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1447  structures 10443  species 0  interactions 160342  sequences 2112  architectures

Clan: PDDEXK (CL0236)

Summary

PD-(D/E)XK nuclease superfamily Add an annotation

This clan includes a large number of nuclease families related to holliday junction resolvases [1,2].

This clan contains 145 families and the total number of domains in the clan is 160342. The clan was built by A Bateman.

Literature references

  1. Aravind L, Makarova KS, Koonin EV; , Nucleic Acids Res. 2000;28:3417-3432.: Holliday junction resolvases and related nucleases: identification of new families, phyletic distribution and evolutionary trajectories. PUBMED:10982859 EPMC:10982859
  2. Feder M, Bujnicki JM; , BMC Genomics. 2005;6:21-21.: Identification of a new family of putative PD-(D/E)XK nucleases with unusual phylogenomic distribution and a new type of the active site. PUBMED:15720711 EPMC:15720711
  3. Knizewski L, Kinch L, Grishin NV, Rychlewski L, Ginalski K; , J Virol. 2006;80:2575-2577.: Human herpesvirus 1 UL24 gene encodes a potential PD-(D/E)XK endonuclease. PUBMED:16474163 EPMC:16474163
  4. Kinch LN, Ginalski K, Rychlewski L, Grishin NV; , Nucleic Acids Res. 2005;33:3598-3605.: Identification of novel restriction endonuclease-like fold families among hypothetical proteins. PUBMED:15972856 EPMC:15972856
  5. Steczkiewicz K, Muszewska A, Knizewski L, Rychlewski L, Ginalski K;, Nucleic Acids Res. 2012;40:7016-7045.: Sequence, structure and functional diversity of PD-(D/E)XK phosphodiesterase superfamily. PUBMED:22638584 EPMC:22638584

Members

This clan contains the following 145 member families:

AHJR-like ArenaCapSnatch BamHI BpuJI_N BpuSI_N Bse634I BsuBI_PstI_RE Cas_APE2256 Cas_Cas02710 Cas_Cas4 Cas_Csm6 Cas_DxTHG Cas_NE0113 CdiA_C CdiA_C_tRNase CoiA Csa1 Dna2 DpnI DpnII DpnII-MboI DUF1780 DUF1887 DUF2034 DUF2161 DUF234 DUF2357 DUF2726 DUF2800 DUF2887 DUF3799 DUF3883 DUF4143 DUF4263 DUF4420 DUF559 DUF5614 DUF6035 DUF6293 EC042_2821 EcoRI EcoRII-C eIF-3_zeta Endonuc-BglII Endonuc-BsobI Endonuc-EcoRV Endonuc-FokI_C Endonuc-HincII Endonuc-MspI Endonuc-PvuII Endonuc_BglI Endonuc_Holl ERCC4 Exo5 Flu_PA Herpes_UL24 Hjc HSDR_N HSDR_N_2 L_protein_N McrBC MepB MmcB-like Mrr_cat Mrr_cat_2 MTES_1575 MutH MvaI_BcnI NaeI NERD NgoMIV_restric NotI NucS PDCD9 PDDEXK_1 PDDEXK_10 PDDEXK_2 PDDEXK_3 PDDEXK_4 PDDEXK_5 PDDEXK_7 PDDEXK_9 Pet127 Phage_endo_I PND R-HINP1I Rad10 RAI1 RAP RE_AlwI RE_ApaLI RE_Bpu10I RE_BsaWI RE_Bsp6I RE_CfrBI RE_Eco47II RE_EcoO109I RE_endonuc RE_HaeII RE_HindIII RE_HindVP RE_HpaII RE_LlaJI RE_LlaMI RE_MjaI RE_NgoBV RE_NgoPII RE_SacI RE_ScaI RE_SinI RE_TaqI RE_TdeIII RE_XamI RE_XcyI RecC_C RecU RestrictionMunI RestrictionSfiI RmuC RNA_pol_Rpb5_N Sen15 SfsA Spo0A_C TBPIP_N ThaI Tn7_Tnp_TnsA_N Tox-REase-2 Tox-REase-3 Tox-REase-5 Tox-REase-7 Tox-REase-9 Transposase_31 tRNA_int_endo Tsp45I Uma2 UPF0102 Viral_alk_exo VirArc_Nuclease VRR_NUC Vsr XhoI XisH YaeQ YhcG_C YqaJ

External database links

Domain organisation

Below is a listing of the unique domain organisations or architectures from this clan. More...

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Alignments

The table below shows the number of occurrences of each domain throughout the sequence database. More...

