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803  structures 51163  species 66  interactions 294205  sequences 1225  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 294205. 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 DUF1052 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 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...

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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
Flu_PA (PF00603) 37885 (12.9%) View
PDDEXK_1 (PF12705) 29902 (10.2%) View
Transposase_31 (PF04754) 17516 (6.0%) View
HSDR_N (PF04313) 14958 (5.1%) View
DUF4143 (PF13635) 11875 (4.0%) View
UPF0102 (PF02021) 11699 (4.0%) View
Mrr_cat (PF04471) 9078 (3.1%) View
Uma2 (PF05685) 8780 (3.0%) View
RmuC (PF02646) 8653 (2.9%) View
NERD (PF08378) 8397 (2.9%) View
RecU (PF03838) 7534 (2.6%) View
DUF559 (PF04480) 7435 (2.5%) View
CoiA (PF06054) 6912 (2.3%) View
VRR_NUC (PF08774) 6876 (2.3%) View
SfsA (PF03749) 6408 (2.2%) View
YqaJ (PF09588) 5594 (1.9%) View
DUF1016 (PF06250) 5358 (1.8%) View
PDDEXK_2 (PF12784) 5265 (1.8%) View
YaeQ (PF07152) 5138 (1.7%) View
DUF3883 (PF13020) 4884 (1.7%) View
DUF2726 (PF10881) 4747 (1.6%) View
Vsr (PF03852) 4343 (1.5%) View
MutH (PF02976) 4167 (1.4%) View
DUF2800 (PF10926) 4114 (1.4%) View
ERCC4 (PF02732) 3917 (1.3%) View
HSDR_N_2 (PF13588) 3906 (1.3%) View
DUF91 (PF01939) 3545 (1.2%) View
PDDEXK_9 (PF08011) 3354 (1.1%) View
Cas_Cas4 (PF01930) 2655 (0.9%) View
McrBC (PF10117) 2641 (0.9%) View
Tn7_Tnp_TnsA_N (PF08722) 2351 (0.8%) View
Mrr_cat_2 (PF13156) 2228 (0.8%) View
Cas_Csm6 (PF09659) 1893 (0.6%) View
Spo0A_C (PF08769) 1791 (0.6%) View
DUF3799 (PF12684) 1717 (0.6%) View
tRNA_int_endo (PF01974) 1525 (0.5%) View
DUF234 (PF03008) 1409 (0.5%) View
RAP (PF08373) 1265 (0.4%) View
EcoRII-C (PF09019) 1182 (0.4%) View
PDDEXK_3 (PF13366) 924 (0.3%) View
Endonuc_Holl (PF10107) 817 (0.3%) View
RNA_pol_Rpb5_N (PF03871) 811 (0.3%) View
DpnII (PF04556) 811 (0.3%) View
PDDEXK_4 (PF14281) 752 (0.3%) View
L_protein_N (PF15518) 738 (0.3%) View
eIF-3_zeta (PF05091) 729 (0.2%) View
DUF1052 (PF06319) 695 (0.2%) View
Dna2 (PF08696) 655 (0.2%) View
Rad10 (PF03834) 641 (0.2%) View
Exo5 (PF09810) 639 (0.2%) View
RAI1 (PF08652) 606 (0.2%) View
DUF1887 (PF09002) 569 (0.2%) View
DpnI (PF06044) 509 (0.2%) View
RE_ApaLI (PF09499) 500 (0.2%) View
DUF2357 (PF09823) 494 (0.2%) View
DUF2887 (PF11103) 487 (0.2%) View
RE_AlwI (PF09491) 487 (0.2%) View
PDDEXK_7 (PF04411) 463 (0.2%) View
BsuBI_PstI_RE (PF06616) 417 (0.1%) View
DUF4263 (PF14082) 399 (0.1%) View
DUF2034 (PF10356) 392 (0.1%) View
DUF4420 (PF14390) 386 (0.1%) View
