User:Julie Holzinger/1g25

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(Difference between revisions)

Revision as of 07:58, 13 June 2024

SOLUTION STRUCTURE OF THE N-TERMINAL DOMAIN OF THE HUMAN TFIIH MAT1 SUBUNIT

Mat1 is a 36kDa protein and subunit of TFIIH, which, with cyclin H and Cdk7, forms a trimeric kinase complex that has been implicated in the activation of cyclin dependent kinases (CDK) that tightly regulate transcription and cell cycle control.

Structural highlights

1g25 is a 1 chain structure with sequence from Homo sapiens. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance. The N terminal of Mat1 features a RING finger, a specialized form of zinc finger with a C3HC4 sequence motif. ^[1]. The analysis of the MAT1 human RING domain reveals that the N terminal domain presents the expected beta alpha beta beta topology with two interleaved zinc binding sites. Conserved hydrophobic residue near the Beta1 strand (Leu19, Leu21, Met22, and Val23) could possibly be involved to a Mat1 activity regulation and constitute an interesting feature; two of these residues (Leu19 and Met22) are involved in the hydrophobic packing of the RING structure, as the two others are exposed to the solvent. The N terminal domain features a unique structured region including one turn of an alpha helix, which corresponds to the sequence insertion between the first and second pairs of zinc-binding ligands, only observed in Mat1 sequences. A solvent exposed tyrosine (Tyr15), conserved among all Mat1 sequences, could be a potential phosphorylation target and involved in activity regulation. The MAT1 RING domain is also remarkably positively charged because of the presence of several basic side chains of arginines and lysines. ^[2]
Method:	Solution NMR
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

MAT1_HUMAN Stabilizes the cyclin H-CDK7 complex to form a functional CDK-activating kinase (CAK) enzymatic complex. CAK activates the cyclin-associated kinases CDK1, CDK2, CDK4 and CDK6 by threonine phosphorylation. CAK complexed to the core-TFIIH basal transcription factor activates RNA polymerase II by serine phosphorylation of the repetitive C-terminus domain (CTD) of its large subunit (POLR2A), allowing its escape from the promoter and elongation of the transcripts. Involved in cell cycle control and in RNA transcription by RNA polymerase II ^[3]

RNA polymerase II is a 12-subunit enzyme, involved in the transcription of protein coding eukaryotic genes, giving ARNm as a product. The transcription initiation of polymerase II requires 5 general transcription factors (TFIIB, TFIID, TFIIE, TFIIF and TFIIH). Associated with PolII and the Mediator, those 5 general transcription factors form the Pre-Initiation Complex (PIC) on the promoter.

The general transcription factor IIH (TFIIH) is a 10 subunits transcription factor involved in the transcription initiation (promoter melting) but also in the transition from initiation to elongation (promoter escape). TFIIH consists of a 7 subunits core and a kinase module. Cyclin H, Cdk7 and Mat1 form the kinase module that can reversibly associate with TFIIH, also known as CAK (Cdk activating kinase) based on the activity of Cdk7.

TFIIH is one of the two transcription factors needed for promoter DNA opening, as it contains essential DNA dependent ATPase activity. The kinase module is not required for DNA repair, however, only the complete TFIIH is transcription competent. ^[4]

In its unphosphorylated form, the PolII C-terminal domain (CTD) has a high affinity interaction with the mediator in the PIC. PolII phosphorylation by Cdk7 (targeting the residues Ser5 and Ser7 in the CTD heptad repeat) releases mediator interaction with the CTD, which may help the promoter escaping process and therefore, initiate the transcription initiation. Cdk7 also controls the cell cycle by phosphorylating the cell cycle Cdk, including Cdk1, 2, 3, 4 and 6 in their T-loops to promote their activity. ^[5]

Mat1, also known as « ménage à trois », acts as a regulatory subunit and is required for stability of the kinase module and efficient global transcription. ^[6] Indeed, Cdk7 activity and substrate specificity is regulated by cyclin H and Mat1. Mat 1 helps direct Cdk7 dependent phosphorylation towards DNA-binding transcription factors. Mat 1 also stabilizes Cyclin H and Cdk7 in the CAK complex and anchor it to the TFIIH core through interaction with TfIIH core subunits. ^[7]

While the C-terminal domain of Mat1 was found to bind to the Cdk7-CyclinH complex and activate the cdk7 activity, and the median portion, containing a coiled-coil motif, allows the binding of CAK to the TFIIH core, the N terminal RING domain is crucial for transcription as it plays an essential role within the transcription complex by interacting with other factors and participates to the phosphorylation of PolII CTD. ^[8]

Diseases

Studies showed that MAT1 facilitates the lung metastasis of osteosarcoma through increasing AKT1 expression. ^[9] and that MAT1 expression is elevated in breast cancer tissues. ^[10] . This suggests that MAT1 could be a potential target for new anti-cancer drugs.

