5X20 | pdb_00005x20

The ternary structure of D-mandelate dehydrogenase with NADH and anilino(oxo)acetate

PDB DOI: https://doi.org/10.2210/pdb5X20/pdb

Classification: OXIDOREDUCTASE
Organism(s): Enterococcus faecium DO
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2017-01-29 Released: 2017-04-05
Deposition Author(s): Furukawa, N., Miyanaga, A., Nakajima, M., Taguchi, H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.218 (Depositor), 0.224 (DCC)
R-Value Work:
0.184 (Depositor), 0.194 (DCC)
R-Value Observed:
0.186 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

The ternary complex structure of d-mandelate dehydrogenase with NADH and anilino(oxo)acetate.

Furukawa, N., Miyanaga, A., Nakajima, M., Taguchi, H.

(2017) Biochem Biophys Res Commun 486: 665-670

PubMed: 28327357 Search on PubMed
DOI: https://doi.org/10.1016/j.bbrc.2017.03.088
Primary Citation Related Structures:
5X20

PubMed Abstract:
Enterococcus faecium NAD-dependent d-mandelate dehydrogenase (d-ManDH) belongs to a ketopantoate reductase (KPR)-related d-2-hydroxyacid dehydrogenase family, and exhibits broad substrate specificity toward bulky hydrophobic 2-ketoacids, preferring C3-branched substrates. The ternary complex structure of d-ManDH with NADH and anilino(oxo)acetate (AOA) revealed that the substrate binding induces a shear motion of the N-terminal domain along the C-terminal domain, following the hinge motion induced by the NADH binding, and allows the bound NADH molecule to form favorable interactions with a 2-ketoacid substrate. d-ManDH possesses a sufficiently wide pocket that accommodates the C3 branched side chains of substrates like KPR, but unlike the pocket of KPR, the pocket of d-ManDH comprises an entirely hydrophobic surface and an expanded space, in which the AOA benzene is accommodated. The expanded space mostly comprises a mobile loop structure, which likely modulates the shape and size of the space depending on the substrate.

Organizational Affiliation

Department of Applied Biological Science, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan.

