3UNC | pdb_00003unc

Crystal Structure of Bovine Milk Xanthine Dehydrogenase to 1.65A Resolution

PDB DOI: https://doi.org/10.2210/pdb3UNC/pdb

Classification: OXIDOREDUCTASE
Organism(s): Bos taurus
Mutation(s): No

Deposited: 2011-11-15 Released: 2012-05-09
Deposition Author(s): Eger, B.T., Okamoto, K., Nishino, T., Pai, E.F.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free:
0.196 (Depositor), 0.188 (DCC)
R-Value Work:
0.177 (Depositor), 0.166 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Protein conformational gating of enzymatic activity in xanthine oxidoreductase.

Ishikita, H., Eger, B.T., Okamoto, K., Nishino, T., Pai, E.F.

(2012) J Am Chem Soc 134: 999-1009

PubMed: 22145797 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/ja207173p
Primary Citation Related Structures:
3AX7, 3AX9, 3UNA, 3UNC, 3UNI

PubMed Abstract:
In mammals, xanthine oxidoreductase can exist as xanthine dehydrogenase (XDH) and xanthine oxidase (XO). The two enzymes possess common redox active cofactors, which form an electron transfer (ET) pathway terminated by a flavin cofactor. In spite of identical protein primary structures, the redox potential difference between XDH and XO for the flavin semiquinone/hydroquinone pair (E(sq/hq)) is ~170 mV, a striking difference. The former greatly prefers NAD(+) as ultimate substrate for ET from the iron-sulfur cluster FeS-II via flavin while the latter only accepts dioxygen. In XDH (without NAD(+)), however, the redox potential of the electron donor FeS-II is 180 mV higher than that for the acceptor flavin, yielding an energetically uphill ET. On the basis of new 1.65, 2.3, 1.9, and 2.2 Å resolution crystal structures for XDH, XO, the NAD(+)- and NADH-complexed XDH, E(sq/hq) were calculated to better understand how the enzyme activates an ET from FeS-II to flavin. The majority of the E(sq/hq) difference between XDH and XO originates from a conformational change in the loop at positions 423-433 near the flavin binding site, causing the differences in stability of the semiquinone state. There was no large conformational change observed in response to NAD(+) binding at XDH. Instead, the positive charge of the NAD(+) ring, deprotonation of Asp429, and capping of the bulk surface of the flavin by the NAD(+) molecule all contribute to altering E(sq/hq) upon NAD(+) binding to XDH.

Organizational Affiliation

Career-Path Promotion Unit for Young Life Scientists, Kyoto University, 202 Building E, Graduate School of Medicine, Kyoto 606-8501, Japan. hiro@cp.kyoto-u.ac.jp