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

The human MAT1 protein belongs to the cyclin-dependent kinase-activating kinase complex, which is functionally associated to the transcription/DNA repair factor TFIIH. The N-terminal region of MAT1 consists of a C3HC4 RING finger, which contributes to optimal TFIIH transcriptional activities. We report here the solution structure of the human MAT1 RING finger domain (Met(1)-Asp(65)) as determined by (1)H NMR spectroscopy. The MAT1 RING finger domain presents the expected betaalphabetabeta topology with two interleaved zinc-binding sites conserved among the RING family. However, the presence of an additional helical segment in the N-terminal part of the domain and a conserved hydrophobic central beta strand are the defining features of this new structure and more generally of the MAT1 RING finger subfamily. Comparison of electrostatic surfaces of RING finger structures shows that the RING finger domain of MAT1 presents a remarkable positively charged surface. The functional implications of these MAT1 RING finger features are discussed.

Solution structure of the N-terminal domain of the human TFIIH MAT1 subunit: new insights into the RING finger family.,Gervais V, Busso D, Wasielewski E, Poterszman A, Egly JM, Thierry JC, Kieffer B J Biol Chem. 2001 Mar 9;276(10):7457-64. Epub 2000 Oct 30. PMID:11056162^[11]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Tassan JP, Jaquenoud M, Fry AM, Frutiger S, Hughes GJ, Nigg EA. In vitro assembly of a functional human CDK7-cyclin H complex requires MAT1, a novel 36 kDa RING finger protein. EMBO J. 1995 Nov 15;14(22):5608-17. PMID:8521818 doi:10.1002/j.1460-2075.1995.tb00248.x
↑ Gervais V, Busso D, Wasielewski E, Poterszman A, Egly JM, Thierry JC, Kieffer B. Solution structure of the N-terminal domain of the human TFIIH MAT1 subunit: new insights into the RING finger family. J Biol Chem. 2001 Mar 9;276(10):7457-64. Epub 2000 Oct 30. PMID:11056162 doi:http://dx.doi.org/10.1074/jbc.M007963200
↑ Tirode F, Busso D, Coin F, Egly JM. Reconstitution of the transcription factor TFIIH: assignment of functions for the three enzymatic subunits, XPB, XPD, and cdk7. Mol Cell. 1999 Jan;3(1):87-95. PMID:10024882
↑ Sainsbury S, Bernecky C, Cramer P. Structural basis of transcription initiation by RNA polymerase II. Nat Rev Mol Cell Biol. 2015 Mar;16(3):129-43. PMID:25693126 doi:10.1038/nrm3952
↑ Sava GP, Fan H, Coombes RC, Buluwela L, Ali S. CDK7 inhibitors as anticancer drugs. Cancer Metastasis Rev. 2020 Sep;39(3):805-823. PMID:32385714 doi:10.1007/s10555-020-09885-8
↑ Helenius K, Yang Y, Tselykh TV, Pessa HK, Frilander MJ, Mäkelä TP. Requirement of TFIIH kinase subunit Mat1 for RNA Pol II C-terminal domain Ser5 phosphorylation, transcription and mRNA turnover. Nucleic Acids Res. 2011 Jul;39(12):5025-35. PMID:21385826 doi:10.1093/nar/gkr107
↑ Rimel JK, Taatjes DJ. The essential and multifunctional TFIIH complex. Protein Sci. 2018 Jun;27(6):1018-1037. PMID:29664212 doi:10.1002/pro.3424
↑ Busso D, Keriel A, Sandrock B, Poterszman A, Gileadi O, Egly JM. Distinct regions of MAT1 regulate cdk7 kinase and TFIIH transcription activities. J Biol Chem. 2000 Jul 28;275(30):22815-23. PMID:10801852 doi:10.1074/jbc.M002578200
↑ Wang J, Ni J, Song D, Ding M, Huang J, Li W, He G. MAT1 facilitates the lung metastasis of osteosarcoma through upregulation of AKT1 expression. Life Sci. 2019 Oct 1;234:116771. PMID:31421084 doi:10.1016/j.lfs.2019.116771
↑ Patel H, Abduljabbar R, Lai CF, Periyasamy M, Harrod A, Gemma C, Steel JH, Patel N, Busonero C, Jerjees D, Remenyi J, Smith S, Gomm JJ, Magnani L, Gyorffy B, Jones LJ, Fuller-Pace F, Shousha S, Buluwela L, Rakha EA, Ellis IO, Coombes RC, Ali S. Expression of CDK7, Cyclin H, and MAT1 Is Elevated in Breast Cancer and Is Prognostic in Estrogen Receptor-Positive Breast Cancer. Clin Cancer Res. 2016 Dec 1;22(23):5929-5938. doi: 10.1158/1078-0432.CCR-15-1104., Epub 2016 Jun 14. PMID:27301701 doi:http://dx.doi.org/10.1158/1078-0432.CCR-15-1104
↑ Gervais V, Busso D, Wasielewski E, Poterszman A, Egly JM, Thierry JC, Kieffer B. Solution structure of the N-terminal domain of the human TFIIH MAT1 subunit: new insights into the RING finger family. J Biol Chem. 2001 Mar 9;276(10):7457-64. Epub 2000 Oct 30. PMID:11056162 doi:http://dx.doi.org/10.1074/jbc.M007963200