continued
Pfam family Num. domains Alignment
Hjc (PF01870) 381 (0.1%) View
DUF1780 (PF08682) 378 (0.1%) View
XisH (PF08814) 376 (0.1%) View
Sen15 (PF09631) 371 (0.1%) View
RE_NgoBV (PF09564) 323 (0.1%) View
RE_HpaII (PF09561) 302 (0.1%) View
DUF2161 (PF09929) 292 (0.1%) View
Herpes_alk_exo (PF01771) 292 (0.1%) View
Pet127 (PF08634) 286 (0.1%) View
RE_LlaJI (PF09563) 244 (0.1%) View
Herpes_UL24 (PF01646) 231 (0.1%) View
RE_CfrBI (PF09516) 218 (0.1%) View
MvaI_BcnI (PF15515) 195 (0.1%) View
RE_Eco47II (PF09553) 179 (0.1%) View
Endonuc-BglII (PF09195) 177 (0.1%) View
Cas_Cas02710 (PF09670) 170 (0.1%) View
RE_EcoO109I (PF14511) 159 (0.1%) View
Cas_NE0113 (PF09623) 158 (0.1%) View
Cas_APE2256 (PF09651) 155 (0.1%) View
NotI (PF12183) 147 (0.0%) View
EcoRI (PF02963) 147 (0.0%) View
PDDEXK_10 (PF07788) 137 (0.0%) View
RE_TdeIII (PF09520) 128 (0.0%) View
RE_NgoPII (PF09521) 121 (0.0%) View
Tsp45I (PF06300) 118 (0.0%) View
RE_HindVP (PF09519) 117 (0.0%) View
Phage_endo_I (PF05367) 107 (0.0%) View
Endonuc-EcoRV (PF09233) 101 (0.0%) View
NgoMIV_restric (PF09015) 96 (0.0%) View
RE_HindIII (PF09518) 94 (0.0%) View
XhoI (PF04555) 87 (0.0%) View
DUF911 (PF06023) 86 (0.0%) View
RE_SinI (PF09570) 81 (0.0%) View
RE_MjaI (PF09568) 73 (0.0%) View
PDDEXK_5 (PF11645) 72 (0.0%) View
NaeI (PF09126) 67 (0.0%) View
RE_Bpu10I (PF09549) 62 (0.0%) View
Endonuc-BsobI (PF09194) 60 (0.0%) View
RE_XamI (PF09572) 54 (0.0%) View
Endonuc-FokI_C (PF09254) 51 (0.0%) View
ThaI (PF15514) 50 (0.0%) View
R-HINP1I (PF11463) 49 (0.0%) View
RE_HaeII (PF09554) 39 (0.0%) View
Endonuc-PvuII (PF09225) 39 (0.0%) View
BpuJI_N (PF11564) 34 (0.0%) View
BamHI (PF02923) 33 (0.0%) View
RE_SacI (PF09566) 29 (0.0%) View
RE_Bsp6I (PF09504) 27 (0.0%) View
RE_ScaI (PF09569) 26 (0.0%) View
Bse634I (PF07832) 23 (0.0%) View
Endonuc-MspI (PF09208) 19 (0.0%) View
TBPIP_N (PF15517) 18 (0.0%) View
RE_XcyI (PF09571) 17 (0.0%) View
VirArc_Nuclease (PF12187) 16 (0.0%) View
Endonuc-HincII (PF09226) 16 (0.0%) View
RE_TaqI (PF09573) 13 (0.0%) View
RestrictionMunI (PF11407) 12 (0.0%) View
BpuSI_N (PF15516) 11 (0.0%) View
RE_LlaMI (PF09562) 11 (0.0%) View
RestrictionSfiI (PF11487) 7 (0.0%) View
Endonuc_BglI (PF14562) 5 (0.0%) View
Total: 123 Total: 294205 Clan alignment
 

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Family relationships

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

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Species distribution

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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.

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