Macromolecule Content

Total Structure Weight: 300.01 kDa
Atom Count: 22,475
Modeled Residue Count: 2,575
Deposited Residue Count: 2,664
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Xanthine dehydrogenase/oxidase	A, B	1,332	Bos taurus	Mutation(s): 0 EC: 1.17.1.4 (PDB Primary Data), 1.17.3.2 (PDB Primary Data)
UniProt
Find proteins for P80457 (Bos taurus) Explore P80457 Go to UniProtKB: P80457
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P80457
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain Z [auth B] MOL2 format, chain G [auth A] MOL2 format, chain Z [auth B] mmCIF format, chain G [auth A] mmCIF format, chain Z [auth B]	G [auth A], Z [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain G [auth A] Focus chain Z [auth B] Interactions & Density Focus chain G [auth A] Focus chain Z [auth B]
MTE Query on MTE Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain X [auth B] MOL2 format, chain E [auth A] MOL2 format, chain X [auth B] mmCIF format, chain E [auth A] mmCIF format, chain X [auth B]	E [auth A], X [auth B]	PHOSPHONIC ACIDMONO-(2-AMINO-5,6-DIMERCAPTO-4-OXO-3,7,8A,9,10,10A-HEXAHYDRO-4H-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-7-YLMETHYL)ESTER C₁₀ H₁₄ N₅ O₆ P S₂ HPEUEJRPDGMIMY-IFQPEPLCSA-N		Interactions Focus chain E [auth A] Focus chain X [auth B] Interactions & Density Focus chain E [auth A] Focus chain X [auth B]
FES Query on FES Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain V [auth B] SDF format, chain W [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B]	C [auth A], D [auth A], V [auth B], W [auth B]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain V [auth B] Focus chain W [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain V [auth B] Focus chain W [auth B]
MOS Query on MOS Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain Y [auth B] MOL2 format, chain F [auth A] MOL2 format, chain Y [auth B] mmCIF format, chain F [auth A] mmCIF format, chain Y [auth B]	F [auth A], Y [auth B]	DIOXOTHIOMOLYBDENUM(VI) ION H Mo O₂ S BDSRWPHSAKXXRG-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain Y [auth B] Interactions & Density Focus chain F [auth A] Focus chain Y [auth B]
SAL Query on SAL Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain AA [auth B] MOL2 format, chain H [auth A] MOL2 format, chain AA [auth B] mmCIF format, chain H [auth A] mmCIF format, chain AA [auth B]	AA [auth B], H [auth A]	2-HYDROXYBENZOIC ACID C₇ H₆ O₃ YGSDEFSMJLZEOE-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain H [auth A] Interactions & Density Focus chain AA [auth B] Focus chain H [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain BA [auth B] SDF format, chain CA [auth B] SDF format, chain DA [auth B] SDF format, chain EA [auth B] SDF format, chain FA [auth B] SDF format, chain GA [auth B] SDF format, chain HA [auth B] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain JA [auth B] SDF format, chain K [auth A] SDF format, chain KA [auth B] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain MA [auth B] SDF format, chain N [auth A] SDF format, chain NA [auth B] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain LA [auth B] SDF format, chain IA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain FA [auth B] MOL2 format, chain GA [auth B] MOL2 format, chain HA [auth B] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth B] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth B] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth B] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth B] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain LA [auth B] MOL2 format, chain IA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain DA [auth B] mmCIF format, chain EA [auth B] mmCIF format, chain FA [auth B] mmCIF format, chain GA [auth B] mmCIF format, chain HA [auth B] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain JA [auth B] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth B] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth B] mmCIF format, chain N [auth A] mmCIF format, chain NA [auth B] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF format, chain S [auth A] mmCIF format, chain LA [auth B] mmCIF format, chain IA [auth B]	BA [auth B] CA [auth B] DA [auth B] EA [auth B] FA [auth B] BA [auth B], CA [auth B], DA [auth B], EA [auth B], FA [auth B], GA [auth B], HA [auth B], I [auth A], IA [auth B], J [auth A], JA [auth B], K [auth A], KA [auth B], L [auth A], LA [auth B], M [auth A], MA [auth B], N [auth A], NA [auth B], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain HA [auth B] Focus chain I [auth A] Focus chain IA [auth B] Focus chain J [auth A] Focus chain JA [auth B] Focus chain K [auth A] Focus chain KA [auth B] Focus chain L [auth A] Focus chain LA [auth B] Focus chain M [auth A] Focus chain MA [auth B] Focus chain N [auth A] Focus chain NA [auth B] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Interactions & Density Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain HA [auth B] Focus chain I [auth A] Focus chain IA [auth B] Focus chain J [auth A] Focus chain JA [auth B] Focus chain K [auth A] Focus chain KA [auth B] Focus chain L [auth A] Focus chain LA [auth B] Focus chain M [auth A] Focus chain MA [auth B] Focus chain N [auth A] Focus chain NA [auth B] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A]
CO3 Query on CO3 Download:Ideal Coordinates CCD File SDF format, chain OA [auth B] SDF format, chain T [auth A] MOL2 format, chain OA [auth B] MOL2 format, chain T [auth A] mmCIF format, chain OA [auth B] mmCIF format, chain T [auth A]	OA [auth B], T [auth A]	CARBONATE ION C O₃ BVKZGUZCCUSVTD-UHFFFAOYSA-L		Interactions Focus chain OA [auth B] Focus chain T [auth A] Interactions & Density Focus chain OA [auth B] Focus chain T [auth A]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain PA [auth B] SDF format, chain U [auth A] MOL2 format, chain PA [auth B] MOL2 format, chain U [auth A] mmCIF format, chain PA [auth B] mmCIF format, chain U [auth A]	PA [auth B], U [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain PA [auth B] Focus chain U [auth A] Interactions & Density Focus chain PA [auth B] Focus chain U [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
SAL	BindingDB: 3UNC	Ki: 1.00e+8 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.196 (Depositor), 0.188 (DCC)
R-Value Work: 0.177 (Depositor), 0.166 (DCC)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 167.573	α = 90
b = 124.37	β = 91.02
c = 148.177	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2012-05-09

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-05-09
Type: Initial release
Version 1.1: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description