2VLD,5GKH


Conserved Protein Domain Family
NucS-like

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cd22341: NucS-like 
Click on image for an interactive view with Cn3D
Mismatch restriction endonuclease NucS and similar nucleases
Archaeal mismatch restriction endonuclease NucS and its ortholog EndoMS specifically cleave dsDNA containing mismatched bases. They belong to a 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.
Statistics
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PSSM-Id: 411745
Aligned: 172 rows
Threshold Bit Score: 82.8351
Created: 29-Jun-2020
Updated: 25-Oct-2021
Structure
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Program:
Drawing:
Aligned Rows:
 
Conserved site includes 3 residues -Click on image for an interactive view with Cn3D
Feature 1: active site [active site], 3 residue positions
Conserved feature residue pattern:D E KClick to see conserved feature residue pattern help
Evidence:
  • Structure:5GKH: Thermococcus kodakarensis EndoMS nuclease active site interacts with substrate DNA and divalent cation; contacts at 4A
    View structure with Cn3D

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1                                                                                        
2VLD_A         4 VIIKENPse---------eEIKELLDLAEKHg---------gVVTIFAr-----CKVHYEg--RAKSELg-------eGD 51  Pyrococcus abyssi
5GKH_A         6 VTVITSPst---------eELVSLVNSALLEe---------aMLTIFAr-----CKVHYDg--RAKSELg-------sGD 53  Thermococcus ko...
KKT35218      80 LKSLQKGdvlff---httiAGKKYITAYYVVe----------RVLDTGe----aVKDKYIsskYCNPHI---------GE 133 Parcubacteria g...
KXH76756      14 MIHADRE------------EIKAYMYKKRKRks--------aIPADAG------AFIRFRd-dIQIGDLvfa----yvGS 62  Candidatus Thor...
OGY78038       4 MRNNFLKgdyvf--fhasiEGKKYITAYYVVd---------rVLDTAGavkdklIVAKYKn-pHLKMYLqnp---gkyQD 68  Candidatus Jack...
WP_076560808   7 YKDPEKNggh------edpVLREFTYGHRKK-----------LKQVKPg-----DYLFFHtmiYNKRYItay----yyVQ 60  Salimicrobium f...
WP_085867265   3 TTHKSYSngihveehahglLVRQYGEAYVARnwrltpavdelISTALA------CGLDWMi--RSDHPLrkarwpnprGV 74  Pseudoruegeria ...
WP_096390021  47 LAEEHYGqg--------pgYILNILKCFAGQpag------drTPMRAGd----iVIVDGQkdiRGKSVLrgv---arvGE 105 Halopenitus per...
WP_102335652  30 LTTVEKNeyiff---htkiLDKRYITAFYKVfd-------kkTVEEIN------QDSFLNg-kVKNPHIn-------eGE 85  Salimicrobium j...
RME71443      32 LKSQVNKgdyif--fhtsrNGKRYITAYYVVdrv------lyVSEAAEdd---nICLKYKn-hHIHDYLrkka--patGD 97  Chloroflexi bac...
Feature 1                                                                                        
2VLD_A        52 RIIIIKPd-------GSFLIHQnkk-----------rePVNWQPPGSKVTFKe--------------nSXISIRRRp--- 96  Pyrococcus abyssi
5GKH_A        54 RVIIVKPd-------GSFLIHQskk-----------rePVNWQPPGSRVRLElre-----------npVLVSIRRKp--- 101 Thermococcus ko...
KKT35218     134 YTQAGRKldddvivfGDPILSRkl------------ekPLPFDKNLAKKLSLkmpfkdnlsdtqnigsATRQWRRLtkrd 201 Parcubacteria g...
KXH76756      63 NIVGLVGev-----eGDVFFDDenevgdv--fyypnqrRVNWWPEPRFFDRRelp-----------hdVSEWIKMRgt-- 122 Candidatus Thor...
OGY78038      69 DVILFGDp------iLSRKLERpllfdkn--lasqlslSIKFKDGFTDTQIIg--------------sAARNWRKLs--- 123 Candidatus Jack...
WP_076560808  61 EVTLVKDavkdalitQKFTNHHlydaf------seeeeRIAFGNPIRSRVLEkple--------vtkeLLESLENKcn-- 124 Salimicrobium f...
WP_085867265  75 VYLGFSPspd---lqWSVAIDSf--------------rPARGDYGQAVFNGK----------------YLAQFEAKgipf 121 Pseudoruegeria ...
WP_096390021 106 PQKWDSFid----ddFPHILYRdaewlynegpvakselPAKFQMGGSSSTHLp--------------gTLQQWNPSe--- 164 Halopenitus per...
WP_102335652  86 KSDILVFg-------NPVYSHVler-----------pvPLDDELLHKFFNGKrin----------qgkLIMNKAKDp--- 134 Salimicrobium j...
