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Book ; Online ; Thesis: Structure-function analysis of human nucleotide excision DNA repair

Kokic, Goran [Verfasser]

2021

Author's details	Goran Kokic
Keywords	Biowissenschaften, Biologie ; Life Science, Biology
Subject code	sg570
Language	English
Publisher	Niedersächsische Staats- und Universitätsbibliothek Göttingen
Publishing place	Göttingen
Document type	Book ; Online ; Thesis
Database	Digital theses on the web

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Article ; Online: Structure of the transcribing RNA polymerase II-Elongin complex.

Chen, Ying / Kokic, Goran / Dienemann, Christian / Dybkov, Olexandr / Urlaub, Henning / Cramer, Patrick

Nature structural & molecular biology

2023 Volume 30, Issue 12, Page(s) 1925–1935

Abstract: Elongin is a heterotrimeric elongation factor for RNA polymerase (Pol) II transcription that is conserved among metazoa. Here, we report three cryo-EM structures of human Elongin bound to transcribing Pol II. The structures show that Elongin subunit ELOA ...

Abstract	Elongin is a heterotrimeric elongation factor for RNA polymerase (Pol) II transcription that is conserved among metazoa. Here, we report three cryo-EM structures of human Elongin bound to transcribing Pol II. The structures show that Elongin subunit ELOA binds the RPB2 side of Pol II and anchors the ELOB-ELOC subunit heterodimer. ELOA contains a 'latch' that binds between the end of the Pol II bridge helix and funnel helices, thereby inducing a conformational change near the polymerase active center. The latch is required for the elongation-stimulatory activity of Elongin, but not for Pol II binding, indicating that Elongin functions by allosterically regulating the conformational mobility of the polymerase active center. Elongin binding to Pol II is incompatible with association of the super elongation complex, PAF1 complex and RTF1, which also contain an elongation-stimulatory latch element.
MeSH term(s)	Humans ; Elongin/genetics ; Elongin/metabolism ; Transcription Factors/metabolism ; RNA Polymerase II/metabolism ; Cell Nucleus/metabolism ; Transcription, Genetic
Chemical Substances	Elongin ; Transcription Factors ; RNA Polymerase II (EC 2.7.7.-) ; PAF1 protein, human
Language	English
Publishing date	2023-11-06
Publishing country	United States
Document type	Journal Article
ZDB-ID	2126708-X
ISSN	1545-9985 ; 1545-9993
ISSN (online)	1545-9985
ISSN	1545-9993
DOI	10.1038/s41594-023-01138-w
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Article: [No title information]

Cramer, Patrick / Kokic, Goran / Dienemann, Christian / Höbartner, Claudia / Hillen, Hauke S

Biospektrum : Zeitschrift der Gesellschaft fur Biologishe Chemie (GBCH) und der Vereinigung fur Allgemeine und Angewandte Mikrobiologie (VAAM)

2021 Volume 27, Issue 1, Page(s) 49–53

Abstract: Coronaviruses use an RNA-dependent RNA polymerase to replicate and transcribe their RNA genome. The structure of the SARS-CoV-2 polymerase was determined by cryo-electron microscopy within a short time in spring 2020. The structure explains how the viral ...

Title translation	Coronavirus-Replikation: Mechanismus und Inhibition durch Remdesivir.
Abstract	Coronaviruses use an RNA-dependent RNA polymerase to replicate and transcribe their RNA genome. The structure of the SARS-CoV-2 polymerase was determined by cryo-electron microscopy within a short time in spring 2020. The structure explains how the viral enzyme synthesizes RNA and how it replicates the exceptionally large genome in a processive manner. The most recent structure-function studies further reveal the mechanism of polymerase inhibition by remdesivir, an approved drug for the treatment of COVID-19.
Language	German
Publishing date	2021-02-12
Publishing country	Germany
Document type	English Abstract ; Journal Article ; Review
ZDB-ID	2203536-9
ISSN	1868-6249 ; 0947-0867
ISSN (online)	1868-6249
ISSN	0947-0867
DOI	10.1007/s12268-021-1516-6
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Article ; Online: Structural basis for RNA polymerase II ubiquitylation and inactivation in transcription-coupled repair.

