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1131  structures 10981  species 67  interactions 146231  sequences 1855  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 142 families and the total number of domains in the clan is 146231. 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 142 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 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_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) 16216 (11.1%) View
Uma2 (PF05685) 14438 (9.9%) View
UPF0102 (PF02021) 6746 (4.6%) View
DUF4143 (PF13635) 6667 (4.6%) View
HSDR_N (PF04313) 5721 (3.9%) View
Mrr_cat (PF04471) 5612 (3.8%) View
RmuC (PF02646) 5254 (3.6%) View
DUF559 (PF04480) 4541 (3.1%) View
NERD (PF08378) 4231 (2.9%) View
ERCC4 (PF02732) 3763 (2.6%) View
PDDEXK_2 (PF12784) 2967 (2.0%) View
HSDR_N_2 (PF13588) 2932 (2.0%) View
tRNA_int_endo (PF01974) 2561 (1.8%) View
PDDEXK_3 (PF13366) 2507 (1.7%) View
PDDEXK_9 (PF08011) 2429 (1.7%) View
YhcG_C (PF06250) 2426 (1.7%) View
Cas_Cas4 (PF01930) 2404 (1.6%) View
SfsA (PF03749) 2295 (1.6%) View
YqaJ (PF09588) 2237 (1.5%) View
VRR_NUC (PF08774) 2220 (1.5%) View
Transposase_31 (PF04754) 2014 (1.4%) View
NucS (PF01939) 1889 (1.3%) View
Vsr (PF03852) 1857 (1.3%) View
MTES_1575 (PF18741) 1854 (1.3%) View
RAP (PF08373) 1839 (1.3%) View
RecC_C (PF17946) 1542 (1.1%) View
RNA_pol_Rpb5_N (PF03871) 1468 (1.0%) View
YaeQ (PF07152) 1391 (1.0%) View
DUF3883 (PF13020) 1371 (0.9%) View
Spo0A_C (PF08769) 1343 (0.9%) View
eIF-3_zeta (PF05091) 1305 (0.9%) View
McrBC (PF10117) 1286 (0.9%) View
DUF234 (PF03008) 1269 (0.9%) View
Exo5 (PF09810) 1228 (0.8%) View
Dna2 (PF08696) 1158 (0.8%) View
RecU (PF03838) 1152 (0.8%) View
Rad10 (PF03834) 1105 (0.8%) View
RAI1 (PF08652) 1040 (0.7%) View
DUF2726 (PF10881) 1039 (0.7%) View
CoiA (PF06054) 960 (0.7%) View
MmcB-like (PF06319) 917 (0.6%) View
Tn7_Tnp_TnsA_N (PF08722) 804 (0.5%) View
DUF2034 (PF10356) 746 (0.5%) View
PDDEXK_4 (PF14281) 702 (0.5%) View
Sen15 (PF09631) 702 (0.5%) View
MutH (PF02976) 690 (0.5%) View
DUF2887 (PF11103) 669 (0.5%) View
DUF3799 (PF12684) 591 (0.4%) View
XisH (PF08814) 591 (0.4%) View
DUF2161 (PF09929) 585 (0.4%) View
PDCD9 (PF07147) 577 (0.4%) View
Pet127 (PF08634) 555 (0.4%) View
DUF2800 (PF10926) 547 (0.4%) View
DUF4420 (PF14390) 485 (0.3%) View
MepB (PF08877) 470 (0.3%) View
DUF4263 (PF14082) 420 (0.3%) View
DUF2357 (PF09823) 417 (0.3%) View
Hjc (PF01870) 404 (0.3%) View
PDDEXK_7 (PF04411) 386 (0.3%) View
Mrr_cat_2 (PF13156) 365 (0.2%) View
DUF1887 (PF09002) 355 (0.2%) View
Cas_DxTHG (PF09455) 354 (0.2%) View
DUF5614 (PF18474) 285 (0.2%) View
DpnII (PF04556) 284 (0.2%) View
MvaI_BcnI (PF15515) 264 (0.2%) View
BsuBI_PstI_RE (PF06616) 263 (0.2%) View
Endonuc-BglII (PF09195) 259 (0.2%) View