RME71443      98 DVIVFGDp------iTSYILERpllfdkn--lvnklslKINFLPNLTQNQSIa--------------sATRAWRELtded 155 Chloroflexi bac...
Feature 1                                                                                        
2VLD_A        97 ----YERLEVEIi--------------ePYSLVVFLAEDYEELALTg----------SEAEXANLIFENPr-------VI 141 Pyrococcus abyssi
5GKH_A       102 ----RETLEVELe--------------eVYMVSVFRAEDYEELALTg----------SEAEMAELIFENPe-------VI 146 Thermococcus ko...
KKT35218     202 vgilREAIDKNQ----------------DTGKRVGRIFSTDEVTEV-----------IEKDLENFIEVSPt-------IL 247 Parcubacteria g...
KXH76756     123 --ilRRKYKVKSl--------------kQEIRKIKSGVMKDSLETE-----------NEIEIQDFIENNIe-------KI 168 Candidatus Thor...
OGY78038     124 ----KADVNALLg--------------aIKANDQKGIEINKVFSTNevt------eiIERDLENFLETTHh-------FL 172 Candidatus Jack...
WP_076560808 125 ---iNEQMTLQAamsaslriwktlgkedITLLLERIEEEEREGTLGrklrteevvqvLERDIEEYISEHPe-------EL 194 Salimicrobium f...
WP_085867265 122 vferRNRTSGHLvvar---------ervLPTLTEVAGFDHGVLALNraprh-akgftTEYVIQHTLLSGWaqtpwadrYR 191 Pseudoruegeria ...
WP_096390021 165 ---dPEKTLDKL----------------VTALEEAPLIQPKSYDFEf----------SEKVIQEHIADHAelf--qenLD 213 Halopenitus per...
WP_102335652 135 ----LDLIEYLMe---------------FQQIPLQNIKLTTNDIYHl----------RESDIENFIESYPd------cLE 179 Salimicrobium j...
RME71443     156 veqlKESIKELI----------------ASKAPPNILRSTEEVAET-----------LEKDIEDIIAVNPd-------KI 201 Chloroflexi bac...
Feature 1                           #              # #                                           
2VLD_A       142 EegFKPIYREKPIr-hGIVDVXGVDKd-GNIVVLELKRRkADLHAVSQXKRYVDSLKEey---geNVRGILVAPs--lTE 214 Pyrococcus abyssi
5GKH_A       147 EpgFKPLFREKAIg-tGIVAVLGRDSd-GNIVVLELKRRrAELHAVRQLKSYVEILREey---gdKVRGILVAPs--lTS 219 Thermococcus ko...
KKT35218     248 GkeLKITKRQCNTp-vGRMDLICEDNq-GKKIIVELKLNkIGRDAVQQLRRYMHHLKKet---kqNVEGILVCKg--vMP 320 Parcubacteria g...
KXH76756     169 EegLVLVERERTVa-gKSMDFLARDKr-GFYTVIEVKQL-AKPDALTQLRGYIRDYKKetg--lkEVRGMLVALd--fSR 241 Candidatus Thor...
OGY78038     173 GdgLKVVRRQFDTp-vGRMDLVFENKk-GKMIIAELKLNkIGREAINQLRRYMDYLEKet---nqAVKGLIVCSg---VM 244 Candidatus Jack...
WP_076560808 195 EqgMKVLRRQYIFrnqRRLDLLMKDKd-GELVVVEVKKGrIGRDAKQQIHHYMKQVKKewd--vaHVRGIIICAg--vLP 269 Salimicrobium f...
WP_085867265 192 DvrDEFPVDGGHTs--RRIDILARDRhsGDTLVIELKRAeATPDAVRQVAGYLRALGRrddfangALSGVLVAEr--iSE 267 Pseudoruegeria ...
WP_096390021 214 ItpGEMEREYQTEs-gGFADFVVLPSd-DEVTVIETKIDiAGPQAAKQLREYIEDLQKey---nqAIQGILVAEefsnYE 288 Halopenitus per...
WP_102335652 180 NnlQLVGRQKRFSd-kSRLDLLFKDKa-GIYVVVEIKKGlIDEDTYQQLKGYVDALKKekn--lrEVRGMIVCRgf-aSD 254 Salimicrobium j...
RME71443     202 GtgLKLSARQLPIa-sGRIDLLFENAq-GHLVVVEVKLHkIGREALRQVQRYVKELKQkn----kNVKGVLVCSg--vMP 273 Chloroflexi bac...
Feature 1                                  
2VLD_A       215 GAKKLLEKEg------LEFRKLEPPK 234 Pyrococcus abyssi
5GKH_A       220 GAKRLLEKEg------LEFRKLEPPK 239 Thermococcus kodakarensis KOD1
KKT35218     321 AFEEELKTLrk----iKVFKYGWELK 342 Parcubacteria group bacterium GW2011_GWA2_44_12
KXH76756     242 RCTEEWEELse---agFEIDLVRVKK 264 Candidatus Thorarchaeota archaeon SMTZ-45
OGY78038     245 PAFEDELRH-------LKNIEIYRYG 263 Candidatus Jacksonbacteria bacterium RIFOXYD2_FULL_43_21
WP_076560808 270 YFEEELVKAqk---dgVFVKRYGWRM 292 Salimicrobium flavidum
WP_085867265 268 SARALARAEg------IEAYEIAWPM 287 Pseudoruegeria aquimaris
WP_096390021 289 GIEDEVGEYd------IMLRRYHVTL 308 Halopenitus persicus
WP_102335652 255 KSKDFYVDKinkgkveLSFHAWKFDL 280 Salimicrobium jeotgali
RME71443     274 AYENELRKQndi-kilTYGWELKIQK 298 Chloroflexi bacterium

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