7x8k

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

Structural highlights

7x8k is a 4 chain structure with sequence from Arabidopsis thaliana. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 3Å
Ligands:FLC, GDD, PPV, SO4
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

GMPP1_ARATH Essential protein during embryogenesis (PubMed:15266054). Catalyzes a reaction of the Smirnoff-Wheeler pathway, the major route to ascorbate biosynthesis in plants. Plays an essential role in plant growth and development and cell-wall architecture. Provides GDP-mannose, used for cell wall carbohydrate biosynthesis, protein N-glycosylation, as well as for the biosynthesis of the antioxidant ascorbate.[1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12]

Publication Abstract from PubMed

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 A, 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 beta-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.

Crystal Structures of Arabidopsis thaliana GDP-D-Mannose Pyrophosphorylase VITAMIN C DEFECTIVE 1.,Zhang C, Zhao S, Li YS, He C, Wang X, Liu L Front Plant Sci. 2022 May 23;13:899738. doi: 10.3389/fpls.2022.899738., eCollection 2022. PMID:35677252[13]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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References

  1. ↑ Conklin PL, Norris SR, Wheeler GL, Williams EH, Smirnoff N, Last RL. Genetic evidence for the role of GDP-mannose in plant ascorbic acid (vitamin C) biosynthesis. Proc Natl Acad Sci U S A. 1999 Mar 30;96(7):4198-203. doi:, 10.1073/pnas.96.7.4198. PMID:10097187 doi:http://dx.doi.org/10.1073/pnas.96.7.4198
  2. ↑ Conklin PL, Saracco SA, Norris SR, Last RL. Identification of ascorbic acid-deficient Arabidopsis thaliana mutants. Genetics. 2000 Feb;154(2):847-56. doi: 10.1093/genetics/154.2.847. PMID:10655235 doi:http://dx.doi.org/10.1093/genetics/154.2.847
  3. ↑ Lukowitz W, Nickle TC, Meinke DW, Last RL, Conklin PL, Somerville CR. Arabidopsis cyt1 mutants are deficient in a mannose-1-phosphate guanylyltransferase and point to a requirement of N-linked glycosylation for cellulose biosynthesis. Proc Natl Acad Sci U S A. 2001 Feb 27;98(5):2262-7. doi: 10.1073/pnas.051625798. , Epub 2001 Feb 20. PMID:11226227 doi:http://dx.doi.org/10.1073/pnas.051625798
  4. ↑ Pastori GM, Kiddle G, Antoniw J, Bernard S, Veljovic-Jovanovic S, Verrier PJ, Noctor G, Foyer CH. Leaf vitamin C contents modulate plant defense transcripts and regulate genes that control development through hormone signaling. Plant Cell. 2003 Apr;15(4):939-51. doi: 10.1105/tpc.010538. PMID:12671089 doi:http://dx.doi.org/10.1105/tpc.010538
  5. ↑ Barth C, Moeder W, Klessig DF, Conklin PL. The timing of senescence and response to pathogens is altered in the ascorbate-deficient Arabidopsis mutant vitamin c-1. Plant Physiol. 2004 Apr;134(4):1784-92. doi: 10.1104/pp.103.032185. Epub 2004 Apr, 2. PMID:15064386 doi:http://dx.doi.org/10.1104/pp.103.032185
  6. ↑ Tzafrir I, Pena-Muralla R, Dickerman A, Berg M, Rogers R, Hutchens S, Sweeney TC, McElver J, Aux G, Patton D, Meinke D. Identification of genes required for embryo development in Arabidopsis. Plant Physiol. 2004 Jul;135(3):1206-20. doi: 10.1104/pp.104.045179. PMID:15266054 doi:http://dx.doi.org/10.1104/pp.104.045179
  7. ↑ Pavet V, Olmos E, Kiddle G, Mowla S, Kumar S, Antoniw J, Alvarez ME, Foyer CH. Ascorbic acid deficiency activates cell death and disease resistance responses in Arabidopsis. Plant Physiol. 2005 Nov;139(3):1291-303. doi: 10.1104/pp.105.067686. Epub 2005, Oct 21. PMID:16244149 doi:http://dx.doi.org/10.1104/pp.105.067686
  8. ↑ Olmos E, Kiddle G, Pellny T, Kumar S, Foyer Ch. Modulation of plant morphology, root architecture, and cell structure by low vitamin C in Arabidopsis thaliana. J Exp Bot. 2006;57(8):1645-55. doi: 10.1093/jxb/erl010. Epub 2006 May 23. PMID:16720601 doi:http://dx.doi.org/10.1093/jxb/erl010
  9. ↑ Colville L, Smirnoff N. Antioxidant status, peroxidase activity, and PR protein transcript levels in ascorbate-deficient Arabidopsis thaliana vtc mutants. J Exp Bot. 2008;59(14):3857-68. doi: 10.1093/jxb/ern229. Epub 2008 Oct 9. PMID:18849295 doi:http://dx.doi.org/10.1093/jxb/ern229
  10. ↑ Qin C, Qian W, Wang W, Wu Y, Yu C, Jiang X, Wang D, Wu P. GDP-mannose pyrophosphorylase is a genetic determinant of ammonium sensitivity in Arabidopsis thaliana. Proc Natl Acad Sci U S A. 2008 Nov 25;105(47):18308-13. doi:, 10.1073/pnas.0806168105. Epub 2008 Nov 14. PMID:19011088 doi:http://dx.doi.org/10.1073/pnas.0806168105
  11. ↑ Conklin PL, Williams EH, Last RL. Environmental stress sensitivity of an ascorbic acid-deficient Arabidopsis mutant. Proc Natl Acad Sci U S A. 1996 Sep 3;93(18):9970-4. doi: 10.1073/pnas.93.18.9970. PMID:8790441 doi:http://dx.doi.org/10.1073/pnas.93.18.9970
  12. ↑ Conklin PL, Pallanca JE, Last RL, Smirnoff N. L-ascorbic acid metabolism in the ascorbate-deficient arabidopsis mutant vtc1. Plant Physiol. 1997 Nov;115(3):1277-85. doi: 10.1104/pp.115.3.1277. PMID:9390448 doi:http://dx.doi.org/10.1104/pp.115.3.1277
  13. ↑ Zhang C, Zhao S, Li YS, He C, Wang X, Liu L. Crystal Structures of Arabidopsis thaliana GDP-D-Mannose Pyrophosphorylase VITAMIN C DEFECTIVE 1. Front Plant Sci. 2022 May 23;13:899738. doi: 10.3389/fpls.2022.899738., eCollection 2022. PMID:35677252 doi:http://dx.doi.org/10.3389/fpls.2022.899738

Contents


PDB ID 7x8k

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