7Q5N | pdb_00007q5n

Crystal structure of Chaetomium thermophilum Ahp1-Urm1 complex

PDB DOI: https://doi.org/10.2210/pdb7Q5N/pdb

Classification: LIGASE
Organism(s): Thermochaetoides thermophila DSM 1495
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2021-11-04 Released: 2022-08-24
Deposition Author(s): Ravichandran, K.E., Wilk, P., Grudnik, P., Glatt, S.
Funding Organization(s): Foundation for Polish Science, European Research Council (ERC), Polish National Science Centre

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.272 (Depositor), 0.280 (DCC)
R-Value Work:
0.234 (Depositor), 0.244 (DCC)
R-Value Observed:
0.236 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

E2/E3-independent ubiquitin-like protein conjugation by Urm1 is directly coupled to cysteine persulfidation.

Ravichandran, K.E., Kaduhr, L., Skupien-Rabian, B., Shvetsova, E., Sokolowski, M., Krutyholowa, R.C., Kwasna, D., Brachmann, C., Lin, S., Guzman Perez, S., Wilk, P., Kosters, M., Grudnik, P., Jankowska, U., Leidel, S.A., Schaffrath, R., Glatt, S.

(2022) EMBO J 41: e111318-e111318

PubMed: 36102610 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.15252/embj.2022111318
Primary Citation Related Structures:
7Q5N, 7Q68, 7Q69, 7Q6A

PubMed Abstract:
Post-translational modifications by ubiquitin-like proteins (UBLs) are essential for nearly all cellular processes. Ubiquitin-related modifier 1 (Urm1) is a unique UBL, which plays a key role in tRNA anticodon thiolation as a sulfur carrier protein (SCP) and is linked to the noncanonical E1 enzyme Uba4 (ubiquitin-like protein activator 4). While Urm1 has also been observed to conjugate to target proteins like other UBLs, the molecular mechanism of its attachment remains unknown. Here, we reconstitute the covalent attachment of thiocarboxylated Urm1 to various cellular target proteins in vitro, revealing that, unlike other known UBLs, this process is E2/E3-independent and requires oxidative stress. Furthermore, we present the crystal structures of the peroxiredoxin Ahp1 before and after the covalent attachment of Urm1. Surprisingly, we show that urmylation is accompanied by the transfer of sulfur to cysteine residues in the target proteins, also known as cysteine persulfidation. Our results illustrate the role of the Uba4-Urm1 system as a key evolutionary link between prokaryotic SCPs and the UBL modifications observed in modern eukaryotes.

Organizational Affiliation

Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow, Poland.

Macromolecule Content

Total Structure Weight: 186.54 kDa
Atom Count: 12,664
Modeled Residue Count: 1,641
Deposited Residue Count: 1,710
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thioredoxin domain-containing protein	A, B, C, D, E A, B, C, D, E, F	174	Thermochaetoides thermophila DSM 1495	Mutation(s): 1 Gene Names: CTHT_0014370 EC: 1.11.1.24
UniProt
Find proteins for G0S1P8 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)) Explore G0S1P8 Go to UniProtKB: G0S1P8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	G0S1P8
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-related modifier 1	G, H, I, J, K G, H, I, J, K, L	111	Thermochaetoides thermophila DSM 1495	Mutation(s): 1 Gene Names: URM1, CTHT_0062030
UniProt
Find proteins for G0SE11 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)) Explore G0SE11 Go to UniProtKB: G0SE11
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	G0SE11
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain GA [auth H] SDF format, chain HA [auth H] SDF format, chain KA [auth I] SDF format, chain LA [auth I] SDF format, chain M [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain R [auth C] SDF format, chain SA [auth K] SDF format, chain T [auth D] SDF format, chain U [auth D] SDF format, chain UA [auth K] SDF format, chain W [auth E] SDF format, chain ZA [auth L] SDF format, chain Z [auth F] SDF format, chain YA [auth L] SDF format, chain Y [auth F] SDF format, chain XA [auth K] SDF format, chain X [auth E] SDF format, chain WA [auth K] SDF format, chain VA [auth K] SDF format, chain V [auth E] SDF format, chain TA [auth K] SDF format, chain S [auth C] SDF format, chain RA [auth J] SDF format, chain QA [auth J] SDF format, chain Q [auth C] SDF format, chain PA [auth J] SDF format, chain OA [auth J] SDF format, chain NA [auth I] SDF format, chain N [auth B] SDF format, chain MA [auth I] SDF format, chain JA [auth I] SDF format, chain IA [auth H] SDF format, chain FA [auth H] SDF format, chain EA [auth H] SDF format, chain DA [auth H] SDF format, chain CA [auth H] SDF format, chain BA [auth H] SDF format, chain AB [auth L] SDF format, chain AA [auth G] MOL2 format, chain GA [auth H] MOL2 format, chain HA [auth H] MOL2 format, chain KA [auth I] MOL2 format, chain LA [auth I] MOL2 format, chain M [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain R [auth C] MOL2 format, chain SA [auth K] MOL2 format, chain T [auth D] MOL2 format, chain U [auth D] MOL2 format, chain UA [auth K] MOL2 format, chain W [auth E] MOL2 format, chain ZA [auth L] MOL2 format, chain Z [auth F] MOL2 format, chain YA [auth L] MOL2 format, chain Y [auth F] MOL2 format, chain XA [auth K] MOL2 format, chain X [auth E] MOL2 format, chain WA [auth K] MOL2 format, chain VA [auth K] MOL2 format, chain V [auth E] MOL2 format, chain TA [auth K] MOL2 format, chain S [auth C] MOL2 format, chain RA [auth J] MOL2 format, chain QA [auth J] MOL2 format, chain Q [auth C] MOL2 format, chain PA [auth J] MOL2 format, chain OA [auth J] MOL2 format, chain NA [auth I] MOL2 format, chain N [auth B] MOL2 format, chain MA [auth I] MOL2 format, chain JA [auth I] MOL2 format, chain IA [auth H] MOL2 format, chain FA [auth H] MOL2 format, chain EA [auth H] MOL2 format, chain DA [auth H] MOL2 format, chain CA [auth H] MOL2 format, chain BA [auth H] MOL2 format, chain AB [auth L] MOL2 format, chain AA [auth G] mmCIF format, chain GA [auth H] mmCIF format, chain HA [auth H] mmCIF format, chain KA [auth I] mmCIF format, chain LA [auth I] mmCIF format, chain M [auth A] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain R [auth C] mmCIF format, chain SA [auth K] mmCIF format, chain T [auth D] mmCIF format, chain U [auth D] mmCIF format, chain UA [auth K] mmCIF format, chain W [auth E] mmCIF format, chain ZA [auth L] mmCIF format, chain Z [auth F] mmCIF format, chain YA [auth L] mmCIF format, chain Y [auth F] mmCIF format, chain XA [auth K] mmCIF format, chain X [auth E] mmCIF format, chain WA [auth K] mmCIF format, chain VA [auth K] mmCIF format, chain V [auth E] mmCIF format, chain TA [auth K] mmCIF format, chain S [auth C] mmCIF format, chain RA [auth J] mmCIF format, chain QA [auth J] mmCIF format, chain Q [auth C] mmCIF format, chain PA [auth J] mmCIF format, chain OA [auth J] mmCIF format, chain NA [auth I] mmCIF format, chain N [auth B] mmCIF format, chain MA [auth I] mmCIF format, chain JA [auth I] mmCIF format, chain IA [auth H] mmCIF format, chain FA [auth H] mmCIF format, chain EA [auth H] mmCIF format, chain DA [auth H] mmCIF format, chain CA [auth H] mmCIF format, chain BA [auth H] mmCIF format, chain AB [auth L] mmCIF format, chain AA [auth G]	AA [auth G] AB [auth L] BA [auth H] CA [auth H] DA [auth H] AA [auth G], AB [auth L], BA [auth H], CA [auth H], DA [auth H], EA [auth H], FA [auth H], GA [auth H], HA [auth H], IA [auth H], JA [auth I], KA [auth I], LA [auth I], M [auth A], MA [auth I], N [auth B], NA [auth I], O [auth B], OA [auth J], P [auth B], PA [auth J], Q [auth C], QA [auth J], R [auth C], RA [auth J], S [auth C], SA [auth K], T [auth D], TA [auth K], U [auth D], UA [auth K], V [auth E], VA [auth K], W [auth E], WA [auth K], X [auth E], XA [auth K], Y [auth F], YA [auth L], Z [auth F], ZA [auth L]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain AA [auth G] Focus chain AB [auth L] Focus chain BA [auth H] Focus chain CA [auth H] Focus chain DA [auth H] Focus chain EA [auth H] Focus chain FA [auth H] Focus chain GA [auth H] Focus chain HA [auth H] Focus chain IA [auth H] Focus chain JA [auth I] Focus chain KA [auth I] Focus chain LA [auth I] Focus chain M [auth A] Focus chain MA [auth I] Focus chain N [auth B] Focus chain NA [auth I] Focus chain O [auth B] Focus chain OA [auth J] Focus chain P [auth B] Focus chain PA [auth J] Focus chain Q [auth C] Focus chain QA [auth J] Focus chain R [auth C] Focus chain RA [auth J] Focus chain S [auth C] Focus chain SA [auth K] Focus chain T [auth D] Focus chain TA [auth K] Focus chain U [auth D] Focus chain UA [auth K] Focus chain V [auth E] Focus chain VA [auth K] Focus chain W [auth E] Focus chain WA [auth K] Focus chain X [auth E] Focus chain XA [auth K] Focus chain Y [auth F] Focus chain YA [auth L] Focus chain Z [auth F] Focus chain ZA [auth L] Interactions & Density Focus chain AA [auth G] Focus chain AB [auth L] Focus chain BA [auth H] Focus chain CA [auth H] Focus chain DA [auth H] Focus chain EA [auth H] Focus chain FA [auth H] Focus chain GA [auth H] Focus chain HA [auth H] Focus chain IA [auth H] Focus chain JA [auth I] Focus chain KA [auth I] Focus chain LA [auth I] Focus chain M [auth A] Focus chain MA [auth I] Focus chain N [auth B] Focus chain NA [auth I] Focus chain O [auth B] Focus chain OA [auth J] Focus chain P [auth B] Focus chain PA [auth J] Focus chain Q [auth C] Focus chain QA [auth J] Focus chain R [auth C] Focus chain RA [auth J] Focus chain S [auth C] Focus chain SA [auth K] Focus chain T [auth D] Focus chain TA [auth K] Focus chain U [auth D] Focus chain UA [auth K] Focus chain V [auth E] Focus chain VA [auth K] Focus chain W [auth E] Focus chain WA [auth K] Focus chain X [auth E] Focus chain XA [auth K] Focus chain Y [auth F] Focus chain YA [auth L] Focus chain Z [auth F] Focus chain ZA [auth L]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSS Query on CSS	A, B, C, D, E A, B, C, D, E, F	L-PEPTIDE LINKING	C₃ H₇ N O₂ S₂		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.272 (Depositor), 0.280 (DCC)
R-Value Work: 0.234 (Depositor), 0.244 (DCC)
R-Value Observed: 0.236 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 185.43	α = 90
b = 197.22	β = 90
c = 139.18	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2022-08-24

Deposition Author(s):

Funding Organization	Location	Grant Number
Foundation for Polish Science	Poland	TEAM TECH CORE FACILITY/2017-4/6
European Research Council (ERC)	Poland	101001394
Polish National Science Centre	Poland	2018/31/B/NZ1/03559
Foundation for Polish Science	Poland	FirstTEAM/2016-1/2