3PND | pdb_00003pnd

FAD binding by ApbE protein from Salmonella enterica: a new class of FAD binding proteins

PDB DOI: https://doi.org/10.2210/pdb3PND/pdb

Classification: PROTEIN BINDING
Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-11-18 Released: 2011-01-05
Deposition Author(s): Boyd, J.M., Endrizzi, J.A., Hamilton, T.L., Christopherson, M.R., Mulder, D.W., Downs, D.M., Peters, J.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free:
0.254 (Depositor), 0.258 (DCC)
R-Value Work:
0.202 (Depositor), 0.205 (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

FAD binding by ApbE protein from Salmonella enterica: a new class of FAD-binding proteins.

Boyd, J.M., Endrizzi, J.A., Hamilton, T.L., Christopherson, M.R., Mulder, D.W., Downs, D.M., Peters, J.W.

(2011) J Bacteriol 193: 887-895

PubMed: 21148731 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1128/JB.00730-10
Primary Citation Related Structures:
3PND

PubMed Abstract:
The periplasmic protein ApbE was identified through the analysis of several mutants defective in thiamine biosynthesis and was implicated as having a role in iron-sulfur cluster biosynthesis or repair. While mutations in apbE cause decreased activity of several iron-sulfur enzymes in vivo, the specific role of ApbE remains unknown. Members of the AbpE family include NosX and RnfF, which have been implicated in oxidation-reduction associated with nitrous oxide and nitrogen metabolism, respectively. In this work, we show that ApbE binds one FAD molecule per monomeric unit. The structure of ApbE in the presence of bound FAD reveals a new FAD-binding motif. Protein variants that are nonfunctional in vivo were generated by random and targeted mutagenesis. Each variant was substituted in the environment of the FAD and analyzed for FAD binding after reconstitution. The variant that altered a key tyrosine residue involved in FAD binding prevented reconstitution of the protein.

Organizational Affiliation

Department of Bacteriology, University of Wisconsin, Madison, WI 53706, USA.