Kokic, Goran / Yakoub, George / van den Heuvel, Diana / Wondergem, Annelotte P / van der Meer, Paula J / van der Weegen, Yana / Chernev, Aleksandar / Fianu, Isaac / Fokkens, Thornton J / Lorenz, Sonja / Urlaub, Henning / Cramer, Patrick / Luijsterburg, Martijn S

Nature structural & molecular biology

2024 Volume 31, Issue 3, Page(s) 536–547

Abstract: During transcription-coupled DNA repair (TCR), RNA polymerase II (Pol II) transitions from a transcriptionally active state to an arrested state that allows for removal of DNA lesions. This transition requires site-specific ubiquitylation of Pol II by ... ...

Abstract	During transcription-coupled DNA repair (TCR), RNA polymerase II (Pol II) transitions from a transcriptionally active state to an arrested state that allows for removal of DNA lesions. This transition requires site-specific ubiquitylation of Pol II by the CRL4
MeSH term(s)	RNA Polymerase II/metabolism ; Transcription, Genetic ; Excision Repair ; DNA Repair ; DNA/metabolism ; Ubiquitination ; Ligases ; Receptors, Antigen, T-Cell
Chemical Substances	RNA Polymerase II (EC 2.7.7.-) ; DNA (9007-49-2) ; Ligases (EC 6.-) ; Receptors, Antigen, T-Cell
Language	English
Publishing date	2024-02-05
Publishing country	United States
Document type	Journal Article
ZDB-ID	2126708-X
ISSN	1545-9985 ; 1545-9993
ISSN (online)	1545-9985
ISSN	1545-9993
DOI	10.1038/s41594-023-01207-0
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Article ; Online: Structural basis of human transcription-DNA repair coupling.

Kokic, Goran / Wagner, Felix R / Chernev, Aleksandar / Urlaub, Henning / Cramer, Patrick

Nature

2021 Volume 598, Issue 7880, Page(s) 368–372

Abstract: Transcription-coupled DNA repair removes bulky DNA lesions from the ... ...

Abstract	Transcription-coupled DNA repair removes bulky DNA lesions from the genome
MeSH term(s)	Carrier Proteins/chemistry ; Carrier Proteins/metabolism ; Carrier Proteins/ultrastructure ; Cryoelectron Microscopy ; DNA Helicases/chemistry ; DNA Helicases/metabolism ; DNA Helicases/ultrastructure ; DNA Repair ; DNA Repair Enzymes/chemistry ; DNA Repair Enzymes/metabolism ; DNA Repair Enzymes/ultrastructure ; DNA-Binding Proteins/chemistry ; DNA-Binding Proteins/metabolism ; DNA-Binding Proteins/ultrastructure ; Humans ; Models, Molecular ; Multiprotein Complexes/chemistry ; Multiprotein Complexes/metabolism ; Multiprotein Complexes/ultrastructure ; Poly-ADP-Ribose Binding Proteins/chemistry ; Poly-ADP-Ribose Binding Proteins/metabolism ; Poly-ADP-Ribose Binding Proteins/ultrastructure ; RNA Polymerase II/chemistry ; RNA Polymerase II/metabolism ; RNA Polymerase II/ultrastructure ; Transcription Elongation, Genetic ; Transcription Factor TFIIH/chemistry ; Transcription Factor TFIIH/metabolism ; Transcription Factor TFIIH/ultrastructure ; Transcription Factors/chemistry ; Transcription Factors/metabolism ; Transcription Factors/ultrastructure ; Transcription, Genetic ; Ubiquitin-Protein Ligases/chemistry ; Ubiquitin-Protein Ligases/metabolism ; Ubiquitin-Protein Ligases/ultrastructure ; Ubiquitination
Chemical Substances	Carrier Proteins ; DDB1 protein, human ; DNA-Binding Proteins ; IL17RB protein, human ; Multiprotein Complexes ; PCLAF protein, human ; Poly-ADP-Ribose Binding Proteins ; SUPT6H protein, human ; Transcription Factors ; UVSSA protein, human ; Transcription Factor TFIIH (148710-81-0) ; Ubiquitin-Protein Ligases (EC 2.3.2.27) ; RNA Polymerase II (EC 2.7.7.-) ; DNA Helicases (EC 3.6.4.-) ; ERCC6 protein, human (EC 3.6.4.12) ; DNA Repair Enzymes (EC 6.5.1.-)
Language	English
Publishing date	2021-09-15
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	120714-3
ISSN	1476-4687 ; 0028-0836
ISSN (online)	1476-4687
ISSN	0028-0836
DOI	10.1038/s41586-021-03906-4
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Article ; Online: Structure of replicating SARS-CoV-2 polymerase.

