NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|6321595|ref|NP_011672|]
View 

cleavage polyadenylation factor subunit PTI1 [Saccharomyces cerevisiae S288C]

Protein Classification

RRM_SF and CSTF2_hinge domain-containing protein( domain architecture ID 11266533)

RRM_SF and CSTF2_hinge domain-containing protein

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
CSTF2_hinge pfam14327
Hinge domain of cleavage stimulation factor subunit 2; The hinge domain of cleavage ...
 185-255 5.33e-20

Hinge domain of cleavage stimulation factor subunit 2; The hinge domain of cleavage stimulation factor subunit 2 proteins, CSTF2, is necessary for binding to the subunit CstF-77 within the polyadenylation complex and subsequent nuclear localization. This suggests that nuclear import of a pre-formed CSTF complex is an essential step in polyadenylation. Accurate and efficient polyadenylation is essential for transcriptional termination, nuclear export, translation, and stability of eukaryotic mRNAs. CSTF2 is an important regulatory subunit of the polyadenylation complex.


:

Pssm-ID: 433869 [Multi-domain]  Cd Length: 81  Bit Score: 83.74  E-value: 5.33e-20
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 6321595    185 APDKISQNLSKIPPLQLIEIISNLKILSNQeniQKSQLESFLDTNSDITISVTQALLEMGFIDYSVVTKVL 255
Cdd:pfam14327  14 APDAISKTLSSLPPAQLLELLSQMKALAQN---NPAQARELLIQNPQLAYALFQALLLMGLVDPDVITSVL 81
RRM smart00360
RNA recognition motif;
21-90 6.92e-07

RNA recognition motif;


:

Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 46.43  E-value: 6.92e-07
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 6321595      21 TLQITNLPPEWNQDIITSVVAGSGPVIDIKAKNDPRTGKLTGVLF-DYLTSKDCKRAWEILN--RIENFPVKI 90
Cdd:smart00360   1 TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFvEFESEEDAEKALEALNgkELDGRPLKV 73
PABP-1234 super family cl31127
polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins ...
 306-413 7.58e-04

polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed and of unknown tissue range.


The actual alignment was detected with superfamily member TIGR01628:

Pssm-ID: 130689 [Multi-domain]  Cd Length: 562  Bit Score: 41.72  E-value: 7.58e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6321595    306 AMPMPMSTPPFIPLP----------LQQQPFGFaPPGPFMPPAQGPSMG-QPVLANQLGQVQQQNISSTEGPSNANKAND 374
Cdd:TIGR01628 384 QLPMGSPMGGAMGQPpyygqgpqqqFNGQPLGW-PRMSMMPTPMGPGGPlRPNGLAPMNAVRAPSRNAQNAAQKPPMQPV 462

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 6321595    375 SGTINMAKLQLLPENQQDMIKQV----LTLTPAQIQSLPSDQQ 413
Cdd:TIGR01628 463 MYPPNYQSLPLSQDLPQPQSTASqggqNKKLAQVLASATPQMQ 505
 
Name Accession Description Interval E-value
CSTF2_hinge pfam14327
Hinge domain of cleavage stimulation factor subunit 2; The hinge domain of cleavage ...
 185-255 5.33e-20

Hinge domain of cleavage stimulation factor subunit 2; The hinge domain of cleavage stimulation factor subunit 2 proteins, CSTF2, is necessary for binding to the subunit CstF-77 within the polyadenylation complex and subsequent nuclear localization. This suggests that nuclear import of a pre-formed CSTF complex is an essential step in polyadenylation. Accurate and efficient polyadenylation is essential for transcriptional termination, nuclear export, translation, and stability of eukaryotic mRNAs. CSTF2 is an important regulatory subunit of the polyadenylation complex.


Pssm-ID: 433869 [Multi-domain]  Cd Length: 81  Bit Score: 83.74  E-value: 5.33e-20
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 6321595    185 APDKISQNLSKIPPLQLIEIISNLKILSNQeniQKSQLESFLDTNSDITISVTQALLEMGFIDYSVVTKVL 255
Cdd:pfam14327  14 APDAISKTLSSLPPAQLLELLSQMKALAQN---NPAQARELLIQNPQLAYALFQALLLMGLVDPDVITSVL 81
RRM smart00360
RNA recognition motif;
21-90 6.92e-07

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 46.43  E-value: 6.92e-07
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 6321595      21 TLQITNLPPEWNQDIITSVVAGSGPVIDIKAKNDPRTGKLTGVLF-DYLTSKDCKRAWEILN--RIENFPVKI 90
Cdd:smart00360   1 TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFvEFESEEDAEKALEALNgkELDGRPLKV 73
PABP-1234 TIGR01628
polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins ...
 306-413 7.58e-04

polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed and of unknown tissue range.


Pssm-ID: 130689 [Multi-domain]  Cd Length: 562  Bit Score: 41.72  E-value: 7.58e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6321595    306 AMPMPMSTPPFIPLP----------LQQQPFGFaPPGPFMPPAQGPSMG-QPVLANQLGQVQQQNISSTEGPSNANKAND 374
Cdd:TIGR01628 384 QLPMGSPMGGAMGQPpyygqgpqqqFNGQPLGW-PRMSMMPTPMGPGGPlRPNGLAPMNAVRAPSRNAQNAAQKPPMQPV 462

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 6321595    375 SGTINMAKLQLLPENQQDMIKQV----LTLTPAQIQSLPSDQQ 413
Cdd:TIGR01628 463 MYPPNYQSLPLSQDLPQPQSTASqggqNKKLAQVLASATPQMQ 505
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
 22-91 1.34e-03

RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).


