PDBsum entry 4zux

Hydrolase/DNA

PDB id: 4zux

Contents

Protein chains

97 a.a.

83 a.a.

103 a.a.

95 a.a.

78 a.a.

447 a.a.

89 a.a.

90 a.a.

76 a.a.

82 a.a.

90 a.a.

89 a.a.

85 a.a.

DNA/RNA

Metals

_ZN ×32

PDB id:

4zux

Name:

Hydrolase/DNA

Title:

Saga dub module ubp8/sgf11/sus1/sgf73 bound to ubiqitinated nucleosome

Structure:

Histone h3.2. Chain: a, e, k, o. Engineered: yes. Histone h4. Chain: b, f, l, p. Engineered: yes. Histone h2a type 1. Chain: c, g, m, q. Engineered: yes.

Source:

Xenopus laevis. African clawed frog. Organism_taxid: 8355. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic construct. Organism_taxid: 32630. Saccharomyces cerevisiae (strain atcc 204508 / s288c).

Resolution:

3.82Å R-factor: 0.237 R-free: 0.256

Authors:

M.Morgan,C.Wolberger

Key ref:

M.T.Morgan et al. (2016). Structural basis for histone H2B deubiquitination by the SAGA DUB module. Science, 351, 725-728. PubMed id: 26912860 DOI: 10.1126/science.aac5681

Date:

17-May-15 Release date: 24-Feb-16

Protein chains

P84233  (H32_XENLA) -  Histone H3.2 from Xenopus laevis

Seq: 136 a.a.

Struc: 97 a.a.*

Protein chains

P62799  (H4_XENLA) -  Histone H4 from Xenopus laevis

Seq: 103 a.a.

Struc: 83 a.a.

Protein chains

P06897  (H2A1_XENLA) -  Histone H2A type 1 from Xenopus laevis

Seq: 130 a.a.

Struc: 103 a.a.*

Protein chains

P02281  (H2B11_XENLA) -  Histone H2B 1.1 from Xenopus laevis

Seq: 126 a.a.

Struc: 95 a.a.*

Protein chains

P62799  (H4_XENLA) -  Histone H4 from Xenopus laevis

Seq: 103 a.a.

Struc: 78 a.a.

Protein chains

P50102  (UBP8_YEAST) -  Ubiquitin carboxyl-terminal hydrolase 8 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 471 a.a.

Struc: 447 a.a.*

Protein chain

Q6WNK7  (SUS1_YEAST) -  Transcription and mRNA export factor SUS1 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 96 a.a.

Struc: 89 a.a.

Protein chains

Q03067  (SGF11_YEAST) -  SAGA-associated factor 11 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 99 a.a.

Struc: 90 a.a.

Protein chains

P0CG47  (UBB_HUMAN) -  Polyubiquitin-B from Homo sapiens

Seq: 229 a.a.

Struc: 76 a.a.

Protein chain

P53165  (SGF73_YEAST) -  SAGA-associated factor 73 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 657 a.a.

Struc: 82 a.a.

Protein chains

Q6WNK7  (SUS1_YEAST) -  Transcription and mRNA export factor SUS1 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 96 a.a.

Struc: 90 a.a.

Protein chains

P53165  (SGF73_YEAST) -  SAGA-associated factor 73 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 657 a.a.

Struc: 89 a.a.

Protein chain

Q6WNK7  (SUS1_YEAST) -  Transcription and mRNA export factor SUS1 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 96 a.a.

Struc: 85 a.a.

* PDB and UniProt seqs differ at 4 residue positions (black crosses)

DNA/RNA chains

A-T-C-A-G-A-A-T-C-C-C-G-G-T-G-C-C-G-A-G-G-C-C-G-C-T-C-A-A-T-T-G-G-T-C-G-T-A-G- 145 bases

A-T-C-G-A-T-G-T-A-T-A-T-A-T-C-T-G-A-C-A-C-G-T-G-C-C-T-G-G-A-G-A-C-T-A-G-G-G-A- 145 bases

A-T-C-A-G-A-A-T-C-C-C-G-G-T-G-C-C-G-A-G-G-C-C-G-C-T-C-A-A-T-T-G-G-T-C-G-T-A-G- 145 bases

A-T-C-G-A-T-G-T-A-T-A-T-A-T-C-T-G-A-C-A-C-G-T-G-C-C-T-G-G-A-G-A-C-T-A-G-G-G-A- 145 bases

Enzyme reactions

• Enzyme class: Chains U, Z, e, j: E.C.3.4.19.12 - ubiquitinyl hydrolase 1.
• Reaction: Thiol-dependent hydrolysis of ester, thiolester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an intracellular targeting signal).

DOI no: 10.1126/science.aac5681

Science 351:725-728 (2016)

PubMed id: 26912860

Structural basis for histone H2B deubiquitination by the SAGA DUB module.

M.T.Morgan, M.Haj-Yahya, A.E.Ringel, P.Bandi, A.Brik, C.Wolberger.

ABSTRACT

Monoubiquitinated histone H2B plays multiple roles in transcription activation. H2B is deubiquitinated by the Spt-Ada-Gcn5 acetyltransferase (SAGA) coactivator, which contains a four-protein subcomplex known as the deubiquitinating (DUB) module. The crystal structure of the Ubp8/Sgf11/Sus1/Sgf73 DUB module bound to a ubiquitinated nucleosome reveals that the DUB module primarily contacts H2A/H2B, with an arginine cluster on the Sgf11 zinc finger domain docking on the conserved H2A/H2B acidic patch. The Ubp8 catalytic domain mediates additional contacts with H2B, as well as with the conjugated ubiquitin. We find that the DUB module deubiquitinates H2B both in the context of the nucleosome and in H2A/H2B dimers complexed with the histone chaperone, FACT, suggesting that SAGA could target H2B at multiple stages of nucleosome disassembly and reassembly during transcription.