerase, family B, viral insert domain
IPR013620 Exonuclease C-terminal
IPR014735 Transposase, Tn5-like, N-terminal
IPR014736 Transposase, Tn5-like, core
IPR014737 Transposase, Tn5-like, C-terminal
IPR020563 Crossover junction endodeoxyribonuclease RuvC, magnesium-binding site
GO Term annotationHelp
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Function GO:0003676 nucleic acid binding
InterPro annotation
BioMart Logo Entry Details in BioMart
AbstractHelp
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The catalytic domain of several polynucleotidyl transferases share a similar structure, consisting of a 3-layer alpha/beta/alpha fold that contains mixed beta sheets, suggesting that they share a similar mechanism of catalysis. Polynucleotidyl transferases containing this domain include ribonuclease H class I (RNase HI) and class II (RNase HII), HIV RNase (reverse transcriptase domain), retroviral integrase (catalytic domain), Mu transposase (core domain), transposase inhibitor Tn5 (containing additional all-alpha subdomains), DnaQ-like 3'-5' exonucleases (exonuclease domains), RuvC resolvase, and mitochondrial resolvase ydc2 (catalytic domain) [1, 2, 3].
Structural linksHelp
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PDB - click here
1a5v , 1a5w , 1a5x , 1asu , 1asv , 1asw , 1b7e , 1b92 , 1b9d , 1b9f , 1bcm , 1bco , 1bgx , 1bhl , 1bi4 , 1bis , 1biu , 1biz , 1bl3 , 1bqm , 1bqn , 1c0m , 1c0t , 1c0u , 1c1a , 1c1b , 1c1c , 1c6v , 1clq , 1cmw , 1cxq , 1cxu , 1cz9 , 1czb , 1d5a , 1d8y , 1d9d , 1d9f , 1dlo , 1dpi , 1dtq , 1dtt , 1duc , 1dun , 1dut , 1e0e , 1eet , 1eke , 1ep4 , 1ex4 , 1exq , 1f21 , 1f7d , 1f7k , 1f7n , 1f7o , 1f7p , 1f7q , 1f7r , 1fk9 , 1fko , 1fkp , 1fxx , 1g15 , 1goa , 1gob , 1goc , 1hjr , 1hmv , 1hni , 1hnv , 1hpz , 1hqe , 1hqu , 1hrh , 1hvu , 1hys , 1hyv , 1hyz , 1i39 , 1i3a , 1ig9 , 1ih7 , 1ikv , 1ikw , 1ikx , 1iky , 1io2 , 1itg , 1iv0 , 1j53 , 1j54 , 1j5o , 1j9a , 1jkh , 1jl1 , 1jl2 , 1jla , 1jlb , 1jlc , 1jle , 1jlf , 1jlg , 1jlq , 1jxb , 1jxe , 1k6y , 1kcf , 1kfd , 1kfs , 1klm , 1kln , 1krp , 1ksp , 1ktq , 1kva , 1kvb , 