Macromolecule Content

Total Structure Weight: 155.31 kDa
Atom Count: 10,442
Modeled Residue Count: 1,259
Deposited Residue Count: 1,348
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thiamine biosynthesis lipoprotein ApbE	A, B, C, D	337	Salmonella enterica subsp. enterica serovar Typhimurium	Mutation(s): 0 Gene Names: apbE, STM2266 EC: 2.7.1.180
UniProt
Find proteins for P41780 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore P41780 Go to UniProtKB: P41780
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P41780
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download:Ideal Coordinates CCD File SDF format, chain CA [auth B] SDF format, chain L [auth A] SDF format, chain NA [auth C] SDF format, chain WA [auth D] MOL2 format, chain CA [auth B] MOL2 format, chain L [auth A] MOL2 format, chain NA [auth C] MOL2 format, chain WA [auth D] mmCIF format, chain CA [auth B] mmCIF format, chain L [auth A] mmCIF format, chain NA [auth C] mmCIF format, chain WA [auth D]	CA [auth B], L [auth A], NA [auth C], WA [auth D]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain CA [auth B] Focus chain L [auth A] Focus chain NA [auth C] Focus chain WA [auth D] Interactions & Density Focus chain CA [auth B] Focus chain L [auth A] Focus chain NA [auth C] Focus chain WA [auth D]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain BA [auth B] SDF format, chain DA [auth B] SDF format, chain E [auth A] SDF format, chain EA [auth B] SDF format, chain F [auth A] SDF format, chain FA [auth C] SDF format, chain G [auth A] SDF format, chain GA [auth C] SDF format, chain H [auth A] SDF format, chain HA [auth C] SDF format, chain I [auth A] SDF format, chain IA [auth C] SDF format, chain J [auth A] SDF format, chain JA [auth C] SDF format, chain K [auth A] SDF format, chain KA [auth C] SDF format, chain LA [auth C] SDF format, chain M [auth A] SDF format, chain MA [auth C] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain OA [auth C] SDF format, chain P [auth A] SDF format, chain PA [auth C] SDF format, chain Q [auth A] SDF format, chain QA [auth C] SDF format, chain R [auth A] SDF format, chain RA [auth D] SDF format, chain S [auth B] SDF format, chain SA [auth D] SDF format, chain T [auth B] SDF format, chain TA [auth D] SDF format, chain U [auth B] SDF format, chain UA [auth D] SDF format, chain V [auth B] SDF format, chain VA [auth D] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain XA [auth D] SDF format, chain Y [auth B] SDF format, chain YA [auth D] SDF format, chain Z [auth B] SDF format, chain ZA [auth D] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain E [auth A] MOL2 format, chain EA [auth B] MOL2 format, chain F [auth A] MOL2 format, chain FA [auth C] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth C] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth C] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth C] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth C] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth C] MOL2 format, chain LA [auth C] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth C] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth C] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth C] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth C] MOL2 format, chain R [auth A] MOL2 format, chain RA [auth D] MOL2 format, chain S [auth B] MOL2 format, chain SA [auth D] MOL2 format, chain T [auth B] MOL2 format, chain TA [auth D] MOL2 format, chain U [auth B] MOL2 format, chain UA [auth D] MOL2 format, chain V [auth B] MOL2 format, chain VA [auth D] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain XA [auth D] MOL2 format, chain Y [auth B] MOL2 format, chain YA [auth D] MOL2 format, chain Z [auth B] MOL2 format, chain ZA [auth D] mmCIF format, chain AA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain DA [auth B] mmCIF format, chain E [auth A] mmCIF format, chain EA [auth B] mmCIF format, chain F [auth A] mmCIF format, chain FA [auth C] mmCIF format, chain G [auth A] mmCIF format, chain GA [auth C] mmCIF format, chain H [auth A] mmCIF format, chain HA [auth C] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth C] mmCIF format, chain J [auth A] mmCIF format, chain JA [auth C] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth C] mmCIF format, chain LA [auth C] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth C] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain OA [auth C] mmCIF format, chain P [auth A] mmCIF format, chain PA [auth C] mmCIF format, chain Q [auth A] mmCIF format, chain QA [auth C] mmCIF format, chain R [auth A] mmCIF format, chain RA [auth D] mmCIF format, chain S [auth B] mmCIF format, chain SA [auth D] mmCIF format, chain T [auth B] mmCIF format, chain TA [auth D] mmCIF format, chain U [auth B] mmCIF format, chain UA [auth D] mmCIF format, chain V [auth B] mmCIF format, chain VA [auth D] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B] mmCIF format, chain XA [auth D] mmCIF format, chain Y [auth B] mmCIF format, chain YA [auth D] mmCIF format, chain Z [auth B] mmCIF format, chain ZA [auth D]	AA [auth B] BA [auth B] DA [auth B] E [auth A] EA [auth B] AA [auth B], BA [auth B], DA [auth B], E [auth A], EA [auth B], F [auth A], FA [auth C], G [auth A], GA [auth C], H [auth A], HA [auth C], I [auth A], IA [auth C], J [auth A], JA [auth C], K [auth A], KA [auth C], LA [auth C], M [auth A], MA [auth C], N [auth A], O [auth A], OA [auth C], P [auth A], PA [auth C], Q [auth A], QA [auth C], R [auth A], RA [auth D], S [auth B], SA [auth D], T [auth B], TA [auth D], U [auth B], UA [auth D], V [auth B], VA [auth D], W [auth B], X [auth B], XA [auth D], Y [auth B], YA [auth D], Z [auth B], ZA [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain DA [auth B] Focus chain E [auth A] Focus chain EA [auth B] Focus chain F [auth A] Focus chain FA [auth C] Focus chain G [auth A] Focus chain GA [auth C] Focus chain H [auth A] Focus chain HA [auth C] Focus chain I [auth A] Focus chain IA [auth C] Focus chain J [auth A] Focus chain JA [auth C] Focus chain K [auth A] Focus chain KA [auth C] Focus chain LA [auth C] Focus chain M [auth A] Focus chain MA [auth C] Focus chain N [auth A] Focus chain O [auth A] Focus chain OA [auth C] Focus chain P [auth A] Focus chain PA [auth C] Focus chain Q [auth A] Focus chain QA [auth C] Focus chain R [auth A] Focus chain RA [auth D] Focus chain S [auth B] Focus chain SA [auth D] Focus chain T [auth B] Focus chain TA [auth D] Focus chain U [auth B] Focus chain UA [auth D] Focus chain V [auth B] Focus chain VA [auth D] Focus chain W [auth B] Focus chain X [auth B] Focus chain XA [auth D] Focus chain Y [auth B] Focus chain YA [auth D] Focus chain Z [auth B] Focus chain ZA [auth D] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain DA [auth B] Focus chain E [auth A] Focus chain EA [auth B] Focus chain F [auth A] Focus chain FA [auth C] Focus chain G [auth A] Focus chain GA [auth C] Focus chain H [auth A] Focus chain HA [auth C] Focus chain I [auth A] Focus chain IA [auth C] Focus chain J [auth A] Focus chain JA [auth C] Focus chain K [auth A] Focus chain KA [auth C] Focus chain LA [auth C] Focus chain M [auth A] Focus chain MA [auth C] Focus chain N [auth A] Focus chain O [auth A] Focus chain OA [auth C] Focus chain P [auth A] Focus chain PA [auth C] Focus chain Q [auth A] Focus chain QA [auth C] Focus chain R [auth A] Focus chain RA [auth D] Focus chain S [auth B] Focus chain SA [auth D] Focus chain T [auth B] Focus chain TA [auth D] Focus chain U [auth B] Focus chain UA [auth D] Focus chain V [auth B] Focus chain VA [auth D] Focus chain W [auth B] Focus chain X [auth B] Focus chain XA [auth D] Focus chain Y [auth B] Focus chain YA [auth D] Focus chain Z [auth B] Focus chain ZA [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free: 0.254 (Depositor), 0.258 (DCC)
R-Value Work: 0.202 (Depositor), 0.205 (DCC)
R-Value Observed: 0.205 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.103	α = 90
b = 120.85	β = 90
c = 212.058	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2011-01-05

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-01-05
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2011-11-02
Changes: Database references
Version 1.3: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description