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Conserved domains on  [gi|545687459|ref|NP_001269966|]
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replication termination factor 2 isoform d [Homo sapiens]

Protein Classification

replication termination factor 2 family protein( domain architecture ID 10519219)

replication termination factor 2 (RTF2) family protein such as Schizosaccharomyces pombe RTF2, which stabilizes the replication fork stalled at RTS1 until completion of DNA synthesis by a converging replication fork initiated at a flanking origin

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
Rtf2 pfam04641
Rtf2 RING-finger; It is vital for effective cell-replication that replication is not stalled ...
1-198 1.56e-105

Rtf2 RING-finger; It is vital for effective cell-replication that replication is not stalled at any point by, for instance, damaged bases. Replication termination factor 2 (Rtf2) stabilizes the replication fork stalled at the site-specific replication barrier RTS1 by preventing replication restart until completion of DNA synthesis by a converging replication fork initiated at a flanking origin. The RTS1 element terminates replication forks that are moving in the cen2-distal direction while allowing forks moving in the cen2-proximal direction to pass through the region. Rtf2 contains a C2HC2 motif related to the C3HC4 RING-finger motif, and would appear to fold up, creating a RING finger-like structure but forming only one functional Zn2+ ion-binding site. This domain is also found at the N-terminus of peptidyl-prolyl cis-trans isomerase 4, a divergent cyclophilin family.


:

Pssm-ID: 398360 [Multi-domain]  Cd Length: 258  Bit Score: 305.05  E-value: 1.56e-105
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545687459    1 MGCDGGTIPKRHELVKGPKKVEKVDKDAELVAQWNYCTLSQEILRRPIVACELGRLYNKDAVIEFLLDKSaeKALGKAAS 80
Cdd:pfam04641   1 MGNDGGTIPTRDELVKMKKKPEKVDKDEERLARWFLCALSQEPLKKPIVACRLGNLYNKDAVIEALLDKS--ISLPKAFS 78
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545687459   81 HIKSIKNVTELKLSDNPAWEGDKgntkgdKHDDLQRARFICPVVGLEMNGRHRFCFLRCCGCVFSERALKEIKAEVCHTC 160
Cdd:pfam04641  79 HIKGLKDVVELKLTPNPAFEGSK------VYDDTSEAPFICPVTGLEMNGKYKFVALWPCGCVFSEKALKEVKSKNCPVC 152
                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 545687459  161 GAAFQEDDVIMLNGTKEDVDVLKTRMEERRLRAKLEKK 198
Cdd:pfam04641 153 GKPYSEEDVIPLNPTEEEVELLKARMEERRAKKKKKKK 190
 
Name Accession Description Interval E-value
Rtf2 pfam04641
Rtf2 RING-finger; It is vital for effective cell-replication that replication is not stalled ...
1-198 1.56e-105

Rtf2 RING-finger; It is vital for effective cell-replication that replication is not stalled at any point by, for instance, damaged bases. Replication termination factor 2 (Rtf2) stabilizes the replication fork stalled at the site-specific replication barrier RTS1 by preventing replication restart until completion of DNA synthesis by a converging replication fork initiated at a flanking origin. The RTS1 element terminates replication forks that are moving in the cen2-distal direction while allowing forks moving in the cen2-proximal direction to pass through the region. Rtf2 contains a C2HC2 motif related to the C3HC4 RING-finger motif, and would appear to fold up, creating a RING finger-like structure but forming only one functional Zn2+ ion-binding site. This domain is also found at the N-terminus of peptidyl-prolyl cis-trans isomerase 4, a divergent cyclophilin family.


Pssm-ID: 398360 [Multi-domain]  Cd Length: 258  Bit Score: 305.05  E-value: 1.56e-105
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545687459    1 MGCDGGTIPKRHELVKGPKKVEKVDKDAELVAQWNYCTLSQEILRRPIVACELGRLYNKDAVIEFLLDKSaeKALGKAAS 80
Cdd:pfam04641   1 MGNDGGTIPTRDELVKMKKKPEKVDKDEERLARWFLCALSQEPLKKPIVACRLGNLYNKDAVIEALLDKS--ISLPKAFS 78
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545687459   81 HIKSIKNVTELKLSDNPAWEGDKgntkgdKHDDLQRARFICPVVGLEMNGRHRFCFLRCCGCVFSERALKEIKAEVCHTC 160
Cdd:pfam04641  79 HIKGLKDVVELKLTPNPAFEGSK------VYDDTSEAPFICPVTGLEMNGKYKFVALWPCGCVFSEKALKEVKSKNCPVC 152
                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 545687459  161 GAAFQEDDVIMLNGTKEDVDVLKTRMEERRLRAKLEKK 198
Cdd:pfam04641 153 GKPYSEEDVIPLNPTEEEVELLKARMEERRAKKKKKKK 190
RING-like_Rtf2 cd16653
RING-like Rtf2 domain, C2HC2-type, found in the replication termination factor 2 (Rtf2) ...
119-164 5.16e-23