1kvc , 1l3s , 1l3t , 1l3u , 1l3v , 1l5u , 1lav , 1law , 1lv5 , 1lw0 , 1lw2 , 1lwc , 1lwe , 1lwf , 1mm8 , 1mu2 , 1muh , 1mur , 1mus , 1n5y , 1n6q , 1njw , 1njx , 1njy , 1njz , 1nk0 , 1nk4 , 1nk5 , 1nk6 , 1nk7 , 1nk8 , 1nk9 , 1nkb , 1nkc , 1nke , 1nmn , 1noy , 1noz , 1nu0 , 1o1w , 1ovq , 1q8i , 1q9x , 1q9y , 1qe1 , 1qht , 1qqc , 1qs4 , 1qsl , 1qss , 1qsy , 1qtm , 1r0a , 1rbr , 1rbs , 1rbt , 1rbu , 1rbv , 1rch , 1rda , 1rdb , 1rdc , 1rdd , 1rdh , 1rev , 1ril , 1rnh , 1rt1 , 1rt2 , 1rt3 , 1rt4 , 1rt5 , 1rt6 , 1rt7 , 1rtd , 1rth , 1rti , 1rtj , 1s1t , 1s1u , 1s1v , 1s1w , 1s1x , 1s5j , 1s6p , 1s6q , 1s9e , 1s9g , 1skr , 1sks , 1skw , 1sl0 , 1sl1 , 1sl2 , 1suq , 1sv5 , 1t03 , 1t05 , 1t7p , 1t8e , 1taq , 1tau , 1tgo , 1tk0 , 1tk5 , 1tk8 , 1tkd , 1tkt , 1tkx , 1tkz , 1tl1 , 1tl3 , 1tv6 , 1tvr , 1u04 , 1u45 , 1u47 , 1u48 , 1u49 , 1u4b , 1ua0 , 1ua1 , 1uax , 1ug8 , 1uoc , 1uwb , 1vhx , 1vk0 , 1vrt , 1vru , 1vsd , 1vse , 1vsf , 1vsh , 1vsi , 1vsj , 1vsk , 1vsl , 1vsm , 1w0h , 1w9h , 1waf , 1waj , 1wlj , 1wn7 , 1wns , 1wse , 1wsf , 1wsg , 1wsh , 1wsi , 1wsj , 1x1p , 1x9m , 1x9s , 1x9w , 1xc9 , 1xwl , 1y97 , 1yt3 , 1yta , 1ytu , 1yvu , 1z25 , 1z26 , 1zbf , 1zbh , 1zbi , 1zbl , 1zbu , 1zyq , 2ajq , 2atq , 2b4j , 2b5j , 2b6a , 2ban , 2bdp , 2be2 , 2bgg , 2d5r , 2dfe , 2dff , 2dfh , 2dy4 , 2e4l , 2etj , 2f8s , 2f8t , 2f96 , 2g8f , 2g8h , 2g8i , 2g8k , 2g8u , 2g8v , 2g8w , 2gbz , 2gui , 2hbj , 2hbk , 2hbl , 2hbm , 2hhq , 2hhs , 2hht , 2hhu , 2hhv , 2hhw , 2hhx , 2hmi , 2hnd , 2hny , 2hnz , 2hvh , 2hvi , 2hw3 , 2i5j , 2iaj , 2ic3 , 2ido , 2igi , 2ioc , 2itg , 2kfn , 2kfz , 2ktq , 2kzm , 2kzz , 2nub , 2o4g , 2o4i , 2oa8 , 2opp , 2opq , 2opr , 2ops , 2oyq , 2ozm , 2ozs , 2p1j , 2p5g , 2p5o , 2q3s , 2qxf , 2r7y , 2rf2 , 2rki , 2rn2 , 2vg5 , 2vg6 , 2vg7 , 2vwj , 2vwk , 2yv0 , 2z1g , 2z1h , 2z1i , 2z1j , 2zd1 , 2ze2 , 3b6o , 3b6p , 3bdp , 3bgr , 3c6t , 3c6u , 3c94 , 3c95 , 3cq8 , 3d0p , 3di6 , 3dle , 3dlg , 3dlk , 3dm2 , 3dok , 3dol , 3drp , 3drr , 3drs , 3ecp , 3hvt , 3ktq , 4bdp , 4ktq , 5ktq
Database linksHelp
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Enzyme: EC:3.1

