4UUB | pdb_00004uub

Crystal structure of zebrafish Sirtuin 5 in complex with 2R-butyl- succinylated CPS1-peptide

PDB DOI: https://doi.org/10.2210/pdb4UUB/pdb

Classification: HYDROLASE
Organism(s): Danio rerio, Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2014-07-25 Released: 2014-08-20
Deposition Author(s): Pannek, M., Gertz, M., Steegborn, C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free:
0.254 (Depositor), 0.255 (DCC)
R-Value Work:
0.203 (Depositor), 0.206 (DCC)
R-Value Observed:
0.205 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Chemical Probing of the Human Sirtuin 5 Active Site Reveals its Substrate Acyl Specificity and Peptide-Based Inhibitors.

Roessler, C., Nowak, T., Pannek, M., Gertz, M., Nguyen, G.T., Scharfe, M., Born, I., Sippl, W., Steegborn, C., Schutkowski, M.

(2014) Angew Chem Int Ed Engl 53: 10728

PubMed: 25111069 Search on PubMed
DOI: https://doi.org/10.1002/anie.201402679
Primary Citation Related Structures:
4UTN, 4UTR, 4UTV, 4UTX, 4UTZ, 4UU7, 4UU8, 4UUA, 4UUB

PubMed Abstract:
Sirtuins are NAD(+)-dependent deacetylases acting as sensors in metabolic pathways and stress response. In mammals there are seven isoforms. The mitochondrial sirtuin 5 is a weak deacetylase but a very efficient demalonylase and desuccinylase; however, its substrate acyl specificity has not been systematically analyzed. Herein, we investigated a carbamoyl phosphate synthetase 1 derived peptide substrate and modified the lysine side chain systematically to determine the acyl specificity of Sirt5. From that point we designed six potent peptide-based inhibitors that interact with the NAD(+) binding pocket. To characterize the interaction details causing the different substrate and inhibition properties we report several X-ray crystal structures of Sirt5 complexed with these peptides. Our results reveal the Sirt5 acyl selectivity and its molecular basis and enable the design of inhibitors for Sirt5.

Organizational Affiliation

Department of Enzymology, Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Strasse 3, 06120 Halle/Saale (Germany).

Macromolecule Content

Total Structure Weight: 62.59 kDa
Atom Count: 4,250
Modeled Residue Count: 534
Deposited Residue Count: 559
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD-DEPENDENT PROTEIN DEACYLASE SIRTUIN-5, MITOCHONDRIAL	A, B	275	Danio rerio	Mutation(s): 0 EC: 3.5.1 (PDB Primary Data), 2.3.1 (UniProt)
UniProt
Find proteins for Q6DHI5 (Danio rerio) Explore Q6DHI5 Go to UniProtKB: Q6DHI5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6DHI5
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CARBAMOYLPHOSPHATE SYNTHETASE I	C [auth D]	9	Homo sapiens	Mutation(s): 1 EC: 6.3.4.16
UniProt & NIH Common Fund Data Resources
Find proteins for P31327 (Homo sapiens) Explore P31327 Go to UniProtKB: P31327
PHAROS: P31327 GTEx: ENSG00000021826
Entity Groups
UniProt Group	P31327
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EPE Query on EPE Download:Ideal Coordinates CCD File SDF format, chain G [auth B] MOL2 format, chain G [auth B] mmCIF format, chain G [auth B]	G [auth B]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Interactions & Density Focus chain G [auth B]
SU8 Query on SU8 Download:Ideal Coordinates CCD File SDF format, chain K [auth D] MOL2 format, chain K [auth D] mmCIF format, chain K [auth D]	K [auth D]	(2R)-2-butylbutanedioic acid C₈ H₁₄ O₄ WOPLHDNLGYOSPG-ZCFIWIBFSA-N		Interactions Focus chain K [auth D] Interactions & Density Focus chain K [auth D]
DMS Query on DMS Download:Ideal Coordinates CCD File SDF format, chain H [auth B] MOL2 format, chain H [auth B] mmCIF format, chain H [auth B]	H [auth B]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Interactions & Density Focus chain H [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain D [auth A] MOL2 format, chain F [auth B] MOL2 format, chain D [auth A] mmCIF format, chain F [auth B] mmCIF format, chain D [auth A]	D [auth A], F [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain E [auth A] MOL2 format, chain J [auth B] MOL2 format, chain E [auth A] mmCIF format, chain J [auth B] mmCIF format, chain E [auth A]	E [auth A], J [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain J [auth B] Interactions & Density Focus chain E [auth A] Focus chain J [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain I [auth B] MOL2 format, chain I [auth B] mmCIF format, chain I [auth B]	I [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Interactions & Density Focus chain I [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.254 (Depositor), 0.255 (DCC)
R-Value Work: 0.203 (Depositor), 0.206 (DCC)
R-Value Observed: 0.205 (Depositor)

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.44	α = 90
b = 87.44	β = 90
c = 315.06	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2014-08-20

Deposition Author(s):

Pannek, M.

Gertz, M.

Steegborn, C.

Revision History (Full details and data files)

Version 1.0: 2014-08-20
Type: Initial release
Version 1.1: 2014-10-08
Changes: Database references, Other
Version 1.2: 2022-12-07
Changes: Database references, Derived calculations, Other
Version 1.3: 2024-01-31
Changes: Data collection, Refinement description