6hxg

From Proteopedia

Jump to: navigation, search

PDX1.2/PDX1.3 complex (intermediate)

Structural highlights

6hxg is a 8 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 1.9Å
Ligands:SO4
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PDX13_ARATH Catalyzes the formation of pyridoxal 5'-phosphate from ribose 5-phosphate (RBP), glyceraldehyde 3-phosphate (G3P) and ammonia. The ammonia is provided by PDX2. Can also use ribulose 5-phosphate and dihydroxyacetone phosphate as substrates, resulting from enzyme-catalyzed isomerization of RBP and G3P, respectively. Also plays an indirect role in resistance to singlet oxygen-generating photosensitizers.[1] [2] [3]

Publication Abstract from PubMed

Pseudoenzymes have burst into the limelight recently as they provide another dimension to regulation of cellular protein activity. In the eudicot plant lineage, the pseudoenzyme PDX1.2 and its cognate enzyme PDX1.3 interact to regulate vitamin B6 biosynthesis. This partnership is important for plant fitness during environmental stress, in particular heat stress. PDX1.2 increases the catalytic activity of PDX1.3, with an overall increase in vitamin B6 biosynthesis. However, the mechanism by which this is achieved is not known. In this study, the Arabidopsis thaliana PDX1.2-PDX1.3 complex was crystallized in the absence and presence of ligands, and attempts were made to solve the X-ray structures. Three PDX1.2-PDX1.3 complex structures are presented: the PDX1.2-PDX1.3 complex as isolated, PDX1.2-PDX1.3-intermediate (in the presence of substrates) and a catalytically inactive complex, PDX1.2-PDX1.3-K97A. Data were also collected from a crystal of a selenomethionine-substituted complex, PDX1.2-PDX1.3-SeMet. In all cases the protein complexes assemble as dodecamers, similar to the recently reported individual PDX1.3 homomer. Intriguingly, the crystals of the protein complex are statistically disordered owing to the high degree of structural similarity of the individual PDX1 proteins, such that the resulting configuration is a composite of both proteins. Despite the differential methionine content, selenomethionine substitution of the PDX1.2-PDX1.3 complex did not resolve the problem. Furthermore, a comparison of the catalytically competent complex with a noncatalytic complex did not facilitate the resolution of the individual proteins. Interestingly, another catalytic lysine in PDX1.3 (Lys165) that pivots between the two active sites in PDX1 (P1 and P2), and the corresponding glutamine (Gln169) in PDX1.2, point towards P1, which is distinctive to the initial priming for catalytic action. This state was previously only observed upon trapping PDX1.3 in a catalytically operational state, as Lys165 points towards P2 in the resting state. Overall, the study shows that the integration of PDX1.2 into a heteromeric dodecamer assembly with PDX1.3 does not cause a major structural deviation from the overall architecture of the homomeric complex. Nonetheless, the structure of the PDX1.2-PDX1.3 complex highlights enhanced flexibility in key catalytic regions for the initial steps of vitamin B6 biosynthesis. This report highlights what may be an intrinsic limitation of X-ray crystallography in the structural investigation of pseudoenzymes.

Crystal structure of the pseudoenzyme PDX1.2 in complex with its cognate enzyme PDX1.3: a total eclipse.,Robinson GC, Kaufmann M, Roux C, Martinez-Font J, Hothorn M, Thore S, Fitzpatrick TB Acta Crystallogr D Struct Biol. 2019 Apr 1;75(Pt 4):400-415. doi:, 10.1107/S2059798319002912. Epub 2019 Apr 4. PMID:30988257[4]

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

Loading citation details..
Citations
reviews cite this structure
No citations found

References

  1. Tambasco-Studart M, Titiz O, Raschle T, Forster G, Amrhein N, Fitzpatrick TB. Vitamin B6 biosynthesis in higher plants. Proc Natl Acad Sci U S A. 2005 Sep 20;102(38):13687-92. Epub 2005 Sep 12. PMID:16157873 doi:http://dx.doi.org/0506228102
  2. Chen H, Xiong L. Pyridoxine is required for post-embryonic root development and tolerance to osmotic and oxidative stresses. Plant J. 2005 Nov;44(3):396-408. PMID:16236150 doi:http://dx.doi.org/TPJ2538
  3. Tambasco-Studart M, Tews I, Amrhein N, Fitzpatrick TB. Functional analysis of PDX2 from Arabidopsis, a glutaminase involved in vitamin B6 biosynthesis. Plant Physiol. 2007 Jun;144(2):915-25. Epub 2007 Apr 27. PMID:17468224 doi:http://dx.doi.org/10.1104/pp.107.096784
  4. Robinson GC, Kaufmann M, Roux C, Martinez-Font J, Hothorn M, Thore S, Fitzpatrick TB. Crystal structure of the pseudoenzyme PDX1.2 in complex with its cognate enzyme PDX1.3: a total eclipse. Acta Crystallogr D Struct Biol. 2019 Apr 1;75(Pt 4):400-415. doi:, 10.1107/S2059798319002912. Epub 2019 Apr 4. PMID:30988257 doi:http://dx.doi.org/10.1107/S2059798319002912

Contents


PDB ID 6hxg

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Personal tools