Macromolecule Content

Total Structure Weight: 213.76 kDa
Atom Count: 13,694
Modeled Residue Count: 1,671
Deposited Residue Count: 1,872
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-dehydropantoate 2-reductase	A, B, C, D, E A, B, C, D, E, F	312	Enterococcus faecium DO	Mutation(s): 0 Gene Names: panE, HMPREF0351_10295 EC: 1.1.1.169 (PDB Primary Data), 1.1.1.379 (UniProt), 1.1.1 (UniProt)
UniProt
Find proteins for Q3Y316 (Enterococcus faecium (strain ATCC BAA-472 / TX0016 / DO)) Explore Q3Y316 Go to UniProtKB: Q3Y316
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q3Y316
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download:Ideal Coordinates CCD File SDF format, chain SA [auth E] SDF format, chain R [auth B] SDF format, chain NA [auth D] SDF format, chain G [auth A] SDF format, chain AA [auth C] MOL2 format, chain SA [auth E] MOL2 format, chain R [auth B] MOL2 format, chain NA [auth D] MOL2 format, chain G [auth A] MOL2 format, chain AA [auth C] mmCIF format, chain SA [auth E] mmCIF format, chain R [auth B] mmCIF format, chain NA [auth D] mmCIF format, chain G [auth A] mmCIF format, chain AA [auth C]	AA [auth C], G [auth A], NA [auth D], R [auth B], SA [auth E]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain AA [auth C] Focus chain G [auth A] Focus chain NA [auth D] Focus chain R [auth B] Focus chain SA [auth E] Interactions & Density Focus chain AA [auth C] Focus chain G [auth A] Focus chain NA [auth D] Focus chain R [auth B] Focus chain SA [auth E]
AOT Query on AOT Download:Ideal Coordinates CCD File SDF format, chain TA [auth E] SDF format, chain S [auth B] SDF format, chain OA [auth D] SDF format, chain H [auth A] SDF format, chain BA [auth C] MOL2 format, chain TA [auth E] MOL2 format, chain S [auth B] MOL2 format, chain OA [auth D] MOL2 format, chain H [auth A] MOL2 format, chain BA [auth C] mmCIF format, chain TA [auth E] mmCIF format, chain S [auth B] mmCIF format, chain OA [auth D] mmCIF format, chain H [auth A] mmCIF format, chain BA [auth C]	BA [auth C], H [auth A], OA [auth D], S [auth B], TA [auth E]	2-oxidanylidene-2-phenylazanyl-ethanoic acid C₈ H₇ N O₃ PQJZHMCWDKOPQG-UHFFFAOYSA-N		Interactions Focus chain BA [auth C] Focus chain H [auth A] Focus chain OA [auth D] Focus chain S [auth B] Focus chain TA [auth E] Interactions & Density Focus chain BA [auth C] Focus chain H [auth A] Focus chain OA [auth D] Focus chain S [auth B] Focus chain TA [auth E]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain Z [auth B] SDF format, chain YA [auth E] SDF format, chain Y [auth B] SDF format, chain XA [auth E] SDF format, chain X [auth B] SDF format, chain W [auth B] SDF format, chain RA [auth D] SDF format, chain QA [auth D] SDF format, chain P [auth A] SDF format, chain O [auth A] SDF format, chain N [auth A] SDF format, chain MA [auth C] SDF format, chain LA [auth C] SDF format, chain KA [auth C] SDF format, chain JA [auth C] SDF format, chain IA [auth C] SDF format, chain HA [auth C] SDF format, chain GA [auth C] MOL2 format, chain Z [auth B] MOL2 format, chain YA [auth E] MOL2 format, chain Y [auth B] MOL2 format, chain XA [auth E] MOL2 format, chain X [auth B] MOL2 format, chain W [auth B] MOL2 format, chain RA [auth D] MOL2 format, chain QA [auth D] MOL2 format, chain P [auth A] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain MA [auth C] MOL2 format, chain LA [auth C] MOL2 format, chain KA [auth C] MOL2 format, chain JA [auth C] MOL2 format, chain IA [auth C] MOL2 format, chain HA [auth C] MOL2 format, chain GA [auth C] mmCIF format, chain Z [auth B] mmCIF format, chain YA [auth E] mmCIF format, chain Y [auth B] mmCIF format, chain XA [auth E] mmCIF format, chain X [auth B] mmCIF format, chain W [auth B] mmCIF format, chain RA [auth D] mmCIF format, chain QA [auth D] mmCIF format, chain P [auth A] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain MA [auth C] mmCIF format, chain LA [auth C] mmCIF format, chain KA [auth C] mmCIF format, chain JA [auth C] mmCIF format, chain IA [auth C] mmCIF format, chain HA [auth C] mmCIF format, chain GA [auth C]	GA [auth C] HA [auth C] IA [auth C] JA [auth C] KA [auth C] GA [auth C], HA [auth C], IA [auth C], JA [auth C], KA [auth C], LA [auth C], MA [auth C], N [auth A], O [auth A], P [auth A], QA [auth D], RA [auth D], W [auth B], X [auth B], XA [auth E], Y [auth B], YA [auth E], Z [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain GA [auth C] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain KA [auth C] Focus chain LA [auth C] Focus chain MA [auth C] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain QA [auth D] Focus chain RA [auth D] Focus chain W [auth B] Focus chain X [auth B] Focus chain XA [auth E] Focus chain Y [auth B] Focus chain YA [auth E] Focus chain Z [auth B] Interactions & Density Focus chain GA [auth C] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain KA [auth C] Focus chain LA [auth C] Focus chain MA [auth C] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain QA [auth D] Focus chain RA [auth D] Focus chain W [auth B] Focus chain X [auth B] Focus chain XA [auth E] Focus chain Y [auth B] Focus chain YA [auth E] Focus chain Z [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain ZA [auth F] SDF format, chain WA [auth E] SDF format, chain VA [auth E] SDF format, chain V [auth B] SDF format, chain UA [auth E] SDF format, chain U [auth B] SDF format, chain T [auth B] SDF format, chain Q [auth A] SDF format, chain PA [auth D] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain FA [auth C] SDF format, chain EA [auth C] SDF format, chain DA [auth C] SDF format, chain CA [auth C] MOL2 format, chain ZA [auth F] MOL2 format, chain WA [auth E] MOL2 format, chain VA [auth E] MOL2 format, chain V [auth B] MOL2 format, chain UA [auth E] MOL2 format, chain U [auth B] MOL2 format, chain T [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain PA [auth D] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain FA [auth C] MOL2 format, chain EA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain CA [auth C] mmCIF format, chain ZA [auth F] mmCIF format, chain WA [auth E] mmCIF format, chain VA [auth E] mmCIF format, chain V [auth B] mmCIF format, chain UA [auth E] mmCIF format, chain U [auth B] mmCIF format, chain T [auth B] mmCIF format, chain Q [auth A] mmCIF format, chain PA [auth D] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain FA [auth C] mmCIF format, chain EA [auth C] mmCIF format, chain DA [auth C] mmCIF format, chain CA [auth C]	CA [auth C] DA [auth C] EA [auth C] FA [auth C] I [auth A] CA [auth C], DA [auth C], EA [auth C], FA [auth C], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], PA [auth D], Q [auth A], T [auth B], U [auth B], UA [auth E], V [auth B], VA [auth E], WA [auth E], ZA [auth F]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain PA [auth D] Focus chain Q [auth A] Focus chain T [auth B] Focus chain U [auth B] Focus chain UA [auth E] Focus chain V [auth B] Focus chain VA [auth E] Focus chain WA [auth E] Focus chain ZA [auth F] Interactions & Density Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain PA [auth D] Focus chain Q [auth A] Focus chain T [auth B] Focus chain U [auth B] Focus chain UA [auth E] Focus chain V [auth B] Focus chain VA [auth E] Focus chain WA [auth E] Focus chain ZA [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.218 (Depositor), 0.224 (DCC)
R-Value Work: 0.184 (Depositor), 0.194 (DCC)
R-Value Observed: 0.186 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.3	α = 90
b = 111.95	β = 96.65
c = 108.94	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2017-04-05

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2017-04-05
Type: Initial release
Version 1.1: 2017-12-06
Changes: Data collection, Database references
Version 1.2: 2023-11-22
Changes: Data collection, Database references, Refinement description