1 Structural highlights
2 Function
3 Diseases
4 Evolutionary Conservation
5 Publication Abstract from PubMed
6 References

Proteopedia Page Contributors and Editors (what is this?)

Julie Holzinger

Retrieved from "http://52.214.119.220/wiki/index.php/User:Julie_Holzinger/1g25"

@@ Line 1: / Line 1: @@
 ==SOLUTION STRUCTURE OF THE N-TERMINAL DOMAIN OF THE HUMAN TFIIH MAT1 SUBUNIT==
 <StructureSection load='1g25' size='340' side='right'caption='[[1g25]]' scene=''>
+Mat1 is a 36kDa protein and subunit of TFIIH, which, with cyclin H and Cdk7, forms a trimeric kinase complex that has been implicated in the activation of cyclin dependent kinases (CDK) that tightly regulate transcription and cell cycle control.
 == Structural highlights ==
 <table><tr><td colspan='2'>[[1g25]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1G25 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1G25 FirstGlance]. <br>
+The N terminal of Mat1 features a RING finger, a specialized form of zinc finger with a C3HC4 sequence motif. <ref>PMID: 8521818</ref>. The analysis of the MAT1 human RING domain reveals that the N terminal domain presents the expected beta alpha beta beta topology with two interleaved zinc binding sites.
+Conserved hydrophobic residue near the Beta1 strand (Leu19, Leu21, Met22, and Val23) could possibly be involved to a Mat1 activity regulation and constitute an interesting feature; two of these residues (Leu19 and Met22) are involved in the hydrophobic packing of the RING structure, as the two others are exposed to the solvent.
+The N terminal domain features a unique structured region including one turn of an alpha helix, which corresponds to the sequence insertion between the first and second pairs of zinc-binding ligands, only observed in Mat1 sequences. A solvent exposed tyrosine (Tyr15), conserved among all Mat1 sequences, could be a potential phosphorylation target and involved in activity regulation.
+The MAT1 RING domain is also remarkably positively charged because of the presence of several basic side chains of arginines and lysines. <ref>PMID: 11056162</ref>
 </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
 <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
@@ Line 8: / Line 16: @@
 </table>
 == Function ==
-[https://www.uniprot.org/uniprot/MAT1_HUMAN MAT1_HUMAN] Stabilizes the cyclin H-CDK7 complex to form a functional CDK-activating kinase (CAK) enzymatic complex. CAK activates the cyclin-associated kinases CDK1, CDK2, CDK4 and CDK6 by threonine phosphorylation. CAK complexed to the core-TFIIH basal transcription factor activates RNA polymerase II by serine phosphorylation of the repetitive C-terminus domain (CTD) of its large subunit (POLR2A), allowing its escape from the promoter and elongation of the transcripts. Involved in cell cycle control and in RNA transcription by RNA polymerase II.<ref>PMID:10024882</ref>
+[https://www.uniprot.org/uniprot/MAT1_HUMAN MAT1_HUMAN] Stabilizes the cyclin H-CDK7 complex to form a functional CDK-activating kinase (CAK) enzymatic complex. CAK activates the cyclin-associated kinases CDK1, CDK2, CDK4 and CDK6 by threonine phosphorylation. CAK complexed to the core-TFIIH basal transcription factor activates RNA polymerase II by serine phosphorylation of the repetitive C-terminus domain (CTD) of its large subunit (POLR2A), allowing its escape from the promoter and elongation of the transcripts. Involved in cell cycle control and in RNA transcription by RNA polymerase II <ref>PMID:10024882</ref>
