Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser.
912  structures 3485  species 66  interactions 51816  sequences 999  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 123 families and the total number of domains in the clan is 51816. 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 123 member families:

BamHI BpuJI_N BpuSI_N Bse634I BsuBI_PstI_RE Cas_APE2256 Cas_Cas02710 Cas_Cas4 Cas_Csm6 Cas_NE0113 CoiA Dna2 DpnI DpnII DUF1016 DUF1780 DUF1887 DUF2034 DUF2161 DUF234 DUF2357 DUF2726 DUF2800 DUF2887 DUF3799 DUF3883 DUF4143 DUF4263 DUF4420 DUF559 DUF91 DUF911 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_alk_exo Herpes_UL24 Hjc HSDR_N HSDR_N_2 L_protein_N McrBC MmcB-like Mrr_cat Mrr_cat_2 MutH MvaI_BcnI NaeI NERD NgoMIV_restric NotI PDDEXK_1 PDDEXK_10 PDDEXK_2 PDDEXK_3 PDDEXK_4 PDDEXK_5 PDDEXK_7 PDDEXK_9 Pet127 Phage_endo_I R-HINP1I Rad10 RAI1 RAP RE_AlwI RE_ApaLI RE_Bpu10I 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 RecU RestrictionMunI RestrictionSfiI RmuC RNA_pol_Rpb5_N Sen15 SfsA Spo0A_C TBPIP_N ThaI Tn7_Tnp_TnsA_N Transposase_31 tRNA_int_endo Tsp45I Uma2 UPF0102 VirArc_Nuclease VRR_NUC Vsr XhoI XisH YaeQ YqaJ

External database links

Domain organisation

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

Loading domain graphics...

