NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|187936738|dbj|BAG32166|]
View 

rag1, partial [Apodemus latronum]

Protein Classification

RAG1 domain-containing protein( domain architecture ID 139673)

RAG1 domain-containing protein such as RAG1, the recombination activating protein 1, which is the catalytic component of the RAG complex, a multiprotein complex that mediates the DNA cleavage phase during V(D)J recombination and also acts as an E3 ubiquitin-protein ligase that mediates monoubiquitination of histone H3

Gene Ontology:  GO:0033151|GO:0008270|GO:0043565|GO:0061630
PubMed:  29628308|8861909|19621044

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
RAG1 super family cl20149
Recombination-activation protein 1 (RAG1), recombinase; This family is one of the two ...
 1-333 0e+00

Recombination-activation protein 1 (RAG1), recombinase; This family is one of the two different components of the RAG1-RAG2 V(D)J recombinase complex. The RAG complex, consisting of two RAG1 and two RAG2 proteins is a multi-protein complex that mediates DNA cleavage during V(D)J (variable-diversity-joining) recombination. RAG1 mediates DNA-binding to the conserved recombination signal sequences (RSS). Many of the proteins in this family are fragments. Solution of the structure of the complex of RAG1 and RAG2 shows that each protein dimerizes with itself and each pair then complexes together to from the RAG1-RAG2 V(D)J recombinase enzyme. The different structural elements in RAG1 for UniProtKB:P15919 are: an N-terminal nonamer-binding domain from residues 391-459; a dimerization and DNA-binding domain from 459-515; an extended pre-RNase H domain from 515-588; the catalytic RNase H domain from 588-719; a ZnC2 domain from 719-791; and ZnH2 domain from 791-962; and a three-helix C-terminal domain from 962-1008.


The actual alignment was detected with superfamily member pfam12940:

Pssm-ID: 315595  Cd Length: 653  Bit Score: 615.90  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 187936738    1 VKESCDGMGDVSEKHGSGPAVPEKAVRFSFTVMRISI---EHGSQNVKVFEEPKPNSELCCKPLCLMLADESDHETLTAI 77
Cdd:pfam12940 216 IKECCDGMGDVSEKHGGGPAVPEKAVRFSFTIMSVSIladDEEGEEVAIFHELKPNSELCCKPLCLMFADESDHETLTAI 295

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 187936738   78 LSPLIAEREAMKSSELTLEMGGIPRTFKFIFRGTGYDEKLVREVEGLEASGSVYICTLCDATRLEASQNLVFHSITRSHA 157
Cdd:pfam12940 296 LAPIMAEREAMKESRLILSIGGLLRSFRFHFRGTGYDEKLVRDMEGLEASGSTYICTLCDSSRAEASKNKVLHAITRSHE 375

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 187936738  158 ENLQRYEVWRSNPYHESVEELRDRVKGVSAKPFIETVPSIDALHCDIGNAAEFYKIFQLEIGEVYKNPNASKEERKRWQA 237
Cdd:pfam12940 376 ENLERYEIWRTNPFSESADDLRDRVKGISAKPFLETQACIDALHCDIGNATEFYKIFQDEIGEVHKKANPSKEERKRWQA 455

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 187936738  238 TLDKHLRKRMNLKPIMRMNGNFARKLMTQETVDAVCELIPSEERHEALRELMDLYLKMKPVWRSSCPAKECPESLCQYSF 317
Cdd:pfam12940 456 ALDKQLRKKMKLKPVMRMNGNFARKLMTQEAVDAVCELVPSEERQEALRELMHLYLQMKPVWRATCPAKECPDLLCRYSF 535

                         330
                  ....*....|....*.
gi 187936738  318 NSQRFAELLSTKFKYR 333
Cdd:pfam12940 536 NSQRFADLLSTTFKYR 551
 
Name Accession Description Interval E-value
RAG1 pfam12940
Recombination-activation protein 1 (RAG1), recombinase; This family is one of the two ...
 1-333 0e+00

Recombination-activation protein 1 (RAG1), recombinase; This family is one of the two different components of the RAG1-RAG2 V(D)J recombinase complex. The RAG complex, consisting of two RAG1 and two RAG2 proteins is a multi-protein complex that mediates DNA cleavage during V(D)J (variable-diversity-joining) recombination. RAG1 mediates DNA-binding to the conserved recombination signal sequences (RSS). Many of the proteins in this family are fragments. Solution of the structure of the complex of RAG1 and RAG2 shows that each protein dimerizes with itself and each pair then complexes together to from the RAG1-RAG2 V(D)J recombinase enzyme. The different structural elements in RAG1 for UniProtKB:P15919 are: an N-terminal nonamer-binding domain from residues 391-459; a dimerization and DNA-binding domain from 459-515; an extended pre-RNase H domain from 515-588; the catalytic RNase H domain from 588-719; a ZnC2 domain from 719-791; and ZnH2 domain from 791-962; and a three-helix C-terminal domain from 962-1008.


