7X8K

Arabidopsis GDP-D-mannose pyrophosphorylase (VTC1) structure (product-bound)

PDB DOI: https://doi.org/10.2210/pdb7X8K/pdb

Classification: TRANSFERASE
Organism(s): Arabidopsis thaliana
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-03-13 Released: 2022-05-18
Deposition Author(s): Zhao, S., Zhang, C., Liu, L.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.260
R-Value Work: 0.234
R-Value Observed: 0.235

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal Structures of Arabidopsis thaliana GDP-D-Mannose Pyrophosphorylase VITAMIN C DEFECTIVE 1.

Zhang, C., Zhao, S., Li, Y.S., He, C., Wang, X., Liu, L.

(2022) Front Plant Sci 13: 899738-899738

PubMed: 35677252 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.3389/fpls.2022.899738
Primary Citation of Related Structures:
7X8J, 7X8K

PubMed Abstract:
Plant GDP-D-mannose pyrophosphorylase (GMPase) catalyzes a committed step in ascorbic acid biosynthesis pathway. Arabidopsis thaliana VTC1 is the first genetically characterized plant GMPase and has unique properties when compared with bacterial and animal homologs. Here we present the crystal structures of VTC1 in the unliganded and product-bound states at resolutions of 2.8 and 3.0 Å, respectively. VTC1 dimerizes in a same way like other known GMPases, but dodecamerizes in a previously unobserved arrangement. The interactions to GDP-D-mannose and inorganic pyrophosphate are revealed by the product-bound VTC1 structure. An in vitro GMPase activity assay confirms the regulatory role of the C-terminal left-handed β-helix domain, and structural analyses suggest the models of VTC1 hetero-complex with its interacting proteins. The structural information advances our insights into the different mechanisms involved in VTC1 regulation.

Organizational Affiliation

School of Life Sciences, Anhui University, Hefei, China.

Macromolecule Content

Total Structure Weight: 168.53 kDa
Atom Count: 11,191
Modelled Residue Count: 1,442
Deposited Residue Count: 1,504
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mannose-1-phosphate guanylyltransferase 1	A, B, C, D	376	Arabidopsis thaliana	Mutation(s): 0 Gene Names: CYT1, EMB101, GMP1, HSN1, SOZ1, VTC1, At2g39770, T5I7.7 EC: 2.7.7.13
UniProt
Find proteins for O22287 (Arabidopsis thaliana) Explore O22287 Go to UniProtKB: O22287
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O22287
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GDD (Subject of Investigation/LOI) Query on GDD Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A]	E [auth A]	GUANOSINE-5'-DIPHOSPHATE-ALPHA-D-MANNOSE C₁₆ H₂₅ N₅ O₁₆ P₂ MVMSCBBUIHUTGJ-GDJBGNAASA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
FLC (Subject of Investigation/LOI) Query on FLC Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain S [auth C] MOL2 format, chain F [auth A] MOL2 format, chain S [auth C]	F [auth A], S [auth C]	CITRATE ANION C₆ H₅ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-K		Interactions Focus chain F [auth A] Focus chain S [auth C] Interactions & Density Focus chain F [auth A] Focus chain S [auth C]
PPV (Subject of Investigation/LOI) Query on PPV Download Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain R [auth B] MOL2 format, chain BA [auth D] MOL2 format, chain R [auth B]	BA [auth D], R [auth B]	PYROPHOSPHATE H₄ O₇ P₂ XPPKVPWEQAFLFU-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain R [auth B] Interactions & Density Focus chain BA [auth D] Focus chain R [auth B]
SO4 (Subject of Investigation/LOI) Query on SO4 Download Ideal Coordinates CCD File SDF format, chain AA [auth D] 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 M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain T [auth C] SDF format, chain U [auth C] SDF format, chain V [auth C] SDF format, chain W [auth C] SDF format, chain X [auth D] SDF format, chain Y [auth D] SDF format, chain Z [auth D] MOL2 format, chain AA [auth D] 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 M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain T [auth C] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C] MOL2 format, chain X [auth D] MOL2 format, chain Y [auth D] MOL2 format, chain Z [auth D]	AA [auth D] G [auth A] H [auth A] I [auth A] J [auth A] AA [auth D], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth B], N [auth B], O [auth B], P [auth B], Q [auth B], T [auth C], U [auth C], V [auth C], W [auth C], X [auth D], Y [auth D], Z [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth D] 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 M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth D] Focus chain Y [auth D] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] 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 M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth D] Focus chain Y [auth D] Focus chain Z [auth D]