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Conserved domains on  [gi|1279527268|pdb|5XV8|B]
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Chain B, General transcription factor IIH subunit 1

Protein Classification

TFIIH subunit TFB1 family PH domain-containing protein( domain architecture ID 10192428)

TFIIH subunit TFB1 family PH (Pleckstrin homology) domain-containing protein similar to the PH domain of Homo sapiens general transcription factor IIH subunit 1 (GTF2H1), a component of the general transcription and DNA repair factor IIH (TFIIH) core complex, which is involved in general and transcription-coupled nucleotide excision repair (NER) of damaged DNA and, when complexed to CAK, in RNA transcription by RNA polymerase II

CATH:  2.30.29.30
Gene Ontology:  GO:0005515|GO:0000439
SCOP:  4002395

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
PH_TFIIH cd13229
Transcription Factor II H (TFIIH) Pleckstrin homology (PH) domain; The transcription factor II ...
11-104 2.82e-42

Transcription Factor II H (TFIIH) Pleckstrin homology (PH) domain; The transcription factor II H (TFIIH) is one of the general transcription factors (GTFs) known to be a target of the transactivation domain (TAD) of p53. Human TFIIH and its homologous yeast counterpart (factor b) are composed of ten subunits that can be divided into two groups, the core TFIIH (XPB/Ssl2, p62/Tfb1, p52/Tfb2, p44/Ssl1, p34/Tfb4, and TTDA/Tfb5 in human/yeast) and the CAK complex (cdk7/Kin28, cyclin H/Ccl1, and MAT1/Tfb3). These two complexes are linked by the XPD/Rad3 subunit. The helicase activities of XPB and XPD are essential to the formation of the open complex during transcription initiation and the kinase activity of cdk7 phosphorylates the C-terminal domain (CTD) of the RNA Pol II largest subunit, enabling RNA Pol II to progress from the initiation phase to the elongation phase of transcription. The PH domain of p62/Tfb1 has been shown to interact with herpes simplex virus protein 16 (VP16) TAD and the binding of p53 TAD is mediated by the TAD2 subdomain. TFIIE recruits TFIIH to complete the preinitiation complex (PIC) formation and regulates enzymatic activities of TFIIH. The PH domain of the human TFIIH p62 subunit binds to the C-terminal acidic (AC) domain of the human TFIIEalpha subunit. This interaction could be a switch to replace p53 with TFIIE on TFIIH in transcription. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes.


:

Pssm-ID: 270049  Cd Length: 93  Bit Score: 133.94  E-value: 2.82e-42
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5XV8_B       11 LLIVKKVRqKKQDGALYLMAERIAWAPEGKDRFTISHMYADIKCQKISPEGKAKIQLQLVLHAGDTTNFHFSNESTAVKE 90
Cdd:cd13229   1 LLSGAAVY-KKKDGTLYLSESRLGWKPSGGDSPPISLPYSDIKNQQISPEGSAKVQLKLVLKDGGSFTFHFTNPSGARKD 79
                        90
                ....*....|....
5XV8_B       91 RDAVKDLLQQLLPK 104
Cdd:cd13229  80 RDAVKDLLQQLLAR 93
 
Name Accession Description Interval E-value
PH_TFIIH cd13229
Transcription Factor II H (TFIIH) Pleckstrin homology (PH) domain; The transcription factor II ...
11-104 2.82e-42

Transcription Factor II H (TFIIH) Pleckstrin homology (PH) domain; The transcription factor II H (TFIIH) is one of the general transcription factors (GTFs) known to be a target of the transactivation domain (TAD) of p53. Human TFIIH and its homologous yeast counterpart (factor b) are composed of ten subunits that can be divided into two groups, the core TFIIH (XPB/Ssl2, p62/Tfb1, p52/Tfb2, p44/Ssl1, p34/Tfb4, and TTDA/Tfb5 in human/yeast) and the CAK complex (cdk7/Kin28, cyclin H/Ccl1, and MAT1/Tfb3). These two complexes are linked by the XPD/Rad3 subunit. The helicase activities of XPB and XPD are essential to the formation of the open complex during transcription initiation and the kinase activity of cdk7 phosphorylates the C-terminal domain (CTD) of the RNA Pol II largest subunit, enabling RNA Pol II to progress from the initiation phase to the elongation phase of transcription. The PH domain of p62/Tfb1 has been shown to interact with herpes simplex virus protein 16 (VP16) TAD and the binding of p53 TAD is mediated by the TAD2 subdomain. TFIIE recruits TFIIH to complete the preinitiation complex (PIC) formation and regulates enzymatic activities of TFIIH. The PH domain of the human TFIIH p62 subunit binds to the C-terminal acidic (AC) domain of the human TFIIEalpha subunit. This interaction could be a switch to replace p53 with TFIIE on TFIIH in transcription. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes.


Pssm-ID: 270049  Cd Length: 93  Bit Score: 133.94  E-value: 2.82e-42
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5XV8_B       11 LLIVKKVRqKKQDGALYLMAERIAWAPEGKDRFTISHMYADIKCQKISPEGKAKIQLQLVLHAGDTTNFHFSNESTAVKE 90
Cdd:cd13229   1 LLSGAAVY-KKKDGTLYLSESRLGWKPSGGDSPPISLPYSDIKNQQISPEGSAKVQLKLVLKDGGSFTFHFTNPSGARKD 79
                        90
                ....*....|....
5XV8_B       91 RDAVKDLLQQLLPK 104
Cdd:cd13229  80 RDAVKDLLQQLLAR 93
PH_TFIIH pfam08567
TFIIH p62 subunit, N-terminal domain; The N-terminal domain of the TFIIH basal transcription ...
18-99 5.04e-31

TFIIH p62 subunit, N-terminal domain; The N-terminal domain of the TFIIH basal transcription factor complex p62 subunit (BTF2-p62) forms an interaction with the 3' endonuclease XPG, which is essential for activity. The 3' endonuclease XPG is a major component of the nucleotide excision repair machinery. The structure of the N-terminal domain reveals that it adopts a pleckstrin homology (PH) fold. This PH-type domain has been shown to bind to a mono-phosphorylated inositide.


