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Conserved domains on  [gi|27348126|dbj|BAC45238|]
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posphorylated CTD interacting factor PCIF1 [Homo sapiens]

Protein Classification

WW domain-containing protein( domain architecture ID 10078854)

WW domain-containing protein; the WW domain mediates protein-protein interaction via proline-rich motifs, such as PPxY

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PCIF1_WW pfam12237
Phosphorylated CTD interacting factor 1 WW domain; This domain family is found in bacteria and ...
 446-616 1.59e-107

Phosphorylated CTD interacting factor 1 WW domain; This domain family is found in bacteria and eukaryotes, and is approximately 180 amino acids in length. This domain is the WW domain of PCIF1. PCIF1 interacts with phosphorylated RNA polymerase II carboxy-terminal domain (CTD). The WW domain of PCIF1 can directly and preferentially bind to the phosphorylated CTD compared to the unphosphorylated CTD. PCIF1 binds to the hyperphosphorylated RNAP II (RNAP IIO) in vitro and in vivo. Double immunofluorescence labeling in HeLa cells demonstrated that PCIF1 and endogenous RNAP IIO are co-localized in the cell nucleus. Thus, PCIF1 may play a role in mRNA synthesis by modulating RNAP IIO activity.


:

Pssm-ID: 463502  Cd Length: 172  Bit Score: 323.45  E-value: 1.59e-107
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27348126   446 KLWLLYR-YSCIDDSAFERFLPRVWCLLRRYQMMFGVGLYEGTGLQGSLPVHVFEALHRLFGVSFECFASPLNCYFRQYC 524
Cdd:pfam12237   1 KLEQLYRsYSCFDDKKFEIFLPRLFCLLLRYQTLLGGQSNEGGGTQAALPESVFDCLHRFFGVSFECFASPLNCYFRQYC 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27348126   525 SAFPDTDGYFGSRGPCLDFAPLSGSFEANPPFCEELMDAMVSHFERLLESSPEPLSFIVFIPEWREPPTPALTRMEQSRF 604
Cdd:pfam12237  81 SAFPDTDGYFGSRGSFFDFKPVSGSFEANPPFCEELMDAMADHIERLLEASSEPLSFVVFVPEWRDPPTPALLKLEESRF 160

                         170
                  ....*....|..
gi 27348126   605 KRHQLILPAFEH 616
Cdd:pfam12237 161 KRKQVVIPANEH 172
WW cd00201
Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; ...
 47-77 3.27e-06

Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other peptide recognition proteins such as antibodies and receptors; WW domains have a single groove formed by a conserved Trp and Tyr which recognizes a pair of residues of the sequence X-Pro; variable loops and neighboring domains confer specificity in this domain; there are five distinct groups based on binding: 1) PPXY motifs 2) the PPLP motif; 3) PGM motifs; 4) PSP or PTP motifs; 5) PR motifs.


:

Pssm-ID: 238122 [Multi-domain]  Cd Length: 31  Bit Score: 44.06  E-value: 3.27e-06
                        10        20        30
                ....*....|....*....|....*....|.
gi 27348126  47 AGWEKCWSRrENRPYYFNRFTNQSLWEMPVL 77
Cdd:cd00201   2 PGWEERWDP-DGRVYYYNHNTKETQWEDPRE 31
 
Name Accession Description Interval E-value
PCIF1_WW pfam12237
Phosphorylated CTD interacting factor 1 WW domain; This domain family is found in bacteria and ...
 446-616 1.59e-107

Phosphorylated CTD interacting factor 1 WW domain; This domain family is found in bacteria and eukaryotes, and is approximately 180 amino acids in length. This domain is the WW domain of PCIF1. PCIF1 interacts with phosphorylated RNA polymerase II carboxy-terminal domain (CTD). The WW domain of PCIF1 can directly and preferentially bind to the phosphorylated CTD compared to the unphosphorylated CTD. PCIF1 binds to the hyperphosphorylated RNAP II (RNAP IIO) in vitro and in vivo. Double immunofluorescence labeling in HeLa cells demonstrated that PCIF1 and endogenous RNAP IIO are co-localized in the cell nucleus. Thus, PCIF1 may play a role in mRNA synthesis by modulating RNAP IIO activity.


