5yjl

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of Arabidopsis glutamyl-tRNA reductase in complex with NADPH and GBP

Structural highlights

5yjl 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 2.7Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

HEM11_ARATH Catalyzes the NADPH-dependent reduction of glutamyl-tRNA(Glu) to glutamate 1-semialdehyde (GSA). Probably involved in the tetrapyrrole synthesis required for the chlorophyll biosynthesis.^[1] ^[2]

Publication Abstract from PubMed

In higher plants, the tetrapyrrole biosynthesis pathway starts from the reaction catalyzed by the rate-limiting enzyme, glutamyl-tRNA(Glu) reductase (GTR). In Arabidopsis thaliana, GTR is controlled by post-transcriptional regulators such as GTR binding protein (GBP), which stimulates AtGTR activity. The NADPH-binding domain of AtGTR undergoes a substantial movement upon GBP binding. Here, we report the crystal structure of AtGTR-NADPH-GBP ternary complex. NADPH binding causes slight structural changes compared with the AtGTR-GBP binary complex, and possibly take a part of the space needed by the substrate glutamyl-tRNA(Glu). The highly reactive sulfhydryl group of the active-site residue Cys144 shows an obvious rotation, which may facilitate the hydride transfer from NADPH to the thioester intermediate to form glutamate-1-semialdehyde. Furthermore, Lys271, Lys274, Ser275, Asn278, and Gln282 of GBP participate in the interaction between AtGTR and GBP, and the stimulating effect of GBP decreased when all of these residues were mutated to Ala. When the Cys144 of AtGTR was mutated to Ser, AtGTR activity could not be detected even in the presence of GBP.

Crystal structure of Arabidopsis thaliana glutamyl-tRNA(Glu) reductase in complex with NADPH and glutamyl-tRNA(Glu) reductase binding protein.,Zhao A, Han F Photosynth Res. 2018 May 21. pii: 10.1007/s11120-018-0518-8. doi:, 10.1007/s11120-018-0518-8. PMID:29785497^[3]

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

References

↑ Ilag LL, Kumar AM, Soll D. Light regulation of chlorophyll biosynthesis at the level of 5-aminolevulinate formation in Arabidopsis. Plant Cell. 1994 Feb;6(2):265-75. PMID:7908550 doi:http://dx.doi.org/10.1105/tpc.6.2.265
↑ Ujwal ML, McCormac AC, Goulding A, Kumar AM, Soll D, Terry MJ. Divergent regulation of the HEMA gene family encoding glutamyl-tRNA reductase in Arabidopsis thaliana: expression of HEMA2 is regulated by sugars, but is independent of light and plastid signalling. Plant Mol Biol. 2002 Sep;50(1):83-91. PMID:12139011
↑ Zhao A, Han F. Crystal structure of Arabidopsis thaliana glutamyl-tRNA(Glu) reductase in complex with NADPH and glutamyl-tRNA(Glu) reductase binding protein. Photosynth Res. 2018 May 21. pii: 10.1007/s11120-018-0518-8. doi:, 10.1007/s11120-018-0518-8. PMID:29785497 doi:http://dx.doi.org/10.1007/s11120-018-0518-8

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5yjl"

Categories: Arabidopsis thaliana | Large Structures | Han F | Zhao A

@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 5yjl is ON HOLD  until Paper Publication
+==Crystal structure of Arabidopsis glutamyl-tRNA reductase in complex with NADPH and GBP==
+<StructureSection load='5yjl' size='340' side='right'caption='[[5yjl]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[5yjl]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YJL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5YJL FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.7&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5yjl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yjl OCA], [https://pdbe.org/5yjl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5yjl RCSB], [https://www.ebi.ac.uk/pdbsum/5yjl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5yjl ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/HEM11_ARATH HEM11_ARATH] Catalyzes the NADPH-dependent reduction of glutamyl-tRNA(Glu) to glutamate 1-semialdehyde (GSA). Probably involved in the tetrapyrrole synthesis required for the chlorophyll biosynthesis.<ref>PMID:7908550</ref> <ref>PMID:12139011</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+In higher plants, the tetrapyrrole biosynthesis pathway starts from the reaction catalyzed by the rate-limiting enzyme, glutamyl-tRNA(Glu) reductase (GTR). In Arabidopsis thaliana, GTR is controlled by post-transcriptional regulators such as GTR binding protein (GBP), which stimulates AtGTR activity. The NADPH-binding domain of AtGTR undergoes a substantial movement upon GBP binding. Here, we report the crystal structure of AtGTR-NADPH-GBP ternary complex. NADPH binding causes slight structural changes compared with the AtGTR-GBP binary complex, and possibly take a part of the space needed by the substrate glutamyl-tRNA(Glu). The highly reactive sulfhydryl group of the active-site residue Cys144 shows an obvious rotation, which may facilitate the hydride transfer from NADPH to the thioester intermediate to form glutamate-1-semialdehyde. Furthermore, Lys271, Lys274, Ser275, Asn278, and Gln282 of GBP participate in the interaction between AtGTR and GBP, and the stimulating effect of GBP decreased when all of these residues were mutated to Ala. When the Cys144 of AtGTR was mutated to Ser, AtGTR activity could not be detected even in the presence of GBP.
-Authors:
+Crystal structure of Arabidopsis thaliana glutamyl-tRNA(Glu) reductase in complex with NADPH and glutamyl-tRNA(Glu) reductase binding protein.,Zhao A, Han F Photosynth Res. 2018 May 21. pii: 10.1007/s11120-018-0518-8. doi:, 10.1007/s11120-018-0518-8. PMID:29785497<ref>PMID:29785497</ref>
-Description:
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
+<div class="pdbe-citations 5yjl" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Arabidopsis thaliana]]
+[[Category: Large Structures]]
+[[Category: Han F]]
+[[Category: Zhao A]]

5yjl

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Current revision

Crystal structure of Arabidopsis glutamyl-tRNA reductase in complex with NADPH and GBP

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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