1CW0,1QPS,1KNV,4DAP,4DA2,1ZP7,1M0D,1D2I,2AZO,3HRL,2FQZ,1NA6,1GEF,5AMR,2VLD,1J22,2OA9,1Y0K,5EAN,4RI9,4RVE,1W36,4ESJ,1VRR,4XJX,1XHU,6UKE,4F0P,1DC1,1F1Z,1FIU,1XMX,3R3P,2FOK,2CV8,1D02,1YFI,4XQK,4QBL,3NDH,3IMB,5DWA,1WTE,3BVQ,3ODH,2INB,1EV7,4ZSF,3DW9,3BM3,2FLC,1Y88,1AVQ,2A1I,1WDJ,1W36,1PVU,5LIQ,1DMU,2REU,2E52,2OT9


Conserved Protein Domain Family
PDDEXK_nuclease-like

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cd01037: PDDEXK_nuclease-like 
PDDEXK family nucleases
Superfamily of PDDEXK nucleases including very short patch repair (Vsr) endonucleases, archaeal Holliday junction resolvases, MutH methyl-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and FokI.
Links
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Statistics
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PSSM-Id: 411707
Aligned: 153 rows
Threshold Bit Score: 28.3977
Created: 4-Sep-2001
Updated: 30-Sep-2020
Structure
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Program:
Drawing:
Aligned Rows:
 
putative active
Conserved site includes 3 residues -Click on image for an interactive view with Cn3D
Feature 1: putative active site [active site], 3 residue positions
Conserved feature residue pattern:[D] [EDQNH] [KH]Click to see conserved feature residue pattern help
Evidence:
  • Structure:1CW0: Escherichia coli Vsr endonuclease putative active site forms complex with a DNA duplex and Mg ions
    View structure with Cn3D
  • Comment:conserved residues in these columns may be essential for endonuclease activity

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1                                                                                         
1CW0_A         22 AIEKRL-------ASlltgqglafr-----------------------------------------------vqdaslpg 47   Escherichia coli
3BVQ_A         85 ALDPLF-------XSaasrklfgygpteplqfiaaptladqavrdgirewldrgvhvvayfqeklggelsisktdsspef 157  Nocardia otit...
1W36_C        884 LLNALV-------EQddaerlfrrfraagdlpygafgeifwetqcqe--mqqladrviacrqpgqsmeidlacngvqitg 954  Escherichia coli
WP_012966224  180 KFAEKLe-----sLSk---------------------------------------------------------------- 190  Ferroglobus p...
AKG91892      179 EFAKVLre----aYEs---------------------------------------------------------------- 190  Geoglobus aha...
OGS42909      571 AVEAGI-------ESelegagfn--------------------------------------------------aevkdle 593  Euryarchaeota...
OGD45095      100 ASKMGL-------KDelegsgfa--------------------------------------------------veerdle 122  Candidatus Ba...
XP_009434022   30 EVPPGVakplfrsTQslptvdts--------------------------------------------------aqaapqt 59   chimpanzee
RLG64557      196 LLYESMrk----aWLk---------------------------------------------------------------- 207  archaeon
XP_021536742   27 APPAGVkpl-fksTRslptveas--------------------------------------------------pqaapqt 55   Hawaiian monk...
Feature 1           #                     # #                                                     
1CW0_A         48 rPDFvvd-----------eyrCVIFTHGCfwhhhhcylfkvpatrtefwle--------------------------kig 90   Escherichia coli
3BVQ_A        158 sFDWtlaevesiypvpkikryGVLEIQTXdfhgsykhavgaidialvegidfhgwlptpagraalskkxegpnlsnvfkr 237  Nocardia otit...
1W36_C        955 wLPQvq-------------pdGLLRWRPSllsvaqgmqlwl--------------------------------------- 982  Escherichia coli
WP_012966224  191 kIEI-----------------KAAKLNPVvengtl--------------------------------------------- 208  Ferroglobus p...
AKG91892      191 gVDV-----------------RAALLRPEvqgdcl--------------------------------------------- 208  Geoglobus aha...
OGS42909      594 sADVvvs------------grVAVSVRTVdefirgisdgsiq-------------------------------------- 623  Euryarchaeota...
OGD45095      123 nADVvis------------prVAASIHTVdqfiqgisdgsvf-------------------------------------- 152  Candidatus Ba...
XP_009434022   60 yAEYaisq---------plegAGATCPTGseplagetpn----------------------------------------- 89   chimpanzee
RLG64557      208 gVYV-----------------TAYKIKLVn-------------------------------------------------- 220  archaeon
XP_021536742   56 yAEYaisg---------ppggVGAPHHRGpeplagetpnqapkpgaks-------------------------------- 94   Hawaiian monk...
Feature 1                                  
1CW0_A         91 knverdrrdisrlqelgwrVLIVWE 115  Escherichia coli
3BVQ_A        238 tfyqxaykfalsghqrcagTGFAIP 262  Nocardia otitidiscaviarum
1W36_C        983 -------ehlvycasggngESRLFL 1000 Escherichia coli
WP_012966224  209 --------------kiyhsGYIPVV 219  Ferroglobus placidus
AKG91892      209 --------------tigfeRYLPVE 219  Geoglobus ahangari
OGS42909      624 -------stlaklkheylhPILIVQ 641  Euryarchaeota archaeon RBG_16_62_10
OGD45095      153 -------atlaklkheylhPILIVQ 170  Candidatus Bathyarchaeota archaeon RBG_16_57_9
XP_009434022   90 ----------qalkpgaksNSIIVS 104  chimpanzee
RLG64557      221 ------------------gRILPVE 227  archaeon
XP_021536742   95 ssiivsprqvrrgwrsgalRFLVGN 119  Hawaiian monk seal

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