RE_AlwI (PF09491) 250 (0.2%) View
Cas_Cas02710 (PF09670) 245 (0.2%) View
PDDEXK_5 (PF11645) 226 (0.2%) View
CdiA_C (PF18451) 208 (0.1%) View
Cas_APE2256 (PF09651) 201 (0.1%) View
continued
Pfam family Num. domains Alignment
EcoRII-C (PF09019) 199 (0.1%) View
Viral_alk_exo (PF01771) 199 (0.1%) View
Tox-REase-5 (PF15648) 191 (0.1%) View
Cas_NE0113 (PF09623) 191 (0.1%) View
RE_TdeIII (PF09520) 187 (0.1%) View
RE_EcoO109I (PF14511) 178 (0.1%) View
Endonuc_Holl (PF10107) 153 (0.1%) View
DpnI (PF06044) 151 (0.1%) View
DpnII-MboI (PF18742) 146 (0.1%) View
RE_LlaJI (PF09563) 143 (0.1%) View
RE_HpaII (PF09561) 142 (0.1%) View
PND (PF17949) 136 (0.1%) View
RE_MjaI (PF09568) 133 (0.1%) View
NaeI (PF09126) 133 (0.1%) View
PDDEXK_10 (PF07788) 130 (0.1%) View
XhoI (PF04555) 125 (0.1%) View
EC042_2821 (PF18740) 118 (0.1%) View
Phage_endo_I (PF05367) 116 (0.1%) View
Cas_Csm6 (PF09659) 112 (0.1%) View
NotI (PF12183) 107 (0.1%) View
RE_Eco47II (PF09553) 105 (0.1%) View
L_protein_N (PF15518) 101 (0.1%) View
Endonuc-EcoRV (PF09233) 99 (0.1%) View
NgoMIV_restric (PF09015) 90 (0.1%) View
DUF1780 (PF08682) 87 (0.1%) View
RE_BsaWI (PF18643) 86 (0.1%) View
Flu_PA (PF00603) 75 (0.1%) View
Tsp45I (PF06300) 74 (0.1%) View
Herpes_UL24 (PF01646) 73 (0.0%) View
AHJR-like (PF18743) 71 (0.0%) View
RE_XamI (PF09572) 71 (0.0%) View
Csa1 (PF06023) 64 (0.0%) View
Endonuc-FokI_C (PF09254) 61 (0.0%) View
Endonuc-BsobI (PF09194) 59 (0.0%) View
RE_HindVP (PF09519) 58 (0.0%) View
RE_SacI (PF09566) 57 (0.0%) View
Tox-REase-7 (PF15649) 56 (0.0%) View
RE_Bpu10I (PF09549) 54 (0.0%) View
RE_NgoPII (PF09521) 50 (0.0%) View
RE_CfrBI (PF09516) 50 (0.0%) View
EcoRI (PF02963) 48 (0.0%) View
BamHI (PF02923) 44 (0.0%) View
R-HINP1I (PF11463) 41 (0.0%) View
RE_ApaLI (PF09499) 38 (0.0%) View
BpuJI_N (PF11564) 35 (0.0%) View
RE_HaeII (PF09554) 35 (0.0%) View
RE_SinI (PF09570) 31 (0.0%) View
Tox-REase-2 (PF15646) 28 (0.0%) View
CdiA_C_tRNase (PF18664) 28 (0.0%) View
ThaI (PF15514) 27 (0.0%) View
RE_HindIII (PF09518) 27 (0.0%) View
RE_NgoBV (PF09564) 26 (0.0%) View
Tox-REase-9 (PF15650) 25 (0.0%) View
Tox-REase-3 (PF15647) 25 (0.0%) View
RE_ScaI (PF09569) 25 (0.0%) View
Endonuc-PvuII (PF09225) 24 (0.0%) View
RE_TaqI (PF09573) 23 (0.0%) View
RE_Bsp6I (PF09504) 21 (0.0%) View
RE_XcyI (PF09571) 20 (0.0%) View
Bse634I (PF07832) 20 (0.0%) View
TBPIP_N (PF15517) 16 (0.0%) View
Endonuc-MspI (PF09208) 16 (0.0%) View
VirArc_Nuclease (PF12187) 15 (0.0%) View
RestrictionMunI (PF11407) 15 (0.0%) View
ArenaCapSnatch (PF17296) 13 (0.0%) View
Endonuc-HincII (PF09226) 12 (0.0%) View
RestrictionSfiI (PF11487) 11 (0.0%) View
Endonuc_BglI (PF14562) 6 (0.0%) View
RE_LlaMI (PF09562) 6 (0.0%) View
BpuSI_N (PF15516) 5 (0.0%) View
Total: 142 Total: 146231
No alignment ℹ
 