Pssm-ID: 409669 [Multi-domain]  Cd Length: 72  Bit Score: 37.26  E-value: 1.34e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 6321595   22 LQITNLPPEWNQDIITSVVAGSGPVIDIKAKNDpRTGKLTGVLF-DYLTSKDCKRAWEILNR--IENFPVKIE 91
Cdd:cd00590   1 LFVGNLPPDTTEEDLRELFSKFGEVVSVRIVRD-RDGKSKGFAFvEFESPEDAEKALEALNGteLGGRPLKVS 72
 
Name Accession Description Interval E-value
CSTF2_hinge pfam14327
Hinge domain of cleavage stimulation factor subunit 2; The hinge domain of cleavage ...
 185-255 5.33e-20

Hinge domain of cleavage stimulation factor subunit 2; The hinge domain of cleavage stimulation factor subunit 2 proteins, CSTF2, is necessary for binding to the subunit CstF-77 within the polyadenylation complex and subsequent nuclear localization. This suggests that nuclear import of a pre-formed CSTF complex is an essential step in polyadenylation. Accurate and efficient polyadenylation is essential for transcriptional termination, nuclear export, translation, and stability of eukaryotic mRNAs. CSTF2 is an important regulatory subunit of the polyadenylation complex.


Pssm-ID: 433869 [Multi-domain]  Cd Length: 81  Bit Score: 83.74  E-value: 5.33e-20
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 6321595    185 APDKISQNLSKIPPLQLIEIISNLKILSNQeniQKSQLESFLDTNSDITISVTQALLEMGFIDYSVVTKVL 255
Cdd:pfam14327  14 APDAISKTLSSLPPAQLLELLSQMKALAQN---NPAQARELLIQNPQLAYALFQALLLMGLVDPDVITSVL 81
RRM smart00360
RNA recognition motif;
21-90 6.92e-07

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 46.43  E-value: 6.92e-07
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 6321595      21 TLQITNLPPEWNQDIITSVVAGSGPVIDIKAKNDPRTGKLTGVLF-DYLTSKDCKRAWEILN--RIENFPVKI 90
Cdd:smart00360   1 TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFvEFESEEDAEKALEALNgkELDGRPLKV 73
PABP-1234 TIGR01628
polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins ...
 306-413 7.58e-04

polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed and of unknown tissue range.


Pssm-ID: 130689 [Multi-domain]  Cd Length: 562  Bit Score: 41.72  E-value: 7.58e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6321595    306 AMPMPMSTPPFIPLP----------LQQQPFGFaPPGPFMPPAQGPSMG-QPVLANQLGQVQQQNISSTEGPSNANKAND 374
Cdd:TIGR01628 384 QLPMGSPMGGAMGQPpyygqgpqqqFNGQPLGW-PRMSMMPTPMGPGGPlRPNGLAPMNAVRAPSRNAQNAAQKPPMQPV 462

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 6321595    375 SGTINMAKLQLLPENQQDMIKQV----LTLTPAQIQSLPSDQQ 413
Cdd:TIGR01628 463 MYPPNYQSLPLSQDLPQPQSTASqggqNKKLAQVLASATPQMQ 505
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
 22-91 1.34e-03

RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).


Pssm-ID: 409669 [Multi-domain]  Cd Length: 72  Bit Score: 37.26  E-value: 1.34e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 6321595   22 LQITNLPPEWNQDIITSVVAGSGPVIDIKAKNDpRTGKLTGVLF-DYLTSKDCKRAWEILNR--IENFPVKIE 91
Cdd:cd00590   1 LFVGNLPPDTTEEDLRELFSKFGEVVSVRIVRD-RDGKSKGFAFvEFESPEDAEKALEALNGteLGGRPLKVS 72
RRM2_gar2 cd12448
RNA recognition motif 2 (RRM2) found in yeast protein gar2 and similar proteins; This ...
 24-91 3.52e-03

RNA recognition motif 2 (RRM2) found in yeast protein gar2 and similar proteins; This subfamily corresponds to the RRM2 of yeast protein gar2, a novel nucleolar protein required for 18S rRNA and 40S ribosomal subunit accumulation. It shares similar domain architecture with nucleolin from vertebrates and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of gar2 is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of gar2 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RGG (or GAR) domain of gar2 is rich in glycine, arginine and phenylalanine residues.


Pssm-ID: 409882 [Multi-domain]  Cd Length: 73  Bit Score: 36.23  E-value: 3.52e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 6321595   24 ITNLPPEWNQDIITSVVAGSGPVIDIKAKNDPRTGKLTGVLF-DYLTSKDCKRAWEILN--RIENFPVKIE 91
Cdd:cd12448   3 VGNLPFSATQDALYEAFSQHGSIVSVRLPTDRETGQPKGFGYvDFSTIDSAEAAIDALGgeYIDGRPIRLD 73
 
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