Conserved Protein Domain Family
RMtype1_S_MmaGORF2198P_TRD1-CR1_like

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cd17500: RMtype1_S_MmaGORF2198P_TRD1-CR1_like 
Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Methanosarcina mazei Goe1 S subunit (S.MmaGORF2198P) TRD1-CR1, and Flavobacterium psychrophilum FPG3 S subunit (S.FpsFPG3ORF6820P) TRD1-CR1
The recognition sequences of Methanosarcina mazei Goe1 S subunit (S.MmaGORF2198P) and Flavobacterium psychrophilum FPG3 S subunit (S.FpsFPG3ORF6820P) are undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains TRD1-CR1. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases.
Statistics
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PSSM-Id: 341191
Aligned: 20 rows
Threshold Bit Score: 277.632
Created: 31-May-2017
Updated: 2-Oct-2020
Structure
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Aligned Rows:
 
putative
Feature 1:putative TRD-CR/TRD-CR interface [polypeptide binding site]
Evidence:
  • Comment:HsdS TRD2-CR2/ HsdS TRD1-CR1 interface
  • Comment:based on related TRD1-CR1/TRD2-CR2 's with structure
  • Comment:HsdS DNA specificity subunit, and HsdM DNA modification subunit; type I RM enzymes, are formed from a core methyltransferase (MTase) comprised of one HsdS subunit and two HsdM subunits, this is complexed with two HsdR DNA restriction subunits (R2M2S1)
  • Comment:CR1 and CR2 refer to two coiled-coiled structures, found at the ends of the primary sequence of S-subunit TRD1 and TRD2 respectively; CR1 and CR2 run antiparallel to each other and interact by hydrophobic contacts between a series of hydrophobic residues