Pssm-ID: 463502  Cd Length: 172  Bit Score: 323.45  E-value: 1.59e-107
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27348126   446 KLWLLYR-YSCIDDSAFERFLPRVWCLLRRYQMMFGVGLYEGTGLQGSLPVHVFEALHRLFGVSFECFASPLNCYFRQYC 524
Cdd:pfam12237   1 KLEQLYRsYSCFDDKKFEIFLPRLFCLLLRYQTLLGGQSNEGGGTQAALPESVFDCLHRFFGVSFECFASPLNCYFRQYC 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27348126   525 SAFPDTDGYFGSRGPCLDFAPLSGSFEANPPFCEELMDAMVSHFERLLESSPEPLSFIVFIPEWREPPTPALTRMEQSRF 604
Cdd:pfam12237  81 SAFPDTDGYFGSRGSFFDFKPVSGSFEANPPFCEELMDAMADHIERLLEASSEPLSFVVFVPEWRDPPTPALLKLEESRF 160

                         170
                  ....*....|..
gi 27348126   605 KRHQLILPAFEH 616
Cdd:pfam12237 161 KRKQVVIPANEH 172
WW cd00201
Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; ...
 47-77 3.27e-06

Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other peptide recognition proteins such as antibodies and receptors; WW domains have a single groove formed by a conserved Trp and Tyr which recognizes a pair of residues of the sequence X-Pro; variable loops and neighboring domains confer specificity in this domain; there are five distinct groups based on binding: 1) PPXY motifs 2) the PPLP motif; 3) PGM motifs; 4) PSP or PTP motifs; 5) PR motifs.


Pssm-ID: 238122 [Multi-domain]  Cd Length: 31  Bit Score: 44.06  E-value: 3.27e-06
                        10        20        30
                ....*....|....*....|....*....|.
gi 27348126  47 AGWEKCWSRrENRPYYFNRFTNQSLWEMPVL 77
Cdd:cd00201   2 PGWEERWDP-DGRVYYYNHNTKETQWEDPRE 31
WW pfam00397
WW domain; The WW domain is a protein module with two highly conserved tryptophans that binds ...
 47-75 5.18e-06

WW domain; The WW domain is a protein module with two highly conserved tryptophans that binds proline-rich peptide motifs in vitro.


Pssm-ID: 459800 [Multi-domain]  Cd Length: 30  Bit Score: 43.26  E-value: 5.18e-06
                          10        20
                  ....*....|....*....|....*....
gi 27348126    47 AGWEKCWSRrENRPYYFNRFTNQSLWEMP 75
Cdd:pfam00397   3 PGWEERWDP-DGRVYYYNHETGETQWEKP 30
WW smart00456
Domain with 2 conserved Trp (W) residues; Also known as the WWP or rsp5 domain. Binds ...
 47-77 1.27e-03

Domain with 2 conserved Trp (W) residues; Also known as the WWP or rsp5 domain. Binds proline-rich polypeptides.


Pssm-ID: 197736 [Multi-domain]  Cd Length: 33  Bit Score: 36.81  E-value: 1.27e-03
                           10        20        30
                   ....*....|....*....|....*....|.
gi 27348126     47 AGWEKCWSRrENRPYYFNRFTNQSLWEMPVL 77
Cdd:smart00456   4 PGWEERKDP-DGRPYYYNHETKETQWEKPRE 33
 
Name Accession Description Interval E-value
PCIF1_WW pfam12237
Phosphorylated CTD interacting factor 1 WW domain; This domain family is found in bacteria and ...
 446-616 1.59e-107