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) 5257 (10.1%) View
Uma2 (PF05685) 5211 (10.1%) View
DUF4143 (PF13635) 2866 (5.5%) View
UPF0102 (PF02021) 2195 (4.2%) View
HSDR_N (PF04313) 1912 (3.7%) View
ERCC4 (PF02732) 1899 (3.7%) View
Mrr_cat (PF04471) 1788 (3.5%) View
RmuC (PF02646) 1718 (3.3%) View
DUF559 (PF04480) 1343 (2.6%) View
NERD (PF08378) 1293 (2.5%) View
PDDEXK_2 (PF12784) 1281 (2.5%) View
tRNA_int_endo (PF01974) 1250 (2.4%) View
PDDEXK_9 (PF08011) 1166 (2.3%) View
RAP (PF08373) 1075 (2.1%) View
DUF1016 (PF06250) 1033 (2.0%) View
Cas_Cas4 (PF01930) 1031 (2.0%) View
HSDR_N_2 (PF13588) 932 (1.8%) View
Transposase_31 (PF04754) 922 (1.8%) View
VRR_NUC (PF08774) 867 (1.7%) View
YqaJ (PF09588) 859 (1.7%) View
SfsA (PF03749) 829 (1.6%) View
RNA_pol_Rpb5_N (PF03871) 801 (1.5%) View
eIF-3_zeta (PF05091) 699 (1.3%) View
Exo5 (PF09810) 661 (1.3%) View
PDDEXK_3 (PF13366) 659 (1.3%) View
Spo0A_C (PF08769) 653 (1.3%) View
Rad10 (PF03834) 591 (1.1%) View
Vsr (PF03852) 571 (1.1%) View
Dna2 (PF08696) 559 (1.1%) View
RAI1 (PF08652) 549 (1.1%) View
DUF91 (PF01939) 539 (1.0%) View
DUF3883 (PF13020) 510 (1.0%) View
DUF234 (PF03008) 505 (1.0%) View
RecU (PF03838) 465 (0.9%) View
DUF2034 (PF10356) 388 (0.7%) View
YaeQ (PF07152) 384 (0.7%) View
McrBC (PF10117) 382 (0.7%) View
DUF2726 (PF10881) 370 (0.7%) View
Sen15 (PF09631) 343 (0.7%) View
CoiA (PF06054) 311 (0.6%) View
DUF2887 (PF11103) 292 (0.6%) View
Pet127 (PF08634) 281 (0.5%) View
MutH (PF02976) 249 (0.5%) View
Tn7_Tnp_TnsA_N (PF08722) 224 (0.4%) View
PDDEXK_4 (PF14281) 214 (0.4%) View
XisH (PF08814) 212 (0.4%) View
MmcB-like (PF06319) 202 (0.4%) View
DUF2800 (PF10926) 162 (0.3%) View
DUF2357 (PF09823) 161 (0.3%) View
DUF3799 (PF12684) 142 (0.3%) View
DUF4420 (PF14390) 135 (0.3%) View
DpnII (PF04556) 135 (0.3%) View
DUF2161 (PF09929) 134 (0.3%) View
Hjc (PF01870) 134 (0.3%) View
PDDEXK_7 (PF04411) 134 (0.3%) View
DUF1887 (PF09002) 128 (0.2%) View
DUF4263 (PF14082) 120 (0.2%) View
Mrr_cat_2 (PF13156) 112 (0.2%) View
MvaI_BcnI (PF15515) 99 (0.2%) View
Cas_APE2256 (PF09651) 97 (0.2%) View
Cas_Cas02710 (PF09670) 96 (0.2%) View
RE_AlwI (PF09491) 92 (0.2%) View
continued
Pfam family Num. domains Alignment
BsuBI_PstI_RE (PF06616) 90 (0.2%) View
Cas_NE0113 (PF09623) 75 (0.1%) View
RE_TdeIII (PF09520) 71 (0.1%) View
Endonuc-BglII (PF09195) 70 (0.1%) View
DpnI (PF06044) 70 (0.1%) View
PDDEXK_10 (PF07788) 66 (0.1%) View
RE_HpaII (PF09561) 65 (0.1%) View
Endonuc_Holl (PF10107) 58 (0.1%) View
Cas_Csm6 (PF09659) 55 (0.1%) View
EcoRII-C (PF09019) 52 (0.1%) View
RE_EcoO109I (PF14511) 49 (0.1%) View
DUF911 (PF06023) 48 (0.1%) View
RE_LlaJI (PF09563) 47 (0.1%) View
RE_MjaI (PF09568) 46 (0.1%) View
Herpes_alk_exo (PF01771) 46 (0.1%) View
RE_Eco47II (PF09553) 43 (0.1%) View
XhoI (PF04555) 37 (0.1%) View
NaeI (PF09126) 33 (0.1%) View
NotI (PF12183) 30 (0.1%) View
Tsp45I (PF06300) 28 (0.1%) View
PDDEXK_5 (PF11645) 27 (0.1%) View
RE_HindVP (PF09519) 27 (0.1%) View
Endonuc-EcoRV (PF09233) 27 (0.1%) View
NgoMIV_restric (PF09015) 24 (0.0%) View
RE_XamI (PF09572) 23 (0.0%) View
RE_Bpu10I (PF09549) 23 (0.0%) View
DUF1780 (PF08682) 21 (0.0%) View
RE_SacI (PF09566) 19 (0.0%) View
RE_NgoPII (PF09521) 19 (0.0%) View
Endonuc-FokI_C (PF09254) 19 (0.0%) View
Endonuc-BsobI (PF09194) 19 (0.0%) View
EcoRI (PF02963) 19 (0.0%) View
BamHI (PF02923) 18 (0.0%) View
RE_ApaLI (PF09499) 16 (0.0%) View
BpuJI_N (PF11564) 14 (0.0%) View
R-HINP1I (PF11463) 14 (0.0%) View
RE_HaeII (PF09554) 14 (0.0%) View
Herpes_UL24 (PF01646) 14 (0.0%) View
RE_TaqI (PF09573) 12 (0.0%) View
RE_SinI (PF09570) 12 (0.0%) View
RE_HindIII (PF09518) 12 (0.0%) View
ThaI (PF15514) 10 (0.0%) View
RestrictionMunI (PF11407) 9 (0.0%) View
Endonuc-HincII (PF09226) 9 (0.0%) View
RE_NgoBV (PF09564) 8 (0.0%) View
Endonuc-MspI (PF09208) 8 (0.0%) View
RE_ScaI (PF09569) 7 (0.0%) View
RE_CfrBI (PF09516) 7 (0.0%) View
Endonuc-PvuII (PF09225) 7 (0.0%) View
Flu_PA (PF00603) 7 (0.0%) View
TBPIP_N (PF15517) 6 (0.0%) View
RE_Bsp6I (PF09504) 6 (0.0%) View
Bse634I (PF07832) 6 (0.0%) View
Phage_endo_I (PF05367) 6 (0.0%) View
L_protein_N (PF15518) 5 (0.0%) View
VirArc_Nuclease (PF12187) 5 (0.0%) View
RestrictionSfiI (PF11487) 5 (0.0%) View
RE_XcyI (PF09571) 5 (0.0%) View
Endonuc_BglI (PF14562) 3 (0.0%) View
RE_LlaMI (PF09562) 2 (0.0%) View
BpuSI_N (PF15516) 1 (0.0%) View
Total: 123 Total: 51816
No alignment ℹ
 

Please note: Clan alignments can be very large and can cause problems for some browsers. Read the note above before viewing.

Family relationships

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

Species distribution

Tree controls

Hide

This tree shows the occurrence of the domains in this clan across different species. More...

Loading...

Interactions

There are 66 interactions for this clan. More...

Interacting families
A B
BamHI BamHI
Bse634I Bse634I
BsuBI_PstI_RE BsuBI_PstI_RE
Cas_APE2256 Cas_APE2256
DpnI DpnI
DUF559 DUF559
DUF91 DUF91
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
Herpes_alk_exo Herpes_alk_exo
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
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
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.

Loading structure mapping...