5VN0 | pdb_00005vn0

Water-forming NADH oxidase from Lactobacillus brevis (LbNOX) bound to NADH.

PDB DOI: https://doi.org/10.2210/pdb5VN0/pdb

Classification: OXIDOREDUCTASE
Organism(s): Levilactobacillus brevis ATCC 367
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2017-04-28 Released: 2017-08-02
Deposition Author(s): Cracan, V., Grabarek, Z.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.225 (Depositor), 0.226 (DCC)
R-Value Work:
0.179 (Depositor), 0.182 (DCC)
R-Value Observed:
0.182 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

A genetically encoded tool for manipulation of NADP(+)/NADPH in living cells.

Cracan, V., Titov, D.V., Shen, H., Grabarek, Z., Mootha, V.K.

(2017) Nat Chem Biol 13: 1088-1095

PubMed: 28805804 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/nchembio.2454
Primary Citation Related Structures:
5VN0, 5VOH

PubMed Abstract:
The redox coenzymes NADH and NADPH are broadly required for energy metabolism, biosynthesis and detoxification. Despite detailed knowledge of specific enzymes and pathways that utilize these coenzymes, a holistic understanding of the regulation and compartmentalization of NADH- and NADPH-dependent pathways is lacking, partly because of a lack of tools with which to investigate these processes in living cells. We have previously reported the use of the naturally occurring Lactobacillus brevis H ₂O-forming NADH oxidase (LbNOX) as a genetic tool for manipulation of the NAD ⁺/NADH ratio in human cells. Here, we present triphosphopyridine nucleotide oxidase (TPNOX), a rationally designed and engineered mutant of LbNOX that is strictly specific to NADPH. We characterized the effects of TPNOX expression on cellular metabolism and used it in combination with LbNOX to show how the redox states of mitochondrial NADPH and NADH pools are connected.

Organizational Affiliation

Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, USA.