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Family relationships

This diagram shows the relationships between members of this clan. More...

Species distribution

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Interactions

There are 67 interactions for this clan. More...

Interacting families
A B
BamHI BamHI
Bse634I Bse634I
BsuBI_PstI_RE BsuBI_PstI_RE
Cas_APE2256 Cas_APE2256
Cas_DxTHG Cas_DxTHG
DpnI DpnI
DUF559 DUF559
EcoRII-C EcoRII-C
EcoRII-N
EcoRII-N EcoRII-C
Endonuc-BglII Endonuc-BglII
Endonuc-BsobI Endonuc-BsobI
Endonuc-EcoRV Endonuc-EcoRV
Endonuc-FokI_C Endonuc-FokI_C
Endonuc-HincII Endonuc-HincII
Endonuc-MspI Endonuc-MspI
Endonuc-PvuII Endonuc-PvuII
ERCC4 ERCC4
Flu_PA Flu_PA
Flu_PB1
FokI_C Endonuc-FokI_C
Hjc Hjc
HSDR_N EcoR124_C
ResIII
HSDR_N_2 ResIII
L_protein_N L_protein_N
MHC_I Flu_PA
MutH MutH
MvaI_BcnI MvaI_BcnI
NaeI NaeI
NgoMIV_restric NgoMIV_restric
NotI NotI
NucS NucS
PDDEXK_1 Exonuc_V_gamma
UvrD_C
PDDEXK_5 PDDEXK_5
Phage_endo_I Phage_endo_I
R-HINP1I R-HINP1I
RE_EcoO109I RE_EcoO109I
RE_HindIII RE_HindIII
RecU RecU
ResIII HSDR_N
RestrictionMunI RestrictionMunI
RestrictionSfiI RestrictionSfiI
RNA_pol_Rpb1_1 RNA_pol_Rpb5_N
RNA_pol_Rpb1_5 RNA_pol_Rpb5_N
RNA_pol_Rpb1_7 RNA_pol_Rpb5_N
RNA_pol_Rpb5_N RNA_pol_Rpb5_C
TFIIS_M
Sen15 Sen15
Spo0A_C Spo0A_C
ThaI ThaI
Tn7_Tnp_TnsA_N Tn7_Tnp_TnsA_C
Tn7_Tnp_TnsA_N
Tn7_TnsC_Int
tRNA_int_endo tRNA_int_endo
tRNA_int_endo_N
tRNA_int_endo_N tRNA_int_endo
Uma2 Uma2
UvrD-helicase PDDEXK_1
UvrD_C PDDEXK_1
Viral_alk_exo Viral_alk_exo
VirArc_Nuclease VirArc_Nuclease
XisH XisH
XRN_N RAI1
YaeQ YaeQ
YqaJ YqaJ

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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