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1                                                                                     
AAM31895    9 KLREIASEIKSGGTPSTKHQEYYGGI-IPWLNTKEIHFnRIRDTDIKITEGGLNNSSAKWVKENSIIVAMYGa--TAGKI 85  Methanosarcina maz...
AKA25098    9 SVLDLCKQVFSGGTPKSTVPEFFDGGtIPWVKTKEVNYsSIRNTENFITELGFLNSSTKIVPVNSIIVAMYGngdTAGRV 88  Pseudomonas chloro...
SHL55718    8 TIGELCSNICSGGTPNRSNDSFYNNGnIPWLNTKEVSFnRIYQTENFITELGLKNSAAKWIPQNTVVVAMYGa--TAGKS 85  Fibrobacter sp. UWH4
OFQ04781    8 TLGELSIRVSSGLTPLKSNKEFWENPiIPWLKTDQLGEkYIFDTNTKISKEALEQTSLRIYPENTISIAMYGegkTRGNL 87  Streptococcus sp. ...
SDX98752    5 RLSEISTRISSGLTPLRSNPEFWKNGtIPWLKTEQLGEkYIYDTNEYISVAAVEKTSIKVFPRNTLSIAMYGegkTRGNL 84  Nitrosomonas sp. Nm33
EOR07185    5 KLSEISLKISSGLTPLRSNPIFWSEGnIPWLKTEQLSLkYIYDTNEYITEAALEKTSIRVYPKDTLALAMYGegkTRGNV 84  Acinetobacter tand...
AEI09871    8 AVEALCSRVTSGGTPSRKRADYYTDEgIPWVKSQELIGaRIATTEEHISEAGLERSSAKLLPPDTVLLAMYGa--NVGQL 85  Corynebacterium re...
GAC08254   11 RIEDLCINVTSGGTPSRKNPDFYTGD-IPWLKTGELKGwFVYDAVEKITEEAIKKSSAKIYPKNTVLMAMYGdgrTIGSV 89  Glaciecola chatham...
ENN96239   25 KRLGEIANISTGGTPSRKKKEYWNGK-INWLKSKEVQDnYIYDTEEKITEKGMKNSNAKRLYPPGTLILAIYaspTAGRV 103 Methanocaldococcus...
KGQ42748    8 AIKDICISITSGGTPSRSISEYYSNGnICWVKTKELNNfYIYDTEEKITENAIRKSSAKLLPKNTVLLAMYGa--TVGET 85  Gallibacterium anatis
Feature 1                                  ##  #                                ###  ##  ##  #
AAM31895   86 AINKIPLTTNQACCNITPDSekadYNFVYYNLCHRYDELVNLSCGaAQQNLNVGLITNLDIILPp-ITEQCAIASVLSSL 164 Methanosarcina maz...
AKA25098   89 AINKIELVTNQACCNLVIDAdhgdYRFIYYYLKSQYEKLVGLKNGgAQQNLNSKLIKEYPILTPp-LWEQKRIGVFLESF 167 Pseudomonas chloro...
SHL55718   86 AIVKIPVTTNQACCNLTIDGskadYRFVYYSLFNRYEHLASLANGgAQQNLNAGLIREFKISVPe-LETQTKIADILSSL 164 Fibrobacter sp. UWH4
OFQ04781   88 SIIKAPMTTNQACCNIELDTkladVEYVYYYLKTQYDALRKLSSG-VRKNLNSNDIKNYKIYIPesVSFQKSIVRILTSL 166 Streptococcus sp. ...
SDX98752   85 SIIKKPMATNQACCNVEIDSdkadYEYIYYFLKTQYEELRNLSSG-VRKNLNSNDIKNYPIRLPktKDEQTKIASVLKSL 163 Nitrosomonas sp. Nm33
EOR07185   85 AIMKKPMATNQACCNIELNKdladNEYVYYFLKNQYKEIRDLASG-VRKNLNTNDIKNFEIRIPesVEKQKSLSKVLKTL 163 Acinetobacter tand...
AEI09871   86 GWLGVEATVNQAICAMVTDPkeadARFLYYALAGARERLVGNAHGaAQQNLSQQLIKPFKLAVPa-LATQQRIGAILRSI 164 Corynebacterium re...
GAC08254   90 AITAIDAASNQASCAMVANQdkclPLFLFYSLKYHRETIVNLALGgAQRNLNQGTIKNFEINCPp-LPQQKRIVDTLSNY 168 Glaciecola chatham...
ENN96239  104 AILKIPSTINQALAAIEGNN----NKFLFFSLIGNRERLLLRASGaAQQNLNLEIVKNFEIPYPq-PEEQTRISTVLSWF 178 Methanocaldococcus...
KGQ42748   86 AILGKEMACNQACCAMIVNEnivdYRFLFYLLILHKTKIKNLATGaAQQNISVKMVKELTFRIPe-KELQIKIANILESL 164 Gallibacterium anatis
Feature 1     #  #   # ##  ## ##  #      
AAM31895  165 DDKIDllHRQNKTLEAMAETLFRQWFV 191 Methanosarcina mazei Go1
AKA25098  168 DDRITllRETNITLESIAETLFKSWFV 194 Pseudomonas chlororaphis
SHL55718  165 DDKIElnNQINRNLEEQAQAIFKNWFI 191 Fibrobacter sp. UWH4
OFQ04781  167 DNKISvnNQINQELEAMAKTLYDYWFV 193 Streptococcus sp. HMSC062D07
SDX98752  164 DAKIElnNRINAELEAMAKTLYDYWFV 190 Nitrosomonas sp. Nm33
EOR07185  164 DDKIElnNLIKSKILIFSKLAYDFWFI 190 Acinetobacter tandoii DSM 14970 = CIP 107469
AEI09871  165 DELIEnnRRRIEVLEKMARAIYREWFV 191 Corynebacterium resistens DSM 45100
GAC08254  169 DNLIEnnNRRIAILEDMAQSLYREWFV 195 Glaciecola chathamensis S18K6
ENN96239  179 DDLIEnkKKQNEILEKMAMAIFKSWFI 205 Methanocaldococcus villosus KIN24-T80
KGQ42748  165 DQKIIlnTQTNQTLEQIAQAIFKHWFI 191 Gallibacterium anatis

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