RING-like Rtf2 domain, C2HC2-type, found in the replication termination factor 2 (Rtf2) protein family; The Rtf2 protein family includes a group of conserved proteins found in eukaryotes ranging from fission yeast to humans. The defining member of the family is Schizosaccharomyces pombe Rtf2 (SpRtf2), which is a proliferating cell nuclear antigen-interacting protein that functions as a key requirement for efficient replication termination at the site-specific replication barrier RTS1. It promotes termination at RTS1 by preventing replication restart. SpRtf2 contains a RING-like Rtf2 domain that is characterized by a C2HC2 motif similar to C3HC4 RING-HC finger motif known to bind two Zn2+ ions and mediate protein-protein interactions. The C2HC2 motif lacks three of the seven conserved cysteines of the C3HC4 motif, and forms only one functional Zn2+ ion-binding site. The RING-like Rtf2 domain in fission yeast is required to stabilize a paused DNA replication fork during imprinting at the mating type locus, possibly by facilitating sumoylation of PCNA. The family also includes Arabidopsis RTF2 (AtRTF2), an essential nuclear protein required for both normal embryo development and for proper expression of the GFP reporter gene. It plays a critical role in splicing the GFP pre-mRNA, and may also have a more transient regulatory role during the spliceosome cycle. The biological function of Rtf2 homologs found in eumetazoa remains unclear. They contain a variant C2HC2 motif where the middle conserved histidine has been replaced by cysteine.


Pssm-ID: 438315  Cd Length: 47  Bit Score: 87.70  E-value: 5.16e-23
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 545687459 119 FICPVVGLEMNGRHRFCFLRCCGCVFSERALKEIKAE-VCHTCGAAF 164
Cdd:cd16653    1 FICPITGLEMNGKYKFVYLWPCGCVFSERALKELKGSkKCPVCGKPF 47
 
Name Accession Description Interval E-value
Rtf2 pfam04641
Rtf2 RING-finger; It is vital for effective cell-replication that replication is not stalled ...
1-198 1.56e-105

Rtf2 RING-finger; It is vital for effective cell-replication that replication is not stalled at any point by, for instance, damaged bases. Replication termination factor 2 (Rtf2) stabilizes the replication fork stalled at the site-specific replication barrier RTS1 by preventing replication restart until completion of DNA synthesis by a converging replication fork initiated at a flanking origin. The RTS1 element terminates replication forks that are moving in the cen2-distal direction while allowing forks moving in the cen2-proximal direction to pass through the region. Rtf2 contains a C2HC2 motif related to the C3HC4 RING-finger motif, and would appear to fold up, creating a RING finger-like structure but forming only one functional Zn2+ ion-binding site. This domain is also found at the N-terminus of peptidyl-prolyl cis-trans isomerase 4, a divergent cyclophilin family.


Pssm-ID: 398360 [Multi-domain]  Cd Length: 258  Bit Score: 305.05  E-value: 1.56e-105
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545687459    1 MGCDGGTIPKRHELVKGPKKVEKVDKDAELVAQWNYCTLSQEILRRPIVACELGRLYNKDAVIEFLLDKSaeKALGKAAS 80
Cdd:pfam04641   1 MGNDGGTIPTRDELVKMKKKPEKVDKDEERLARWFLCALSQEPLKKPIVACRLGNLYNKDAVIEALLDKS--ISLPKAFS 78
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545687459   81 HIKSIKNVTELKLSDNPAWEGDKgntkgdKHDDLQRARFICPVVGLEMNGRHRFCFLRCCGCVFSERALKEIKAEVCHTC 160
Cdd:pfam04641  79 HIKGLKDVVELKLTPNPAFEGSK------VYDDTSEAPFICPVTGLEMNGKYKFVALWPCGCVFSEKALKEVKSKNCPVC 152
                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 545687459  161 GAAFQEDDVIMLNGTKEDVDVLKTRMEERRLRAKLEKK 198
Cdd:pfam04641 153 GKPYSEEDVIPLNPTEEEVELLKARMEERRAKKKKKKK 190
RING-like_Rtf2 cd16653
RING-like Rtf2 domain, C2HC2-type, found in the replication termination factor 2 (Rtf2) ...
119-164 5.16e-23

