3F7J | pdb_00003f7j

B.subtilis YvgN

PDB DOI: https://doi.org/10.2210/pdb3F7J/pdb
Entry: 3F7J supersedes: 3B3E

Classification: OXIDOREDUCTASE
Organism(s): Bacillus subtilis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-11-09 Released: 2008-11-25
Deposition Author(s): Zhou, Y.F., Lei, J., Liang, Y.H., Su, X.-D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.255 (Depositor), 0.255 (DCC)
R-Value Work:
0.212 (Depositor), 0.211 (DCC)
R-Value Observed:
0.214 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Structural and biochemical analyses of YvgN and YtbE from Bacillus subtilis

Lei, J., Zhou, Y.F., Li, L.F., Su, X.-D.

(2009) Protein Sci 18: 1792-1800

PubMed: 19585557 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1002/pro.178
Primary Citation Related Structures:
3B3D, 3D3F, 3F7J

PubMed Abstract:
Bacillus subtilis is one of the most studied gram-positive bacteria. In this work, YvgN and YtbE from B. subtilis, assigned as AKR5G1 and AKR5G2 of aldo-keto reductase (AKR) superfamily. AKR catalyzes the NADPH-dependent reduction of aldehyde or aldose substrates to alcohols. YvgN and YtbE were studied by crystallographic and enzymatic analyses. The apo structures of these proteins were determined by molecular replacement, and the structure of holoenzyme YvgN with NADPH was also solved, revealing the conformational changes upon cofactor binding. Our biochemical data suggest both YvgN and YtbE have preferential specificity for derivatives of benzaldehyde, such as nitryl or halogen group substitution at the 2 or 4 positions. These proteins also showed broad catalytic activity on many standard substrates of AKR, such as glyoxal, dihydroxyacetone, and DL-glyceraldehyde, suggesting a possible role in bacterial detoxification.

Organizational Affiliation

National laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing 100871, China.

Macromolecule Content

Total Structure Weight: 64.05 kDa
Atom Count: 5,046
Modeled Residue Count: 552
Deposited Residue Count: 552
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
YvgN protein	A, B	276	Bacillus subtilis	Mutation(s): 0 Gene Names: yvgN EC: 1.1.1 (UniProt), 1.1.1.283 (UniProt)
UniProt
Find proteins for O32210 (Bacillus subtilis (strain 168)) Explore O32210 Go to UniProtKB: O32210
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O32210
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NO3 Query on NO3 Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth B], I [auth B], J [auth B], K [auth B]	NITRATE ION N O₃ NHNBFGGVMKEFGY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B]	L [auth B], M [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain L [auth B] Focus chain M [auth B] Interactions & Density Focus chain L [auth B] Focus chain M [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.255 (Depositor), 0.255 (DCC)
R-Value Work: 0.212 (Depositor), 0.211 (DCC)
R-Value Observed: 0.214 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.656	α = 90
b = 123.075	β = 90
c = 57.239	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
MOLREP	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2008-11-25

Deposition Author(s):

This entry supersedes: 3B3E

Revision History (Full details and data files)

Version 1.0: 2008-11-25
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2014-01-29
Changes: Database references
Version 1.3: 2023-12-27
Changes: Data collection, Database references, Derived calculations