Hillen, Hauke S / Kokic, Goran / Farnung, Lucas / Dienemann, Christian / Tegunov, Dimitry / Cramer, Patrick

Nature

2020 Volume 584, Issue 7819, Page(s) 154–156

Abstract: The new coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) uses an RNA-dependent RNA polymerase (RdRp) for the replication of its genome and the transcription of its ... ...

Abstract	The new coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) uses an RNA-dependent RNA polymerase (RdRp) for the replication of its genome and the transcription of its genes
MeSH term(s)	Adenosine Monophosphate/analogs & derivatives ; Adenosine Monophosphate/pharmacology ; Alanine/analogs & derivatives ; Alanine/pharmacology ; Betacoronavirus/drug effects ; Betacoronavirus/enzymology ; Betacoronavirus/genetics ; Betacoronavirus/ultrastructure ; Coronavirus RNA-Dependent RNA Polymerase ; Cryoelectron Microscopy ; Models, Molecular ; Protein Conformation ; RNA, Viral/biosynthesis ; RNA, Viral/chemistry ; RNA, Viral/metabolism ; RNA-Dependent RNA Polymerase/chemistry ; RNA-Dependent RNA Polymerase/genetics ; RNA-Dependent RNA Polymerase/metabolism ; RNA-Dependent RNA Polymerase/ultrastructure ; SARS-CoV-2 ; Viral Nonstructural Proteins/chemistry ; Viral Nonstructural Proteins/genetics ; Viral Nonstructural Proteins/metabolism ; Viral Nonstructural Proteins/ultrastructure
Chemical Substances	RNA, Viral ; Viral Nonstructural Proteins ; remdesivir (3QKI37EEHE) ; Adenosine Monophosphate (415SHH325A) ; Coronavirus RNA-Dependent RNA Polymerase (EC 2.7.7.48) ; NSP12 protein, SARS-CoV-2 (EC 2.7.7.48) ; RNA-Dependent RNA Polymerase (EC 2.7.7.48) ; Alanine (OF5P57N2ZX)
Keywords	covid19
Language	English
Publishing date	2020-05-21
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	120714-3
ISSN	1476-4687 ; 0028-0836
ISSN (online)	1476-4687
ISSN	0028-0836
DOI	10.1038/s41586-020-2368-8
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Article ; Online: The structure of a dimeric form of SARS-CoV-2 polymerase.

Jochheim, Florian A / Tegunov, Dimitry / Hillen, Hauke S / Schmitzová, Jana / Kokic, Goran / Dienemann, Christian / Cramer, Patrick

Communications biology

2021 Volume 4, Issue 1, Page(s) 999

Abstract: The coronavirus SARS-CoV-2 uses an RNA-dependent RNA polymerase (RdRp) to replicate and transcribe its genome. Previous structures of the RdRp revealed a monomeric enzyme composed of the catalytic subunit nsp12, two copies of subunit nsp8, and one copy ... ...

Abstract	The coronavirus SARS-CoV-2 uses an RNA-dependent RNA polymerase (RdRp) to replicate and transcribe its genome. Previous structures of the RdRp revealed a monomeric enzyme composed of the catalytic subunit nsp12, two copies of subunit nsp8, and one copy of subunit nsp7. Here we report an alternative, dimeric form of the enzyme and resolve its structure at 5.5 Å resolution. In this structure, the two RdRps contain only one copy of nsp8 each and dimerize via their nsp7 subunits to adopt an antiparallel arrangement. We speculate that the RdRp dimer facilitates template switching during production of sub-genomic RNAs.
MeSH term(s)	Dimerization ; Humans ; RNA-Dependent RNA Polymerase/chemistry ; RNA-Dependent RNA Polymerase/metabolism ; SARS-CoV-2/enzymology
Chemical Substances	RNA-Dependent RNA Polymerase (EC 2.7.7.48)
Language	English
Publishing date	2021-08-24
Publishing country	England
Document type	Journal Article
ISSN	2399-3642
ISSN (online)	2399-3642
DOI	10.1038/s42003-021-02529-9
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Article ; Online: Mechanism of molnupiravir-induced SARS-CoV-2 mutagenesis.