Pssm-ID: 462521  Cd Length: 88  Bit Score: 105.01  E-value: 5.04e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5XV8_B         18 RQKKQDGALYLMAERIAWAPE-GKDRFTISHMYADIKCQKISPEGKAKIQLQLVLH-----AGDTTNFHFSNESTAVKER 91
Cdd:pfam08567   1 SYKKKDGTLTLTEARLEWTPDaGSSAPSVSIPLADITNLQQSPAGSAKVMLKLVLKpdsppDPVTYTFHFTNPSNARKER 80

                  ....*...
5XV8_B         92 DAVKDLLQ 99
Cdd:pfam08567  81 DNIKDLLQ 88
 
Name Accession Description Interval E-value
PH_TFIIH cd13229
Transcription Factor II H (TFIIH) Pleckstrin homology (PH) domain; The transcription factor II ...
11-104 2.82e-42

Transcription Factor II H (TFIIH) Pleckstrin homology (PH) domain; The transcription factor II H (TFIIH) is one of the general transcription factors (GTFs) known to be a target of the transactivation domain (TAD) of p53. Human TFIIH and its homologous yeast counterpart (factor b) are composed of ten subunits that can be divided into two groups, the core TFIIH (XPB/Ssl2, p62/Tfb1, p52/Tfb2, p44/Ssl1, p34/Tfb4, and TTDA/Tfb5 in human/yeast) and the CAK complex (cdk7/Kin28, cyclin H/Ccl1, and MAT1/Tfb3). These two complexes are linked by the XPD/Rad3 subunit. The helicase activities of XPB and XPD are essential to the formation of the open complex during transcription initiation and the kinase activity of cdk7 phosphorylates the C-terminal domain (CTD) of the RNA Pol II largest subunit, enabling RNA Pol II to progress from the initiation phase to the elongation phase of transcription. The PH domain of p62/Tfb1 has been shown to interact with herpes simplex virus protein 16 (VP16) TAD and the binding of p53 TAD is mediated by the TAD2 subdomain. TFIIE recruits TFIIH to complete the preinitiation complex (PIC) formation and regulates enzymatic activities of TFIIH. The PH domain of the human TFIIH p62 subunit binds to the C-terminal acidic (AC) domain of the human TFIIEalpha subunit. This interaction could be a switch to replace p53 with TFIIE on TFIIH in transcription. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes.


Pssm-ID: 270049  Cd Length: 93  Bit Score: 133.94  E-value: 2.82e-42
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5XV8_B       11 LLIVKKVRqKKQDGALYLMAERIAWAPEGKDRFTISHMYADIKCQKISPEGKAKIQLQLVLHAGDTTNFHFSNESTAVKE 90
Cdd:cd13229   1 LLSGAAVY-KKKDGTLYLSESRLGWKPSGGDSPPISLPYSDIKNQQISPEGSAKVQLKLVLKDGGSFTFHFTNPSGARKD 79
                        90
                ....*....|....
5XV8_B       91 RDAVKDLLQQLLPK 104
Cdd:cd13229  80 RDAVKDLLQQLLAR 93
PH_TFIIH pfam08567
TFIIH p62 subunit, N-terminal domain; The N-terminal domain of the TFIIH basal transcription ...
18-99 5.04e-31

TFIIH p62 subunit, N-terminal domain; The N-terminal domain of the TFIIH basal transcription factor complex p62 subunit (BTF2-p62) forms an interaction with the 3' endonuclease XPG, which is essential for activity. The 3' endonuclease XPG is a major component of the nucleotide excision repair machinery. The structure of the N-terminal domain reveals that it adopts a pleckstrin homology (PH) fold. This PH-type domain has been shown to bind to a mono-phosphorylated inositide.


Pssm-ID: 462521  Cd Length: 88  Bit Score: 105.01  E-value: 5.04e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5XV8_B         18 RQKKQDGALYLMAERIAWAPE-GKDRFTISHMYADIKCQKISPEGKAKIQLQLVLH-----AGDTTNFHFSNESTAVKER 91
Cdd:pfam08567   1 SYKKKDGTLTLTEARLEWTPDaGSSAPSVSIPLADITNLQQSPAGSAKVMLKLVLKpdsppDPVTYTFHFTNPSNARKER 80

                  ....*...
5XV8_B         92 DAVKDLLQ 99
Cdd:pfam08567  81 DNIKDLLQ 88
PH-like cd00900
Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like ...
17-94 1.79e-11

Pleckstrin homology-like domain; The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins.


Pssm-ID: 275390  Cd Length: 89  Bit Score: 55.48  E-value: 1.79e-11
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
5XV8_B       17 VRQKKQDGALYLMAERIAWAPEGKDRFTISHMYADIKCQKISPEGKAKIQLQLVLHA-GDTTNFHFSNESTAVKERDAV 94
Cdd:cd00900  11 EPTKRVEGTLYITSDRLILRDKNDGGLELSIPISDIVNVNVSPQGPSSRYLVLVLKDrGEFVGFSFPKEEDAIEISDAL 89
 
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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