+RNA polymerase II is a 12-subunit enzyme, involved in the transcription of protein coding eukaryotic genes, giving ARNm as a product. The transcription initiation of polymerase II requires 5 general transcription factors (TFIIB, TFIID, TFIIE, TFIIF and TFIIH). Associated with PolII and the Mediator, those 5 general transcription factors form the Pre-Initiation Complex (PIC) on the promoter.
+The general transcription factor IIH (TFIIH) is a 10 subunits transcription factor involved in the transcription initiation (promoter melting) but also in the transition from initiation to elongation (promoter escape). TFIIH consists of a 7 subunits core and a kinase module. Cyclin H, Cdk7 and Mat1 form the kinase module that can reversibly associate with TFIIH, also known as CAK (Cdk activating kinase) based on the activity of Cdk7.
+TFIIH is one of the two transcription factors needed for promoter DNA opening, as it contains essential DNA dependent ATPase activity. The kinase module is not required for DNA repair, however, only the complete TFIIH is transcription competent. <ref>PMID:25693126</ref>
+In its unphosphorylated form, the PolII C-terminal domain (CTD) has a high affinity interaction with the mediator in the PIC. PolII phosphorylation by Cdk7 (targeting the residues Ser5 and Ser7 in the CTD heptad repeat) releases mediator interaction with the CTD, which may help the promoter escaping process and therefore, initiate the transcription initiation. Cdk7 also controls the cell cycle by phosphorylating the cell cycle Cdk, including Cdk1, 2, 3, 4 and 6 in their T-loops to promote their activity. <ref>PMID:32385714</ref>
+Mat1, also known as « ménage à trois », acts as a regulatory subunit and is required for stability of the kinase module and efficient global transcription. <ref>PMID:21385826</ref> Indeed, Cdk7 activity and substrate specificity is regulated by cyclin H and Mat1. Mat 1 helps direct Cdk7 dependent phosphorylation towards DNA-binding transcription factors. Mat 1 also stabilizes Cyclin H and Cdk7 in the CAK complex and anchor it to the TFIIH core through interaction with TfIIH core subunits. <ref>PMID:29664212</ref>
+While the C-terminal domain of Mat1 was found to bind to the Cdk7-CyclinH complex and activate the cdk7 activity, and the median portion, containing a coiled-coil motif, allows the binding of CAK to the TFIIH core, the N terminal RING domain is crucial for transcription as it plays an essential role within the transcription complex by interacting with other factors and participates to the phosphorylation of PolII CTD. <ref>PMID:10801852</ref>
+== Diseases ==
+Studies showed that MAT1 facilitates the lung metastasis of osteosarcoma through increasing AKT1 expression. <ref>PMID: 31421084</ref> and that MAT1 expression is elevated in breast cancer tissues. <ref>PMID: 27301701</ref> . This suggests that MAT1 could be a potential target for new anti-cancer drugs.
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]

User:Julie Holzinger/1g25

From Proteopedia

Revision as of 07:58, 13 June 2024

SOLUTION STRUCTURE OF THE N-TERMINAL DOMAIN OF THE HUMAN TFIIH MAT1 SUBUNIT

Structural highlights

Function

Diseases

Evolutionary Conservation

Publication Abstract from PubMed

References

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Proteopedia Page Contributors and Editors (what is this?)

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