Pssm-ID: 315595  Cd Length: 653  Bit Score: 615.90  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 187936738    1 VKESCDGMGDVSEKHGSGPAVPEKAVRFSFTVMRISI---EHGSQNVKVFEEPKPNSELCCKPLCLMLADESDHETLTAI 77
Cdd:pfam12940 216 IKECCDGMGDVSEKHGGGPAVPEKAVRFSFTIMSVSIladDEEGEEVAIFHELKPNSELCCKPLCLMFADESDHETLTAI 295

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 187936738   78 LSPLIAEREAMKSSELTLEMGGIPRTFKFIFRGTGYDEKLVREVEGLEASGSVYICTLCDATRLEASQNLVFHSITRSHA 157
Cdd:pfam12940 296 LAPIMAEREAMKESRLILSIGGLLRSFRFHFRGTGYDEKLVRDMEGLEASGSTYICTLCDSSRAEASKNKVLHAITRSHE 375

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 187936738  158 ENLQRYEVWRSNPYHESVEELRDRVKGVSAKPFIETVPSIDALHCDIGNAAEFYKIFQLEIGEVYKNPNASKEERKRWQA 237
Cdd:pfam12940 376 ENLERYEIWRTNPFSESADDLRDRVKGISAKPFLETQACIDALHCDIGNATEFYKIFQDEIGEVHKKANPSKEERKRWQA 455

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 187936738  238 TLDKHLRKRMNLKPIMRMNGNFARKLMTQETVDAVCELIPSEERHEALRELMDLYLKMKPVWRSSCPAKECPESLCQYSF 317
Cdd:pfam12940 456 ALDKQLRKKMKLKPVMRMNGNFARKLMTQEAVDAVCELVPSEERQEALRELMHLYLQMKPVWRATCPAKECPDLLCRYSF 535

                         330
                  ....*....|....*.
gi 187936738  318 NSQRFAELLSTKFKYR 333
Cdd:pfam12940 536 NSQRFADLLSTTFKYR 551
 
Name Accession Description Interval E-value
RAG1 pfam12940
Recombination-activation protein 1 (RAG1), recombinase; This family is one of the two ...
 1-333 0e+00

Recombination-activation protein 1 (RAG1), recombinase; This family is one of the two different components of the RAG1-RAG2 V(D)J recombinase complex. The RAG complex, consisting of two RAG1 and two RAG2 proteins is a multi-protein complex that mediates DNA cleavage during V(D)J (variable-diversity-joining) recombination. RAG1 mediates DNA-binding to the conserved recombination signal sequences (RSS). Many of the proteins in this family are fragments. Solution of the structure of the complex of RAG1 and RAG2 shows that each protein dimerizes with itself and each pair then complexes together to from the RAG1-RAG2 V(D)J recombinase enzyme. The different structural elements in RAG1 for UniProtKB:P15919 are: an N-terminal nonamer-binding domain from residues 391-459; a dimerization and DNA-binding domain from 459-515; an extended pre-RNase H domain from 515-588; the catalytic RNase H domain from 588-719; a ZnC2 domain from 719-791; and ZnH2 domain from 791-962; and a three-helix C-terminal domain from 962-1008.


Pssm-ID: 315595  Cd Length: 653  Bit Score: 615.90  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 187936738    1 VKESCDGMGDVSEKHGSGPAVPEKAVRFSFTVMRISI---EHGSQNVKVFEEPKPNSELCCKPLCLMLADESDHETLTAI 77
Cdd:pfam12940 216 IKECCDGMGDVSEKHGGGPAVPEKAVRFSFTIMSVSIladDEEGEEVAIFHELKPNSELCCKPLCLMFADESDHETLTAI 295

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 187936738   78 LSPLIAEREAMKSSELTLEMGGIPRTFKFIFRGTGYDEKLVREVEGLEASGSVYICTLCDATRLEASQNLVFHSITRSHA 157
Cdd:pfam12940 296 LAPIMAEREAMKESRLILSIGGLLRSFRFHFRGTGYDEKLVRDMEGLEASGSTYICTLCDSSRAEASKNKVLHAITRSHE 375

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 187936738  158 ENLQRYEVWRSNPYHESVEELRDRVKGVSAKPFIETVPSIDALHCDIGNAAEFYKIFQLEIGEVYKNPNASKEERKRWQA 237
Cdd:pfam12940 376 ENLERYEIWRTNPFSESADDLRDRVKGISAKPFLETQACIDALHCDIGNATEFYKIFQDEIGEVHKKANPSKEERKRWQA 455

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 187936738  238 TLDKHLRKRMNLKPIMRMNGNFARKLMTQETVDAVCELIPSEERHEALRELMDLYLKMKPVWRSSCPAKECPESLCQYSF 317
Cdd:pfam12940 456 ALDKQLRKKMKLKPVMRMNGNFARKLMTQEAVDAVCELVPSEERQEALRELMHLYLQMKPVWRATCPAKECPDLLCRYSF 535

                         330
                  ....*....|....*.
gi 187936738  318 NSQRFAELLSTKFKYR 333
Cdd:pfam12940 536 NSQRFADLLSTTFKYR 551
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH