5XT6

A sulfur-transferring catalytic intermediate of SufS-SufU complex from Bacillus subtilis

PDB DOI: https://doi.org/10.2210/pdb5XT6/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Bacillus subtilis subsp. subtilis str. 168
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2017-06-17 Released: 2017-12-20
Deposition Author(s): Fujishiro, T., Kunichika, K., Takahashi, Y.
Funding Organization(s): JSPS, Sumitomo Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.50 Å
R-Value Free:
0.262 (Depositor), 0.260 (DCC)
R-Value Work:
0.223 (Depositor), 0.220 (DCC)
R-Value Observed:
0.225 (Depositor)

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Zinc-Ligand Swapping Mediated Complex Formation and Sulfur Transfer between SufS and SufU for Iron-Sulfur Cluster Biogenesis in Bacillus subtilis

Fujishiro, T., Terahata, T., Kunichika, K., Yokoyama, N., Maruyama, C., Asai, K., Takahashi, Y.

(2017) J Am Chem Soc 139: 18464-18467

PubMed: 29235855 Search on PubMed
DOI: https://doi.org/10.1021/jacs.7b11307
Primary Citation of Related Structures:
5XT5, 5XT6

PubMed Abstract:
SufU is a zinc-containing protein involved in mobilization of sulfur from SufS for iron-sulfur cluster biogenesis of Bacillus subtilis. Structural basis for the sulfur transfer in SufS-SufU complex was revealed. A zinc-ligand exchange reaction upon SufS-SufU complexation provides a free thiol from Cys41 of SufU as a sulfur acceptor.

Organizational Affiliation

Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University , Shimo-ohkubo 255, Sakura-ku, Saitama 338-8570, Japan.

Macromolecule Content

Total Structure Weight: 128.55 kDa
Atom Count: 8,443
Modelled Residue Count: 1,082
Deposited Residue Count: 1,148
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Zinc-dependent sulfurtransferase SufU	A [auth D]	155	Bacillus subtilis subsp. subtilis str. 168	Mutation(s): 0 Gene Names: sufU, iscU, nifU, yurV, BSU32680 EC: 2
UniProt
Find proteins for O32163 (Bacillus subtilis (strain 168)) Explore O32163 Go to UniProtKB: O32163
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O32163
Sequence Annotations Expand
Reference Sequence LOADING

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cysteine desulfurase SufS	B [auth A], C [auth B]	419	Bacillus subtilis subsp. subtilis str. 168	Mutation(s): 0 Gene Names: sufS, csd, yurW, BSU32690 EC: 2.8.1.7
UniProt
Find proteins for O32164 (Bacillus subtilis (strain 168)) Explore O32164 Go to UniProtKB: O32164
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O32164
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Zinc-dependent sulfurtransferase SufU	D [auth C]	155	Bacillus subtilis subsp. subtilis str. 168	Mutation(s): 0 Gene Names: sufU, iscU, nifU, yurV, BSU32680 EC: 2
UniProt
Find proteins for O32163 (Bacillus subtilis (strain 168)) Explore O32163 Go to UniProtKB: O32163
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O32163
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PDA Query on PDA Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth B] mmCIF format, chain F [auth A] mmCIF format, chain G [auth B]	F [auth A], G [auth B]	2-[(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL)-AMINO]-PROPIONIC ACID C₁₁ H₁₇ N₂ O₇ P WACJCHFWJNNBPR-ZETCQYMHSA-N		Interactions Focus chain F [auth A] Focus chain G [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth B]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain E [auth D] SDF format, chain H [auth C] MOL2 format, chain E [auth D] MOL2 format, chain H [auth C] mmCIF format, chain E [auth D] mmCIF format, chain H [auth C]	E [auth D], H [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth D] Focus chain H [auth C] Interactions & Density Focus chain E [auth D] Focus chain H [auth C]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.50 Å
R-Value Free: 0.262 (Depositor), 0.260 (DCC)
R-Value Work: 0.223 (Depositor), 0.220 (DCC)
R-Value Observed: 0.225 (Depositor)

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.93	α = 90
b = 73.93	β = 90
c = 367.74	γ = 120

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2017-12-20

Deposition Author(s):

Fujishiro, T.

Kunichika, K.

Takahashi, Y.

Funding Organization	Location	Grant Number
JSPS	Japan	15H04472
JSPS	Japan	17K14510
Sumitomo Foundation	Japan	163037

Revision History (Full details and data files)

Version 1.0: 2017-12-20
Type: Initial release
Version 1.1: 2017-12-27
Changes: Database references
Version 1.2: 2018-01-17
Changes: Database references
Version 1.3: 2023-11-22
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.4: 2024-10-23
Changes: Structure summary