4HWK | pdb_00004hwk

Crystal structure of human sepiapterin reductase in complex with sulfapyridine

PDB DOI: https://doi.org/10.2210/pdb4HWK/pdb

Classification: OXIDOREDUCTASE/ANTIBIOTIC
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2012-11-08 Released: 2013-06-05
Deposition Author(s): Groenlund Pedersen, M., Pojer, F., Johnsson, K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.211 (Depositor), 0.210 (DCC)
R-Value Work:
0.194 (Depositor), 0.194 (DCC)
R-Value Observed:
0.195 (Depositor)

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

Tetrahydrobiopterin biosynthesis as an off-target of sulfa drugs.

Haruki, H., Pedersen, M.G., Gorska, K.I., Pojer, F., Johnsson, K.

(2013) Science 340: 987-991

PubMed: 23704574 Search on PubMed
DOI: https://doi.org/10.1126/science.1232972
Primary Citation Related Structures:
4HWK, 4J7U

PubMed Abstract:
The introduction of sulfa drugs for the chemotherapy of bacterial infections in 1935 revolutionized medicine. Although their mechanism of action is understood, the molecular bases for most of their side effects remain obscure. Here, we report that sulfamethoxazole and other sulfa drugs interfere with tetrahydrobiopterin biosynthesis through inhibition of sepiapterin reductase. Crystal structures of sepiapterin reductase with bound sulfa drugs reveal how structurally diverse sulfa drugs achieve specific inhibition of the enzyme. The effect of sulfa drugs on tetrahydrobiopterin-dependent neurotransmitter biosynthesis in cell-based assays provides a rationale for some of their central nervous system-related side effects, particularly in high-dose sulfamethoxazole therapy of Pneumocystis pneumonia. Our findings reveal an unexpected aspect of the pharmacology of sulfa drugs and might translate into their improved medical use.

Organizational Affiliation

EPFL, Institute of Chemical Sciences and Engineering, Institute of Bioengineering, National Centre of Competence in Research in Chemical Biology, 1015 Lausanne, Switzerland.

Macromolecule Content

Total Structure Weight: 130.85 kDa
Atom Count: 8,479
Modeled Residue Count: 1,028
Deposited Residue Count: 1,152
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sepiapterin reductase	A, B, C, D	288	Homo sapiens	Mutation(s): 0 Gene Names: SPR EC: 1.1.1.153
UniProt & NIH Common Fund Data Resources
Find proteins for P35270 (Homo sapiens) Explore P35270 Go to UniProtKB: P35270
PHAROS: P35270 GTEx: ENSG00000116096
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P35270
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAP Query on NAP Download:Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain E [auth A] SDF format, chain O [auth B] SDF format, chain V [auth C] MOL2 format, chain AA [auth D] MOL2 format, chain E [auth A] MOL2 format, chain O [auth B] MOL2 format, chain V [auth C] mmCIF format, chain AA [auth D] mmCIF format, chain E [auth A] mmCIF format, chain O [auth B] mmCIF format, chain V [auth C]	AA [auth D], E [auth A], O [auth B], V [auth C]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain AA [auth D] Focus chain E [auth A] Focus chain O [auth B] Focus chain V [auth C] Interactions & Density Focus chain AA [auth D] Focus chain E [auth A] Focus chain O [auth B] Focus chain V [auth C]
SFY Query on SFY Download:Ideal Coordinates CCD File SDF format, chain CA [auth D] SDF format, chain K [auth A] SDF format, chain T [auth B] SDF format, chain Y [auth C] MOL2 format, chain CA [auth D] MOL2 format, chain K [auth A] MOL2 format, chain T [auth B] MOL2 format, chain Y [auth C] mmCIF format, chain CA [auth D] mmCIF format, chain K [auth A] mmCIF format, chain T [auth B] mmCIF format, chain Y [auth C]	CA [auth D], K [auth A], T [auth B], Y [auth C]	4-amino-N-(pyridin-2-yl)benzenesulfonamide C₁₁ H₁₁ N₃ O₂ S GECHUMIMRBOMGK-UHFFFAOYSA-N		Interactions Focus chain CA [auth D] Focus chain K [auth A] Focus chain T [auth B] Focus chain Y [auth C] Interactions & Density Focus chain CA [auth D] Focus chain K [auth A] Focus chain T [auth B] Focus chain Y [auth C]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain Z [auth C] MOL2 format, chain N [auth A] MOL2 format, chain Z [auth C] mmCIF format, chain N [auth A] mmCIF format, chain Z [auth C]	N [auth A], Z [auth C]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain N [auth A] Focus chain Z [auth C] Interactions & Density Focus chain N [auth A] Focus chain Z [auth C]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain DA [auth D] SDF format, chain F [auth A] SDF format, chain I [auth A] SDF format, chain L [auth A] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain W [auth C] SDF format, chain P [auth B] MOL2 format, chain BA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain F [auth A] MOL2 format, chain I [auth A] MOL2 format, chain L [auth A] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain W [auth C] MOL2 format, chain P [auth B] mmCIF format, chain BA [auth D] mmCIF format, chain DA [auth D] mmCIF format, chain F [auth A] mmCIF format, chain I [auth A] mmCIF format, chain L [auth A] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain W [auth C] mmCIF format, chain P [auth B]	BA [auth D] DA [auth D] F [auth A] I [auth A] L [auth A] BA [auth D], DA [auth D], F [auth A], I [auth A], L [auth A], P [auth B], R [auth B], S [auth B], W [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain BA [auth D] Focus chain DA [auth D] Focus chain F [auth A] Focus chain I [auth A] Focus chain L [auth A] Focus chain P [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain W [auth C] Interactions & Density Focus chain BA [auth D] Focus chain DA [auth D] Focus chain F [auth A] Focus chain I [auth A] Focus chain L [auth A] Focus chain P [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain W [auth C]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain J [auth A] SDF format, chain M [auth A] SDF format, chain Q [auth B] SDF format, chain X [auth C] SDF format, chain U [auth B] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain J [auth A] MOL2 format, chain M [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain X [auth C] MOL2 format, chain U [auth B] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain J [auth A] mmCIF format, chain M [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain X [auth C] mmCIF format, chain U [auth B]	G [auth A] H [auth A] J [auth A] M [auth A] Q [auth B] G [auth A], H [auth A], J [auth A], M [auth A], Q [auth B], U [auth B], X [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth A] Focus chain M [auth A] Focus chain Q [auth B] Focus chain U [auth B] Focus chain X [auth C] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth A] Focus chain M [auth A] Focus chain Q [auth B] Focus chain U [auth B] Focus chain X [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.211 (Depositor), 0.210 (DCC)
R-Value Work: 0.194 (Depositor), 0.194 (DCC)
R-Value Observed: 0.195 (Depositor)

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 148.452	α = 90
b = 148.452	β = 90
c = 179.717	γ = 120

Software Package:

Software Name	Purpose
XDS	data scaling
PHASER	phasing
REFMAC	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2013-06-05

Deposition Author(s):

Groenlund Pedersen, M.

Pojer, F.

Johnsson, K.

Revision History (Full details and data files)

Version 1.0: 2013-06-05
Type: Initial release
Version 1.1: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description