Macromolecule Content

Total Structure Weight: 461.7 kDa
Atom Count: 30,845
Modeled Residue Count: 3,593
Deposited Residue Count: 4,144
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD(FAD)-dependent dehydrogenase	A, B, C, D, E A, B, C, D, E, F, G, H	518	Levilactobacillus brevis ATCC 367	Mutation(s): 0 Gene Names: LVIS_1558
UniProt
Find proteins for Q03Q85 (Levilactobacillus brevis (strain ATCC 367 / BCRC 12310 / CIP 105137 / JCM 1170 / LMG 11437 / NCIMB 947 / NCTC 947)) Explore Q03Q85 Go to UniProtKB: Q03Q85
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q03Q85
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download:Ideal Coordinates CCD File SDF format, chain EA [auth F] SDF format, chain I [auth A] SDF format, chain KA [auth G] SDF format, chain N [auth B] SDF format, chain R [auth C] SDF format, chain V [auth D] SDF format, chain OA [auth H] SDF format, chain AA [auth E] MOL2 format, chain EA [auth F] MOL2 format, chain I [auth A] MOL2 format, chain KA [auth G] MOL2 format, chain N [auth B] MOL2 format, chain R [auth C] MOL2 format, chain V [auth D] MOL2 format, chain OA [auth H] MOL2 format, chain AA [auth E] mmCIF format, chain EA [auth F] mmCIF format, chain I [auth A] mmCIF format, chain KA [auth G] mmCIF format, chain N [auth B] mmCIF format, chain R [auth C] mmCIF format, chain V [auth D] mmCIF format, chain OA [auth H] mmCIF format, chain AA [auth E]	AA [auth E] EA [auth F] I [auth A] KA [auth G] N [auth B] AA [auth E], EA [auth F], I [auth A], KA [auth G], N [auth B], OA [auth H], R [auth C], V [auth D]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain AA [auth E] Focus chain EA [auth F] Focus chain I [auth A] Focus chain KA [auth G] Focus chain N [auth B] Focus chain OA [auth H] Focus chain R [auth C] Focus chain V [auth D] Interactions & Density Focus chain AA [auth E] Focus chain EA [auth F] Focus chain I [auth A] Focus chain KA [auth G] Focus chain N [auth B] Focus chain OA [auth H] Focus chain R [auth C] Focus chain V [auth D]
NAI Query on NAI Download:Ideal Coordinates CCD File SDF format, chain CA [auth E] SDF format, chain GA [auth F] SDF format, chain K [auth A] SDF format, chain MA [auth G] SDF format, chain P [auth B] SDF format, chain QA [auth H] SDF format, chain T [auth C] SDF format, chain X [auth D] MOL2 format, chain CA [auth E] MOL2 format, chain GA [auth F] MOL2 format, chain K [auth A] MOL2 format, chain MA [auth G] MOL2 format, chain P [auth B] MOL2 format, chain QA [auth H] MOL2 format, chain T [auth C] MOL2 format, chain X [auth D] mmCIF format, chain CA [auth E] mmCIF format, chain GA [auth F] mmCIF format, chain K [auth A] mmCIF format, chain MA [auth G] mmCIF format, chain P [auth B] mmCIF format, chain QA [auth H] mmCIF format, chain T [auth C] mmCIF format, chain X [auth D]	CA [auth E] GA [auth F] K [auth A] MA [auth G] P [auth B] CA [auth E], GA [auth F], K [auth A], MA [auth G], P [auth B], QA [auth H], T [auth C], X [auth D]	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE C₂₁ H₂₉ N₇ O₁₄ P₂ BOPGDPNILDQYTO-NNYOXOHSSA-N		Interactions Focus chain CA [auth E] Focus chain GA [auth F] Focus chain K [auth A] Focus chain MA [auth G] Focus chain P [auth B] Focus chain QA [auth H] Focus chain T [auth C] Focus chain X [auth D] Interactions & Density Focus chain CA [auth E] Focus chain GA [auth F] Focus chain K [auth A] Focus chain MA [auth G] Focus chain P [auth B] Focus chain QA [auth H] Focus chain T [auth C] Focus chain X [auth D]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain DA [auth E] SDF format, chain HA [auth F] SDF format, chain IA [auth F] SDF format, chain JA [auth F] SDF format, chain M [auth A] SDF format, chain NA [auth G] SDF format, chain Q [auth B] SDF format, chain RA [auth H] SDF format, chain SA [auth H] SDF format, chain U [auth C] SDF format, chain Y [auth D] SDF format, chain Z [auth D] SDF format, chain L [auth A] MOL2 format, chain DA [auth E] MOL2 format, chain HA [auth F] MOL2 format, chain IA [auth F] MOL2 format, chain JA [auth F] MOL2 format, chain M [auth A] MOL2 format, chain NA [auth G] MOL2 format, chain Q [auth B] MOL2 format, chain RA [auth H] MOL2 format, chain SA [auth H] MOL2 format, chain U [auth C] MOL2 format, chain Y [auth D] MOL2 format, chain Z [auth D] MOL2 format, chain L [auth A] mmCIF format, chain DA [auth E] mmCIF format, chain HA [auth F] mmCIF format, chain IA [auth F] mmCIF format, chain JA [auth F] mmCIF format, chain M [auth A] mmCIF format, chain NA [auth G] mmCIF format, chain Q [auth B] mmCIF format, chain RA [auth H] mmCIF format, chain SA [auth H] mmCIF format, chain U [auth C] mmCIF format, chain Y [auth D] mmCIF format, chain Z [auth D] mmCIF format, chain L [auth A]	DA [auth E] HA [auth F] IA [auth F] JA [auth F] L [auth A] DA [auth E], HA [auth F], IA [auth F], JA [auth F], L [auth A], M [auth A], NA [auth G], Q [auth B], RA [auth H], SA [auth H], U [auth C], Y [auth D], Z [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain DA [auth E] Focus chain HA [auth F] Focus chain IA [auth F] Focus chain JA [auth F] Focus chain L [auth A] Focus chain M [auth A] Focus chain NA [auth G] Focus chain Q [auth B] Focus chain RA [auth H] Focus chain SA [auth H] Focus chain U [auth C] Focus chain Y [auth D] Focus chain Z [auth D] Interactions & Density Focus chain DA [auth E] Focus chain HA [auth F] Focus chain IA [auth F] Focus chain JA [auth F] Focus chain L [auth A] Focus chain M [auth A] Focus chain NA [auth G] Focus chain Q [auth B] Focus chain RA [auth H] Focus chain SA [auth H] Focus chain U [auth C] Focus chain Y [auth D] Focus chain Z [auth D]
OXY Query on OXY Download:Ideal Coordinates CCD File SDF format, chain BA [auth E] SDF format, chain FA [auth F] SDF format, chain J [auth A] SDF format, chain LA [auth G] SDF format, chain O [auth B] SDF format, chain PA [auth H] SDF format, chain S [auth C] SDF format, chain W [auth D] MOL2 format, chain BA [auth E] MOL2 format, chain FA [auth F] MOL2 format, chain J [auth A] MOL2 format, chain LA [auth G] MOL2 format, chain O [auth B] MOL2 format, chain PA [auth H] MOL2 format, chain S [auth C] MOL2 format, chain W [auth D] mmCIF format, chain BA [auth E] mmCIF format, chain FA [auth F] mmCIF format, chain J [auth A] mmCIF format, chain LA [auth G] mmCIF format, chain O [auth B] mmCIF format, chain PA [auth H] mmCIF format, chain S [auth C] mmCIF format, chain W [auth D]	BA [auth E] FA [auth F] J [auth A] LA [auth G] O [auth B] BA [auth E], FA [auth F], J [auth A], LA [auth G], O [auth B], PA [auth H], S [auth C], W [auth D]	OXYGEN MOLECULE O₂ MYMOFIZGZYHOMD-UHFFFAOYSA-N		Interactions Focus chain BA [auth E] Focus chain FA [auth F] Focus chain J [auth A] Focus chain LA [auth G] Focus chain O [auth B] Focus chain PA [auth H] Focus chain S [auth C] Focus chain W [auth D] Interactions & Density Focus chain BA [auth E] Focus chain FA [auth F] Focus chain J [auth A] Focus chain LA [auth G] Focus chain O [auth B] Focus chain PA [auth H] Focus chain S [auth C] Focus chain W [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.225 (Depositor), 0.226 (DCC)
R-Value Work: 0.179 (Depositor), 0.182 (DCC)
R-Value Observed: 0.182 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.525	α = 63.37
b = 107.511	β = 90.04
c = 119.298	γ = 89.95

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
HKL-2000	data reduction
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2017-08-02

Deposition Author(s):

Cracan, V.

Grabarek, Z.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM099683

Revision History (Full details and data files)

Version 1.0: 2017-08-02
Type: Initial release
Version 1.1: 2017-08-30
Changes: Database references, Refinement description
Version 1.2: 2017-09-27
Changes: Database references
Version 1.3: 2020-01-01
Changes: Author supporting evidence
Version 1.4: 2023-10-04
Changes: Data collection, Database references, Refinement description