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Conserved domains on  [gi|171919888|gb|ACB59116|]
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recombination activating protein 1, partial [Glaucidium californicum]

Protein Classification

V(D)J recombination-activating protein 1( domain architecture ID 10564381)

recombination activating protein 1, also known as V(D)J recombination-activating protein 1, endonuclease RAG1, or E3 ubiquitin-protein ligase RAG1, is the catalytic component of the RAG complex, a multiprotein complex that mediates the DNA cleavage phase during V(D)J recombination

Graphical summary

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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 ...
 33-313 1.29e-171

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: 491.10  E-value: 1.29e-171
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 171919888   33 YCHINKGGRPRQHLLSLTRRAQKHRLRELKRQVKAFAEKEEGGDIKAVCMTLFLLALRAKNEHRQADELEAIMQGRGSGL 112
Cdd:pfam12940   3 FLLTNKGGRPRQHLLSLTRRAQKHRLRDLKHQVKVFADKEEGGDIKSVCLTLFLLALRAGNEHRQADELEAMMQGRGFGL 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 171919888  113 HPAVCLAIRVNTFLSCSQYHKMYRTVKAVTGRQIFQPLHALRTAEKALLPGYHPFEWKPPLKNVSINTEVGIIDGLSGLP 192
Cdd:pfam12940  83 HPAVCLAIRVNTFLSCSQYHKMYRTVKATSGRQIFQPLHTLRAAEKALLPGFHHFEWQPALKNVSPSCDVGIIDGLSGWS 162

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 171919888  193 LSIDDYPVDTIAKRFRYDAALVCALKDMEEEILEGMKAKHLDDY-LNGPFTVVVKESCDGMGDVSEKHGSGPAVPEKAVR 271
Cdd:pfam12940 163 PSVDDQPADTITRRFRYDVALVAALKDLEEDILEGLKEQGLDDSaCTEGFSVMIKECCDGMGDVSEKHGGGPAVPEKAVR 242

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*
gi 171919888  272 FSFTVMNIGIALGNESK---RIFEEVKPNSELCCKPLCLMLADES 313
Cdd:pfam12940 243 FSFTIMSVSILADDEEGeevAIFHELKPNSELCCKPLCLMFADES 287
zf-RAG1 pfam10426
Recombination-activating protein 1 zinc-finger domain; This is a C2-H2 zinc-finger domain ...
 1-28 5.19e-11

Recombination-activating protein 1 zinc-finger domain; This is a C2-H2 zinc-finger domain closely resembling the classical TFIIIA-type zinc-finger, CX3FX5LX2-3H, despite having a valine and a tyrosine at the core instead of a phenylalanine and a leucine, hence CX3VX1LX2YX2H. The structure, nevertheless, contains the characteriztic two-stranded beta-sheet and alpha-helix of a classical zinc-finger. The domain binds one zinc and, in complex with the zinc-RING-finger domain, helps to stabilize the whole of the dimerization region of recombination activating protein 1 (RAG1). The function of the whole is to bind double-stranded DNA.


:

Pssm-ID: 431278  Cd Length: 30  Bit Score: 56.75  E-value: 5.19e-11
                          10        20
                  ....*....|....*....|....*...
gi 171919888    1 IRCPVKECDEEIPHGKYGQHLSSHKEMK 28
Cdd:pfam10426   3 IRCPAKDCDEEVRLEKYGQHLSSHKEGK 30
 
Name Accession Description Interval E-value
RAG1 pfam12940
Recombination-activation protein 1 (RAG1), recombinase; This family is one of the two ...
 33-313 1.29e-171

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: 491.10  E-value: 1.29e-171
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 171919888   33 YCHINKGGRPRQHLLSLTRRAQKHRLRELKRQVKAFAEKEEGGDIKAVCMTLFLLALRAKNEHRQADELEAIMQGRGSGL 112
Cdd:pfam12940   3 FLLTNKGGRPRQHLLSLTRRAQKHRLRDLKHQVKVFADKEEGGDIKSVCLTLFLLALRAGNEHRQADELEAMMQGRGFGL 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 171919888  113 HPAVCLAIRVNTFLSCSQYHKMYRTVKAVTGRQIFQPLHALRTAEKALLPGYHPFEWKPPLKNVSINTEVGIIDGLSGLP 192
Cdd:pfam12940  83 HPAVCLAIRVNTFLSCSQYHKMYRTVKATSGRQIFQPLHTLRAAEKALLPGFHHFEWQPALKNVSPSCDVGIIDGLSGWS 162