Pfam family Num. domains Alignment
PDDEXK_1 (PF12705) 16606 (10.4%) View
Uma2 (PF05685) 15869 (9.9%) View
UPF0102 (PF02021) 6610 (4.1%) View
HSDR_N (PF04313) 6129 (3.8%) View
Mrr_cat (PF04471) 5768 (3.6%) View
DUF4143 (PF13635) 5543 (3.5%) View
ERCC4 (PF02732) 5215 (3.3%) View
NERD (PF08378) 5052 (3.2%) View
RmuC (PF02646) 4955 (3.1%) View
DUF559 (PF04480) 4858 (3.0%) View
PDDEXK_2 (PF12784) 3251 (2.0%) View
tRNA_int_endo (PF01974) 3237 (2.0%) View
YqaJ (PF09588) 3095 (1.9%) View
HSDR_N_2 (PF13588) 2858 (1.8%) View
Cas_Cas4 (PF01930) 2682 (1.7%) View
VRR_NUC (PF08774) 2618 (1.6%) View
PDDEXK_9 (PF08011) 2605 (1.6%) View
RAP (PF08373) 2537 (1.6%) View
SfsA (PF03749) 2381 (1.5%) View
YhcG_C (PF06250) 2255 (1.4%) View
RNA_pol_Rpb5_N (PF03871) 2225 (1.4%) View
Vsr (PF03852) 2182 (1.4%) View
NucS (PF01939) 2159 (1.3%) View
PDDEXK_3 (PF13366) 2144 (1.3%) View
Transposase_31 (PF04754) 2097 (1.3%) View
MTES_1575 (PF18741) 2039 (1.3%) View
eIF-3_zeta (PF05091) 1970 (1.2%) View
Exo5 (PF09810) 1933 (1.2%) View
DUF3883 (PF13020) 1733 (1.1%) View
Dna2 (PF08696) 1670 (1.0%) View
Spo0A_C (PF08769) 1593 (1.0%) View
Rad10 (PF03834) 1591 (1.0%) View
RecC_C (PF17946) 1582 (1.0%) View
RAI1 (PF08652) 1444 (0.9%) View
McrBC (PF10117) 1395 (0.9%) View
YaeQ (PF07152) 1364 (0.9%) View
RecU (PF03838) 1195 (0.7%) View
DUF234 (PF03008) 1174 (0.7%) View
DUF2034 (PF10356) 1093 (0.7%) View
MmcB-like (PF06319) 1084 (0.7%) View
DUF2726 (PF10881) 1068 (0.7%) View
Sen15 (PF09631) 1066 (0.7%) View
CoiA (PF06054) 991 (0.6%) View
PDCD9 (PF07147) 859 (0.5%) View
RE_endonuc (PF19778) 838 (0.5%) View
Pet127 (PF08634) 775 (0.5%) View
DUF3799 (PF12684) 774 (0.5%) View
DUF2800 (PF10926) 756 (0.5%) View
Tn7_Tnp_TnsA_N (PF08722) 747 (0.5%) View
MutH (PF02976) 689 (0.4%) View
DUF2161 (PF09929) 660 (0.4%) View
PDDEXK_4 (PF14281) 641 (0.4%) View
DUF2887 (PF11103) 625 (0.4%) View
DUF4420 (PF14390) 551 (0.3%) View
XisH (PF08814) 542 (0.3%) View
DUF2357 (PF09823) 470 (0.3%) View
DUF4263 (PF14082) 430 (0.3%) View
MepB (PF08877) 414 (0.3%) View
PDDEXK_7 (PF04411) 413 (0.3%) View
DUF5614 (PF18474) 397 (0.2%) View
Mrr_cat_2 (PF13156) 392 (0.2%) View
Cas_DxTHG (PF09455) 356 (0.2%) View
Hjc (PF01870) 354 (0.2%) View
DUF1887 (PF09002) 311 (0.2%) View
BsuBI_PstI_RE (PF06616) 286 (0.2%) View
DUF6293 (PF19810) 271 (0.2%) View
PND (PF17949) 267 (0.2%) View
DpnII (PF04556) 265 (0.2%) View
CdiA_C (PF18451) 252 (0.2%) View
Viral_alk_exo (PF01771) 248 (0.2%) View
Cas_Cas02710 (PF09670) 246 (0.2%) View
Endonuc-BglII (PF09195) 227 (0.1%) View
EcoRII-C (PF09019) 223 (0.1%) View
continued
Pfam family Num. domains Alignment
Cas_NE0113 (PF09623) 215 (0.1%) View
MvaI_BcnI (PF15515) 211 (0.1%) View
Phage_endo_I (PF05367) 198 (0.1%) View
Cas_APE2256 (PF09651) 194 (0.1%) View
RE_AlwI (PF09491) 192 (0.1%) View
PDDEXK_5 (PF11645) 182 (0.1%) View
NaeI (PF09126) 166 (0.1%) View
Tox-REase-5 (PF15648) 163 (0.1%) View
