6ISO | pdb_00006iso

Human SIRT3 Recognizing H3K4cr

PDB DOI: https://doi.org/10.2210/pdb6ISO/pdb
Entry: 6ISO supersedes: 4V1C

Classification: HYDROLASE
Organism(s): Homo sapiens, synthetic construct
Expression System: Escherichia coli-Pichia pastoris shuttle vector pPpARG4
Mutation(s): No

Deposited: 2018-11-17 Released: 2019-01-23
Deposition Author(s): Wang, Y., Hao, Q.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.95 Å
R-Value Free:
0.275 (Depositor), 0.273 (DCC)
R-Value Work:
0.221 (Depositor), 0.221 (DCC)
R-Value Observed:
0.224 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Identification of 'erasers' for lysine crotonylated histone marks using a chemical proteomics approach.

Bao, X., Wang, Y., Li, X., Li, X.M., Liu, Z., Yang, T., Wong, C.F., Zhang, J., Hao, Q., Li, X.D.

(2014) Elife 3

PubMed: 25369635 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.7554/eLife.02999
Primary Citation Related Structures:
6ISO

PubMed Abstract:
Posttranslational modifications (PTMs) play a crucial role in a wide range of biological processes. Lysine crotonylation (Kcr) is a newly discovered histone PTM that is enriched at active gene promoters and potential enhancers in mammalian cell genomes. However, the cellular enzymes that regulate the addition and removal of Kcr are unknown, which has hindered further investigation of its cellular functions. Here we used a chemical proteomics approach to comprehensively profile 'eraser' enzymes that recognize a lysine-4 crotonylated histone H3 (H3K4Cr) mark. We found that Sirt1, Sirt2, and Sirt3 can catalyze the hydrolysis of lysine crotonylated histone peptides and proteins. More importantly, Sirt3 functions as a decrotonylase to regulate histone Kcr dynamics and gene transcription in living cells. This discovery not only opens opportunities for examining the physiological significance of histone Kcr, but also helps to unravel the unknown cellular mechanisms controlled by Sirt3, that have previously been considered solely as a deacetylase.

Organizational Affiliation

Department of Chemistry, University of Hong Kong, Hong Kong, Hong Kong.

Macromolecule Content

Total Structure Weight: 189.69 kDa
Atom Count: 12,241
Modeled Residue Count: 1,535
Deposited Residue Count: 1,692
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD-dependent protein deacetylase sirtuin-3, mitochondrial	A C [auth B] E H [auth G] J [auth I] A, C [auth B], E, H [auth G], J [auth I], L [auth K]	275	Homo sapiens	Mutation(s): 0 Gene Names: SIRT3, SIR2L3 EC: 3.5.1 (PDB Primary Data), 2.3.1 (UniProt), 2.3.1.286 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NTG7 (Homo sapiens) Explore Q9NTG7 Go to UniProtKB: Q9NTG7
PHAROS: Q9NTG7 GTEx: ENSG00000142082
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9NTG7
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ARG-THR-LYS-GLN-THR-ALA-ARG	B [auth C] D F G [auth H] I [auth L] B [auth C], D, F, G [auth H], I [auth L], K [auth J]	7	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain O [auth B] SDF format, chain V [auth G] SDF format, chain R [auth E] SDF format, chain AA [auth K] MOL2 format, chain O [auth B] MOL2 format, chain V [auth G] MOL2 format, chain R [auth E] MOL2 format, chain AA [auth K] mmCIF format, chain O [auth B] mmCIF format, chain V [auth G] mmCIF format, chain R [auth E] mmCIF format, chain AA [auth K]	AA [auth K], O [auth B], R [auth E], V [auth G]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth K] Focus chain O [auth B] Focus chain R [auth E] Focus chain V [auth G] Interactions & Density Focus chain AA [auth K] Focus chain O [auth B] Focus chain R [auth E] Focus chain V [auth G]
CRD Query on CRD Download:Ideal Coordinates CCD File SDF format, chain X [auth L] SDF format, chain Z [auth J] SDF format, chain U [auth H] SDF format, chain T [auth F] SDF format, chain Q [auth D] SDF format, chain N [auth C] MOL2 format, chain X [auth L] MOL2 format, chain Z [auth J] MOL2 format, chain U [auth H] MOL2 format, chain T [auth F] MOL2 format, chain Q [auth D] MOL2 format, chain N [auth C] mmCIF format, chain X [auth L] mmCIF format, chain Z [auth J] mmCIF format, chain U [auth H] mmCIF format, chain T [auth F] mmCIF format, chain Q [auth D] mmCIF format, chain N [auth C]	N [auth C] Q [auth D] T [auth F] U [auth H] X [auth L] N [auth C], Q [auth D], T [auth F], U [auth H], X [auth L], Z [auth J]	(2E)-BUT-2-ENAL C₄ H₆ O MLUCVPSAIODCQM-NSCUHMNNSA-N		Interactions Focus chain N [auth C] Focus chain Q [auth D] Focus chain T [auth F] Focus chain U [auth H] Focus chain X [auth L] Focus chain Z [auth J] Interactions & Density Focus chain N [auth C] Focus chain Q [auth D] Focus chain T [auth F] Focus chain U [auth H] Focus chain X [auth L] Focus chain Z [auth J]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain P [auth B] SDF format, chain Y [auth I] SDF format, chain W [auth G] SDF format, chain S [auth E] MOL2 format, chain M [auth A] MOL2 format, chain P [auth B] MOL2 format, chain Y [auth I] MOL2 format, chain W [auth G] MOL2 format, chain S [auth E] mmCIF format, chain M [auth A] mmCIF format, chain P [auth B] mmCIF format, chain Y [auth I] mmCIF format, chain W [auth G] mmCIF format, chain S [auth E]	M [auth A], P [auth B], S [auth E], W [auth G], Y [auth I]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Focus chain P [auth B] Focus chain S [auth E] Focus chain W [auth G] Focus chain Y [auth I] Interactions & Density Focus chain M [auth A] Focus chain P [auth B] Focus chain S [auth E] Focus chain W [auth G] Focus chain Y [auth I]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.95 Å
R-Value Free: 0.275 (Depositor), 0.273 (DCC)
R-Value Work: 0.221 (Depositor), 0.221 (DCC)
R-Value Observed: 0.224 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 138.085	α = 90
b = 138.085	β = 90
c = 225.342	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2019-01-23

Deposition Author(s):

Wang, Y.

Hao, Q.

This entry supersedes: 4V1C

Funding Organization	Location	Grant Number
	Hong Kong	GRF766510

Revision History (Full details and data files)

Version 1.0: 2019-01-23
Type: Initial release
Version 1.1: 2023-11-22
Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2024-11-20
Changes: Structure summary