4R7P | pdb_00004r7p

Human UDP-glucose pyrophosphorylase isoform 1 in complex with UDP-glucose

PDB DOI: https://doi.org/10.2210/pdb4R7P/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2014-08-28 Released: 2015-04-22
Deposition Author(s): Fuehring, J., Cramer, J.T., Schneider, J., Baruch, P., Gerardy-Schahn, R., Fedorov, R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.35 Å
R-Value Free:
0.247 (Depositor), 0.251 (DCC)
R-Value Work:
0.199 (Depositor), 0.205 (DCC)
R-Value Observed:
0.202 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

A Quaternary Mechanism Enables the Complex Biological Functions of Octameric Human UDP-glucose Pyrophosphorylase, a Key Enzyme in Cell Metabolism.

Fuhring, J.I., Cramer, J.T., Schneider, J., Baruch, P., Gerardy-Schahn, R., Fedorov, R.

(null) Sci Rep 5: 9618-9618

PubMed: 25860585 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/srep09618
Primary Citation Related Structures:
4R7P

PubMed Abstract:
In mammals, UDP-glucose pyrophosphorylase (UGP) is the only enzyme capable of activating glucose-1-phosphate (Glc-1-P) to UDP-glucose (UDP-Glc), a metabolite located at the intersection of virtually all metabolic pathways in the mammalian cell. Despite the essential role of its product, the molecular basis of UGP function is poorly understood. Here we report the crystal structure of human UGP in complex with its product UDP-Glc. Beyond providing first insight into the active site architecture, we describe the substrate binding mode and intermolecular interactions in the octameric enzyme that are crucial to its activity. Importantly, the quaternary mechanism identified for human UGP in this study may be common for oligomeric sugar-activating nucleotidyltransferases. Elucidating such mechanisms is essential for understanding nucleotide sugar metabolism and opens the perspective for the development of drugs that specifically inhibit simpler organized nucleotidyltransferases in pathogens.

Organizational Affiliation

Institute for Cellular Chemistry, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany.

Macromolecule Content

Total Structure Weight: 239.45 kDa
Atom Count: 15,591
Modeled Residue Count: 1,935
Deposited Residue Count: 2,104
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UTP--glucose-1-phosphate uridylyltransferase	A, B, C, D	526	Homo sapiens	Mutation(s): 0 Gene Names: UGP2, UGP1 EC: 2.7.7.9
UniProt & NIH Common Fund Data Resources
Find proteins for Q16851 (Homo sapiens) Explore Q16851 Go to UniProtKB: Q16851
PHAROS: Q16851 GTEx: ENSG00000169764
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q16851
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UPG Query on UPG Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	URIDINE-5'-DIPHOSPHATE-GLUCOSE C₁₅ H₂₄ N₂ O₁₇ P₂ HSCJRCZFDFQWRP-JZMIEXBBSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain DA [auth C] SDF format, chain EA [auth C] SDF format, chain F [auth A] SDF format, chain FA [auth C] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain MA [auth D] SDF format, chain NA [auth D] SDF format, chain OA [auth D] SDF format, chain T [auth B] SDF format, chain U [auth B] MOL2 format, chain DA [auth C] MOL2 format, chain EA [auth C] MOL2 format, chain F [auth A] MOL2 format, chain FA [auth C] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain MA [auth D] MOL2 format, chain NA [auth D] MOL2 format, chain OA [auth D] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] mmCIF format, chain DA [auth C] mmCIF format, chain EA [auth C] mmCIF format, chain F [auth A] mmCIF format, chain FA [auth C] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain MA [auth D] mmCIF format, chain NA [auth D] mmCIF format, chain OA [auth D] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B]	DA [auth C] EA [auth C] F [auth A] FA [auth C] G [auth A] DA [auth C], EA [auth C], F [auth A], FA [auth C], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], MA [auth D], NA [auth D], OA [auth D], T [auth B], U [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain DA [auth C] Focus chain EA [auth C] Focus chain F [auth A] Focus chain FA [auth C] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain MA [auth D] Focus chain NA [auth D] Focus chain OA [auth D] Focus chain T [auth B] Focus chain U [auth B] Interactions & Density Focus chain DA [auth C] Focus chain EA [auth C] Focus chain F [auth A] Focus chain FA [auth C] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain MA [auth D] Focus chain NA [auth D] Focus chain OA [auth D] Focus chain T [auth B] Focus chain U [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain BA [auth B] SDF format, chain CA [auth B] SDF format, chain IA [auth C] SDF format, chain JA [auth C] SDF format, chain KA [auth C] SDF format, chain LA [auth C] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain SA [auth D] SDF format, chain TA [auth D] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain IA [auth C] MOL2 format, chain JA [auth C] MOL2 format, chain KA [auth C] MOL2 format, chain LA [auth C] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain SA [auth D] MOL2 format, chain TA [auth D] mmCIF format, chain AA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain IA [auth C] mmCIF format, chain JA [auth C] mmCIF format, chain KA [auth C] mmCIF format, chain LA [auth C] mmCIF format, chain R [auth A] mmCIF format, chain S [auth A] mmCIF format, chain SA [auth D] mmCIF format, chain TA [auth D]	AA [auth B] BA [auth B] CA [auth B] IA [auth C] JA [auth C] AA [auth B], BA [auth B], CA [auth B], IA [auth C], JA [auth C], KA [auth C], LA [auth C], R [auth A], S [auth A], SA [auth D], TA [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain KA [auth C] Focus chain LA [auth C] Focus chain R [auth A] Focus chain S [auth A] Focus chain SA [auth D] Focus chain TA [auth D] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain KA [auth C] Focus chain LA [auth C] Focus chain R [auth A] Focus chain S [auth A] Focus chain SA [auth D] Focus chain TA [auth D]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain HA [auth C] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain RA [auth D] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain Z [auth B] MOL2 format, chain HA [auth C] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain RA [auth D] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] mmCIF format, chain HA [auth C] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain RA [auth D] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth B]	HA [auth C] N [auth A] O [auth A] P [auth A] Q [auth A] HA [auth C], N [auth A], O [auth A], P [auth A], Q [auth A], RA [auth D], V [auth B], W [auth B], X [auth B], Y [auth B], Z [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain HA [auth C] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain RA [auth D] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain HA [auth C] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain RA [auth D] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain GA [auth C] SDF format, chain M [auth A] SDF format, chain PA [auth D] SDF format, chain QA [auth D] MOL2 format, chain GA [auth C] MOL2 format, chain M [auth A] MOL2 format, chain PA [auth D] MOL2 format, chain QA [auth D] mmCIF format, chain GA [auth C] mmCIF format, chain M [auth A] mmCIF format, chain PA [auth D] mmCIF format, chain QA [auth D]	GA [auth C], M [auth A], PA [auth D], QA [auth D]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain GA [auth C] Focus chain M [auth A] Focus chain PA [auth D] Focus chain QA [auth D] Interactions & Density Focus chain GA [auth C] Focus chain M [auth A] Focus chain PA [auth D] Focus chain QA [auth D]