Kabinger, Florian / Stiller, Carina / Schmitzová, Jana / Dienemann, Christian / Kokic, Goran / Hillen, Hauke S / Höbartner, Claudia / Cramer, Patrick

Nature structural & molecular biology

2021 Volume 28, Issue 9, Page(s) 740–746

Abstract: Molnupiravir is an orally available antiviral drug candidate currently in phase III trials for the treatment of patients with COVID-19. Molnupiravir increases the frequency of viral RNA mutations and impairs SARS-CoV-2 replication in animal models and in ...

Abstract	Molnupiravir is an orally available antiviral drug candidate currently in phase III trials for the treatment of patients with COVID-19. Molnupiravir increases the frequency of viral RNA mutations and impairs SARS-CoV-2 replication in animal models and in humans. Here, we establish the molecular mechanisms underlying molnupiravir-induced RNA mutagenesis by the viral RNA-dependent RNA polymerase (RdRp). Biochemical assays show that the RdRp uses the active form of molnupiravir, β-D-N
MeSH term(s)	Animals ; Antiviral Agents/chemistry ; Antiviral Agents/metabolism ; Antiviral Agents/pharmacology ; Base Sequence ; COVID-19/prevention & control ; COVID-19/virology ; Cytidine/analogs & derivatives ; Cytidine/chemistry ; Cytidine/metabolism ; Cytidine/pharmacology ; Humans ; Hydroxylamines/chemistry ; Hydroxylamines/metabolism ; Hydroxylamines/pharmacology ; Models, Molecular ; Molecular Structure ; Mutagenesis/drug effects ; Mutagenesis/genetics ; Mutation/drug effects ; Mutation/genetics ; Nucleic Acid Conformation ; Protein Binding/drug effects ; Protein Conformation ; RNA, Viral/chemistry ; RNA, Viral/genetics ; RNA, Viral/metabolism ; RNA-Dependent RNA Polymerase/chemistry ; RNA-Dependent RNA Polymerase/genetics ; RNA-Dependent RNA Polymerase/metabolism ; SARS-CoV-2/drug effects ; SARS-CoV-2/genetics ; SARS-CoV-2/physiology ; Virus Replication/drug effects ; Virus Replication/genetics ; COVID-19 Drug Treatment
Chemical Substances	Antiviral Agents ; Hydroxylamines ; RNA, Viral ; Cytidine (5CSZ8459RP) ; RNA-Dependent RNA Polymerase (EC 2.7.7.48) ; molnupiravir (YA84KI1VEW)
Language	English
Publishing date	2021-08-11
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2126708-X
ISSN	1545-9985 ; 1545-9993
ISSN (online)	1545-9985
ISSN	1545-9993
DOI	10.1038/s41594-021-00651-0
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Article ; Online: Structure of replicating SARS-CoV-2 polymerase

Hillen, Hauke S. / Kokic, Goran / Farnung, Lucas / Dienemann, Christian / Tegunov, Dimitry / Cramer, Patrick

Nature

2020 Volume 584, Issue 7819, Page(s) 154–156

Keywords	Multidisciplinary ; covid19
Language	English
Publisher	Springer Science and Business Media LLC
Publishing country	us
Document type	Article ; Online
ZDB-ID	120714-3
ISSN	1476-4687 ; 0028-0836
ISSN (online)	1476-4687
ISSN	0028-0836
DOI	10.1038/s41586-020-2368-8
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: The structure of a dimeric form of SARS-CoV-2 polymerase

Florian A. Jochheim / Dimitry Tegunov / Hauke S. Hillen / Jana Schmitzová / Goran Kokic / Christian Dienemann / Patrick Cramer

Communications Biology, Vol 4, Iss 1, Pp 1-

2021 Volume 5

Abstract: Jochheim et al report an alternative, dimeric form of the coronavirus SARS-CoV-2 RNA dependent RNA polymerase (RdRp), which is used to replicate and transcribe its genome. They resolve its structure at 5.5 Å resolution and speculate that the dimer ... ...

Abstract	Jochheim et al report an alternative, dimeric form of the coronavirus SARS-CoV-2 RNA dependent RNA polymerase (RdRp), which is used to replicate and transcribe its genome. They resolve its structure at 5.5 Å resolution and speculate that the dimer facilitates template switching during production of sub-genomic RNAs.
Keywords	Biology (General) ; QH301-705.5
Language	English
Publishing date	2021-08-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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