Phosphorylated CTD interacting factor 1 WW domain; This domain family is found in bacteria and eukaryotes, and is approximately 180 amino acids in length. This domain is the WW domain of PCIF1. PCIF1 interacts with phosphorylated RNA polymerase II carboxy-terminal domain (CTD). The WW domain of PCIF1 can directly and preferentially bind to the phosphorylated CTD compared to the unphosphorylated CTD. PCIF1 binds to the hyperphosphorylated RNAP II (RNAP IIO) in vitro and in vivo. Double immunofluorescence labeling in HeLa cells demonstrated that PCIF1 and endogenous RNAP IIO are co-localized in the cell nucleus. Thus, PCIF1 may play a role in mRNA synthesis by modulating RNAP IIO activity.


Pssm-ID: 463502  Cd Length: 172  Bit Score: 323.45  E-value: 1.59e-107
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27348126   446 KLWLLYR-YSCIDDSAFERFLPRVWCLLRRYQMMFGVGLYEGTGLQGSLPVHVFEALHRLFGVSFECFASPLNCYFRQYC 524
Cdd:pfam12237   1 KLEQLYRsYSCFDDKKFEIFLPRLFCLLLRYQTLLGGQSNEGGGTQAALPESVFDCLHRFFGVSFECFASPLNCYFRQYC 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27348126   525 SAFPDTDGYFGSRGPCLDFAPLSGSFEANPPFCEELMDAMVSHFERLLESSPEPLSFIVFIPEWREPPTPALTRMEQSRF 604
Cdd:pfam12237  81 SAFPDTDGYFGSRGSFFDFKPVSGSFEANPPFCEELMDAMADHIERLLEASSEPLSFVVFVPEWRDPPTPALLKLEESRF 160

                         170
                  ....*....|..
gi 27348126   605 KRHQLILPAFEH 616
Cdd:pfam12237 161 KRKQVVIPANEH 172
WW cd00201
Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; ...
 47-77 3.27e-06

Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other peptide recognition proteins such as antibodies and receptors; WW domains have a single groove formed by a conserved Trp and Tyr which recognizes a pair of residues of the sequence X-Pro; variable loops and neighboring domains confer specificity in this domain; there are five distinct groups based on binding: 1) PPXY motifs 2) the PPLP motif; 3) PGM motifs; 4) PSP or PTP motifs; 5) PR motifs.


Pssm-ID: 238122 [Multi-domain]  Cd Length: 31  Bit Score: 44.06  E-value: 3.27e-06
                        10        20        30
                ....*....|....*....|....*....|.
gi 27348126  47 AGWEKCWSRrENRPYYFNRFTNQSLWEMPVL 77
Cdd:cd00201   2 PGWEERWDP-DGRVYYYNHNTKETQWEDPRE 31
WW pfam00397
WW domain; The WW domain is a protein module with two highly conserved tryptophans that binds ...
 47-75 5.18e-06

WW domain; The WW domain is a protein module with two highly conserved tryptophans that binds proline-rich peptide motifs in vitro.


Pssm-ID: 459800 [Multi-domain]  Cd Length: 30  Bit Score: 43.26  E-value: 5.18e-06
                          10        20
                  ....*....|....*....|....*....
gi 27348126    47 AGWEKCWSRrENRPYYFNRFTNQSLWEMP 75
Cdd:pfam00397   3 PGWEERWDP-DGRVYYYNHETGETQWEKP 30
WW smart00456
Domain with 2 conserved Trp (W) residues; Also known as the WWP or rsp5 domain. Binds ...
 47-77 1.27e-03

Domain with 2 conserved Trp (W) residues; Also known as the WWP or rsp5 domain. Binds proline-rich polypeptides.


Pssm-ID: 197736 [Multi-domain]  Cd Length: 33  Bit Score: 36.81  E-value: 1.27e-03
                           10        20        30
                   ....*....|....*....|....*....|.
gi 27348126     47 AGWEKCWSRrENRPYYFNRFTNQSLWEMPVL 77
Cdd:smart00456   4 PGWEERKDP-DGRPYYYNHETKETQWEKPRE 33
 
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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