DpnII-MboI (PF18742) 162 (0.1%) View
RE_LlaJI (PF09563) 159 (0.1%) View
XhoI (PF04555) 157 (0.1%) View
RE_HpaII (PF09561) 149 (0.1%) View
PDDEXK_10 (PF07788) 149 (0.1%) View
RE_EcoO109I (PF14511) 139 (0.1%) View
EC042_2821 (PF18740) 136 (0.1%) View
NotI (PF12183) 121 (0.1%) View
RE_TdeIII (PF09520) 121 (0.1%) View
NgoMIV_restric (PF09015) 119 (0.1%) View
RE_Eco47II (PF09553) 110 (0.1%) View
L_protein_N (PF15518) 105 (0.1%) View
Cas_Csm6 (PF09659) 101 (0.1%) View
Herpes_UL24 (PF01646) 85 (0.1%) View
DUF6035 (PF19500) 84 (0.1%) View
Endonuc_Holl (PF10107) 82 (0.1%) View
Endonuc-EcoRV (PF09233) 82 (0.1%) View
RE_MjaI (PF09568) 74 (0.0%) View
DpnI (PF06044) 73 (0.0%) View
AHJR-like (PF18743) 69 (0.0%) View
RE_XamI (PF09572) 68 (0.0%) View
Csa1 (PF06023) 68 (0.0%) View
Tox-REase-7 (PF15649) 67 (0.0%) View
Endonuc-FokI_C (PF09254) 61 (0.0%) View
RE_Bpu10I (PF09549) 59 (0.0%) View
Flu_PA (PF00603) 58 (0.0%) View
RE_HindVP (PF09519) 54 (0.0%) View
BamHI (PF02923) 51 (0.0%) View
RE_BsaWI (PF18643) 48 (0.0%) View
RE_SacI (PF09566) 46 (0.0%) View
RE_NgoPII (PF09521) 46 (0.0%) View
DUF1780 (PF08682) 45 (0.0%) View
RE_ApaLI (PF09499) 40 (0.0%) View
Tox-REase-9 (PF15650) 38 (0.0%) View
Tox-REase-2 (PF15646) 35 (0.0%) View
BpuJI_N (PF11564) 35 (0.0%) View
Endonuc-BsobI (PF09194) 35 (0.0%) View
EcoRI (PF02963) 34 (0.0%) View
RE_SinI (PF09570) 30 (0.0%) View
Tsp45I (PF06300) 30 (0.0%) View
RE_NgoBV (PF09564) 28 (0.0%) View
CdiA_C_tRNase (PF18664) 27 (0.0%) View
RE_CfrBI (PF09516) 27 (0.0%) View
Endonuc-PvuII (PF09225) 27 (0.0%) View
R-HINP1I (PF11463) 26 (0.0%) View
RE_HindIII (PF09518) 26 (0.0%) View
RE_XcyI (PF09571) 25 (0.0%) View
Tox-REase-3 (PF15647) 24 (0.0%) View
RE_HaeII (PF09554) 24 (0.0%) View
ArenaCapSnatch (PF17296) 19 (0.0%) View
RE_ScaI (PF09569) 18 (0.0%) View
Bse634I (PF07832) 18 (0.0%) View
VirArc_Nuclease (PF12187) 14 (0.0%) View
Endonuc-MspI (PF09208) 14 (0.0%) View
ThaI (PF15514) 11 (0.0%) View
RE_TaqI (PF09573) 11 (0.0%) View
Endonuc-HincII (PF09226) 11 (0.0%) View
RE_Bsp6I (PF09504) 10 (0.0%) View
RestrictionMunI (PF11407) 9 (0.0%) View
Endonuc_BglI (PF14562) 8 (0.0%) View
RE_LlaMI (PF09562) 8 (0.0%) View
RestrictionSfiI (PF11487) 7 (0.0%) View
BpuSI_N (PF15516) 5 (0.0%) View
TBPIP_N (PF15517) 4 (0.0%) View
Total: 145 Total: 160342
No alignment ℹ
 

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Family relationships

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Species distribution

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Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the MSD group, to allow us to map Pfam domains onto UniProt three-dimensional structures. The table below shows the mapping between the Pfam families in this clan, the corresponding UniProt entries, and the region of the three-dimensional structures that are available for that sequence.

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