RING-like Rtf2 domain, C2HC2-type, found in the replication termination factor 2 (Rtf2) protein family; The Rtf2 protein family includes a group of conserved proteins found in eukaryotes ranging from fission yeast to humans. The defining member of the family is Schizosaccharomyces pombe Rtf2 (SpRtf2), which is a proliferating cell nuclear antigen-interacting protein that functions as a key requirement for efficient replication termination at the site-specific replication barrier RTS1. It promotes termination at RTS1 by preventing replication restart. SpRtf2 contains a RING-like Rtf2 domain that is characterized by a C2HC2 motif similar to C3HC4 RING-HC finger motif known to bind two Zn2+ ions and mediate protein-protein interactions. The C2HC2 motif lacks three of the seven conserved cysteines of the C3HC4 motif, and forms only one functional Zn2+ ion-binding site. The RING-like Rtf2 domain in fission yeast is required to stabilize a paused DNA replication fork during imprinting at the mating type locus, possibly by facilitating sumoylation of PCNA. The family also includes Arabidopsis RTF2 (AtRTF2), an essential nuclear protein required for both normal embryo development and for proper expression of the GFP reporter gene. It plays a critical role in splicing the GFP pre-mRNA, and may also have a more transient regulatory role during the spliceosome cycle. The biological function of Rtf2 homologs found in eumetazoa remains unclear. They contain a variant C2HC2 motif where the middle conserved histidine has been replaced by cysteine.


Pssm-ID: 438315  Cd Length: 47  Bit Score: 87.70  E-value: 5.16e-23
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 545687459 119 FICPVVGLEMNGRHRFCFLRCCGCVFSERALKEIKAE-VCHTCGAAF 164
Cdd:cd16653    1 FICPITGLEMNGKYKFVYLWPCGCVFSERALKELKGSkKCPVCGKPF 47
RING_Ubox cd00162
RING finger (Really Interesting New Gene) domain and U-box domain superfamily; The RING finger ...
121-160 1.44e-08

RING finger (Really Interesting New Gene) domain and U-box domain superfamily; The RING finger is a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc. It is defined by the "cross-brace" motif that chelates zinc atoms by eight amino acid residues, typically Cys or His, arranged in a characteristic spacing. Canonical RING motifs have been categorized into two major subclasses, RING-HC (C3HC4-type) and RING-H2 (C3H2C3-type), according to their Cys/His content. There are also many variants of RING fingers: some have different Cys/His patterns while some lack a single Cys or His residue at typical Zn ligand positions (the fourth or eighth zinc ligand is prevalently exchanged for an Asp, which can indeed chelate Zn in a RING finger as well). C4C4-, C3HC3D-, C2H2C4-, and C3HC5-type RING fingers are closely related to RING-HC fingers. In contrast, C4HC3- (RING-CH alias RINGv), C3H3C2-, C3H2C2D-, C3DHC3-, and C4HC2H-type RING fingers are more closely related to RING-H2 fingers. However, not all RING finger-containing proteins display regular RING finger features, and the RING finger family has turned out to be multifarious. The degenerate RING fingers of the Siz/PIAS RING (SP-RING) family proteins and sporulation protein RMD5, are characterized by lacking the second, fifth, and sixth Zn2+ ion-coordinating residues. They bind only one Zn2+ ion. On the other hand, the RING fingers of the human APC11 and RBX1 proteins can bind a third Zn atom since they harbor four additional Zn ligands. U-box is a modified form of the RING finger domain that lacks metal chelating Cys and His residues. It resembles the cross-brace RING structure consisting of three beta-sheets and a single alpha-helix, which would be stabilized by salt bridges instead of chelated metal ions. U-box proteins are widely distributed among eukaryotic organisms and show a higher prevalence in plants than in other organisms. RING finger/U-box-containing proteins are a group of diverse proteins with a variety of cellular functions, including oncogenesis, development, viral replication, signal transduction, the cell cycle and apoptosis. Many of them are ubiquitin-protein ligases (E3s) that serve as scaffolds for binding to ubiquitin-conjugating enzymes (E2s, also referred to as ubiquitin carrier proteins or UBCs) in close proximity to substrate proteins, which enable efficient transfer of ubiquitin from E2 to the substrates.


Pssm-ID: 438111 [Multi-domain]  Cd Length: 42  Bit Score: 49.38  E-value: 1.44e-08
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 545687459 121 CPVVGLEMNGRHrFCFLRCCGCVFSERALKEIK---AEVCHTC 160
Cdd:cd00162    1 CPICREEMNDRR-PVVLLSCGHTFSRSAIARWLegsKQKCPFC 42
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.20
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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