Taxonomic coverageHelp
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Overlapping InterPro entriesHelp
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IPR012337 Numbers of overlapping proteins Average numbers of overlapping amino acids

Example proteinsHelp
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O09053 Werner syndrome ATP-dependent helicase homolog

O60930 Ribonuclease H1

P13382 DNA polymerase alpha catalytic subunit A

Q10905 Cell death-related nuclease 4

Q9VUQ5 Protein argonaute-2

More proteins


Example Proteins Key


InterPro entry accession number/name and structure databases Colour code
IPR015088 Zinc finger, DNA-directed DNA polymerase, family B, alpha
IPR017966 DNA-directed DNA polymerase, family B, conserved region2
IPR017964 DNA-directed DNA polymerase, family B, conserved site
IPR018329 DNA helicase, ATP-dependent, RecQ type, N-terminal
IPR012337 Polynucleotidyl transferase, ribonuclease H fold
IPR004578 DNA-directed DNA polymerase, family B, pol2
IPR001650 DNA/RNA helicase, C-terminal
IPR009027 Ribosomal protein L9/RNase H1, N-terminal
IPR002156 Ribonuclease H
IPR002562 3'-5' exonuclease
IPR013520 Exonuclease, RNase T/DNA polymerase III
IPR003100 Argonaute/Dicer protein, PAZ
IPR014811 Domain of unknown function DUF1785
IPR018982 RQC domain
IPR006055 Exonuclease
IPR011320 Ribonuclease H1, N-terminal
IPR017067 Ribonuclease H1, eukaryote
IPR014021 Helicase, superfamily 1/2, ATP-binding domain
IPR004589 DNA helicase, ATP-dependent, RecQ type
IPR002121 Helicase/RNase D C-terminal, HRDC domain
IPR006134 DNA-directed DNA polymerase, family B, conserved region
IPR006133 DNA-directed DNA polymerase, family B, exonuclease domain
IPR011545 DNA/RNA helicase, DEAD/DEAH box type, N-terminal
IPR006172 DNA-directed DNA polymerase, family B
IPR003165 Stem cell self-renewal protein Piwi
IPR014001 DEAD-like helicase, N-terminal
ModBase
SWISS-MODEL
PDB Chain
CATH Domain
SCOP Domain

PublicationsHelp
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1. Chattopadhyay D, Finzel BC, Munson SH, Evans DB, Sharma SK, Strakalaitus NA, Brunner DP, Eckenrode FM, Dauter Z, Betzel C, Einspahr HM.
Crystallographic analyses of an active HIV-1 ribonuclease H domain show structural features that distinguish it from the inactive form.
Acta Crystallogr. D Biol. Crystallogr. 49 423-7 1993 [PubMed: 15299518]
http://dx.doi.org/10.1107/S0907444993002409
2. Rice P, Craigie R, Davies DR.
Retroviral integrases and their cousins.
Curr. Opin. Struct. Biol. 6 76-83 1996 [PubMed: 8696976]
http://dx.doi.org/10.1016/S0959-440X(96)80098-4
3. Sigala B, Tsaneva IR.
Functional dissection of the Schizosaccharomyces pombe Holliday junction resolvase Ydc2: in vivo role in mitochondrial DNA maintenance.
Eur. J. Biochem. 270 2837-47 2003 [PubMed: 12823554]
http://dx.doi.org/10.1046/j.1432-1033.2003.03661.x

Additional ReadingHelp
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Kirschberg TA, Balakrishnan M, Huang W, Hluhanich R, Kutty N, Liclican AC, McColl DJ, Squires NH, Lansdon EB.
Triazole derivatives as non-nucleoside inhibitors of HIV-1 reverse transcriptase--structure-activity relationships and crystallographic analysis.
Bioorg. Med. Chem. Lett. 18 2008 1131-4 [PubMed: 18083512]
http://dx.doi.org/10.1016/j.bmcl.2007.11.127
Spallarossa A, Cesarini S, Ranise A, Ponassi M, Unge T, Bolognesi M.
Crystal structures of HIV-1 reverse transcriptase complexes with thiocarbamate non-nucleoside inhibitors.
Biochem. Biophys. Res. Commun. 365 2008 764-70 [PubMed: 18035053]
http://dx.doi.org/10.1016/j.bbrc.2007.11.036
Busam RD.
Structure of Escherichia coli exonuclease I in complex with thymidine 5'-monophosphate.
Acta Crystallogr. D Biol. Crystallogr. 64 2008 206-10 [PubMed: 18219121]
http://dx.doi.org/10.1107/S090744490706012X
Zhao Z, Wolkenberg SE, Lu M, Munshi V, Moyer G, Feng M, Carella AV, Ecto LT, Gabryelski LJ, Lai MT, Prasad SG, Yan Y, McGaughey GB, Miller MD, Lindsley CW, Hartman GD, Vacca JP, Williams TM.
Novel indole-3-sulfonamides as potent HIV non-nucleoside reverse transcriptase inhibitors (NNRTIs).
Bioorg. Med. Chem. Lett. 18 2008 554-9 [PubMed: 18083561]
http://dx.doi.org/10.1016/j.bmcl.2007.11.085
Firbank SJ, Wardle J, Heslop P, Lewis RJ, Connolly BA.
Uracil recognition in archaeal DNA polymerases captured by X-ray crystallography.
J. Mol. Biol. 381 2008 529-39 [PubMed: 18614176]
http://dx.doi.org/10.1016/j.jmb.2008.06.004
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