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 171919888  193 LSIDDYPVDTIAKRFRYDAALVCALKDMEEEILEGMKAKHLDDY-LNGPFTVVVKESCDGMGDVSEKHGSGPAVPEKAVR 271
Cdd:pfam12940 163 PSVDDQPADTITRRFRYDVALVAALKDLEEDILEGLKEQGLDDSaCTEGFSVMIKECCDGMGDVSEKHGGGPAVPEKAVR 242

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*
gi 171919888  272 FSFTVMNIGIALGNESK---RIFEEVKPNSELCCKPLCLMLADES 313
Cdd:pfam12940 243 FSFTIMSVSILADDEEGeevAIFHELKPNSELCCKPLCLMFADES 287
zf-RAG1 pfam10426
Recombination-activating protein 1 zinc-finger domain; This is a C2-H2 zinc-finger domain ...
 1-28 5.19e-11

Recombination-activating protein 1 zinc-finger domain; This is a C2-H2 zinc-finger domain closely resembling the classical TFIIIA-type zinc-finger, CX3FX5LX2-3H, despite having a valine and a tyrosine at the core instead of a phenylalanine and a leucine, hence CX3VX1LX2YX2H. The structure, nevertheless, contains the characteriztic two-stranded beta-sheet and alpha-helix of a classical zinc-finger. The domain binds one zinc and, in complex with the zinc-RING-finger domain, helps to stabilize the whole of the dimerization region of recombination activating protein 1 (RAG1). The function of the whole is to bind double-stranded DNA.


Pssm-ID: 431278  Cd Length: 30  Bit Score: 56.75  E-value: 5.19e-11
                          10        20
                  ....*....|....*....|....*...
gi 171919888    1 IRCPVKECDEEIPHGKYGQHLSSHKEMK 28
Cdd:pfam10426   3 IRCPAKDCDEEVRLEKYGQHLSSHKEGK 30
 
Name Accession Description Interval E-value
RAG1 pfam12940
Recombination-activation protein 1 (RAG1), recombinase; This family is one of the two ...
 33-313 1.29e-171

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: 491.10  E-value: 1.29e-171
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 171919888   33 YCHINKGGRPRQHLLSLTRRAQKHRLRELKRQVKAFAEKEEGGDIKAVCMTLFLLALRAKNEHRQADELEAIMQGRGSGL 112
Cdd:pfam12940   3 FLLTNKGGRPRQHLLSLTRRAQKHRLRDLKHQVKVFADKEEGGDIKSVCLTLFLLALRAGNEHRQADELEAMMQGRGFGL 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 171919888  113 HPAVCLAIRVNTFLSCSQYHKMYRTVKAVTGRQIFQPLHALRTAEKALLPGYHPFEWKPPLKNVSINTEVGIIDGLSGLP 192
Cdd:pfam12940  83 HPAVCLAIRVNTFLSCSQYHKMYRTVKATSGRQIFQPLHTLRAAEKALLPGFHHFEWQPALKNVSPSCDVGIIDGLSGWS 162

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 171919888  193 LSIDDYPVDTIAKRFRYDAALVCALKDMEEEILEGMKAKHLDDY-LNGPFTVVVKESCDGMGDVSEKHGSGPAVPEKAVR 271
Cdd:pfam12940 163 PSVDDQPADTITRRFRYDVALVAALKDLEEDILEGLKEQGLDDSaCTEGFSVMIKECCDGMGDVSEKHGGGPAVPEKAVR 242

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*
gi 171919888  272 FSFTVMNIGIALGNESK---RIFEEVKPNSELCCKPLCLMLADES 313
Cdd:pfam12940 243 FSFTIMSVSILADDEEGeevAIFHELKPNSELCCKPLCLMFADES 287
zf-RAG1 pfam10426
Recombination-activating protein 1 zinc-finger domain; This is a C2-H2 zinc-finger domain ...
 1-28 5.19e-11

Recombination-activating protein 1 zinc-finger domain; This is a C2-H2 zinc-finger domain closely resembling the classical TFIIIA-type zinc-finger, CX3FX5LX2-3H, despite having a valine and a tyrosine at the core instead of a phenylalanine and a leucine, hence CX3VX1LX2YX2H. The structure, nevertheless, contains the characteriztic two-stranded beta-sheet and alpha-helix of a classical zinc-finger. The domain binds one zinc and, in complex with the zinc-RING-finger domain, helps to stabilize the whole of the dimerization region of recombination activating protein 1 (RAG1). The function of the whole is to bind double-stranded DNA.


Pssm-ID: 431278  Cd Length: 30  Bit Score: 56.75  E-value: 5.19e-11
                          10        20
                  ....*....|....*....|....*...
gi 171919888    1 IRCPVKECDEEIPHGKYGQHLSSHKEMK 28
Cdd:pfam10426   3 IRCPAKDCDEEVRLEKYGQHLSSHKEGK 30
 
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.
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