6d1v

From Proteopedia

(Difference between revisions)

Revision as of 10:02, 4 December 2019

Crystal structure of E. coli RppH-DapF complex, monomer bound to RNA

Structural highlights

6d1v is a 3 chain structure with sequence from Ecoli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, ,
NonStd Res:
Gene:	dapF (ECOLI), rppH, nudH, ygdP, b2830, JW2798 (ECOLI)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[DAPF_ECOLI] Catalyzes the stereoinversion of LL-2,6-diaminoheptanedioate (L,L-DAP) to meso-diaminoheptanedioate (meso-DAP), a precursor of L-lysine and an essential component of the bacterial peptidoglycan. Only accepts DAP isomers with the L configuration.^[1] ^[2] ^[3] [RPPH_ECOLI] Master regulator of 5'-dependent mRNA decay. Accelerates the degradation of transcripts by removing pyrophosphate from the 5'-end of triphosphorylated RNA, leading to a more labile monophosphorylated state that can stimulate subsequent ribonuclease cleavage. Preferentially hydrolyzes diadenosine penta-phosphate with ATP as one of the reaction products. Also able to hydrolyze diadenosine hexa- and tetra-phosphate. Has no activity on diadenosine tri-phosphate, ADP-ribose, NADH and UDP-glucose. In the meningitis causing strain E.coli K1, has been shown to play a role in HBMEC (human brain microvascular endothelial cells) invasion in vitro.^[4] ^[5]

Publication Abstract from PubMed

Vitally important for controlling gene expression in eukaryotes and prokaryotes, the deprotection of mRNA 5' termini is governed by enzymes whose activity is modulated by interactions with ancillary factors. In Escherichia coli, 5'-end-dependent mRNA degradation begins with the generation of monophosphorylated 5' termini by the RNA pyrophosphohydrolase RppH, which can be stimulated by DapF, a diaminopimelate epimerase involved in amino acid and cell wall biosynthesis. We have determined crystal structures of RppH-DapF complexes and measured rates of RNA deprotection. These studies show that DapF potentiates RppH activity in two ways, depending on the nature of the substrate. Its stimulatory effect on the reactivity of diphosphorylated RNAs, the predominant natural substrates of RppH, requires a substrate long enough to reach DapF in the complex, while the enhanced reactivity of triphosphorylated RNAs appears to involve DapF-induced changes in RppH itself and likewise increases with substrate length. This study provides a basis for understanding the intricate relationship between cellular metabolism and mRNA decay and reveals striking parallels with the stimulation of decapping activity in eukaryotes.

Structural and kinetic insights into stimulation of RppH-dependent RNA degradation by the metabolic enzyme DapF.,Gao A, Vasilyev N, Luciano DJ, Levenson-Palmer R, Richards J, Marsiglia WM, Traaseth NJ, Belasco JG, Serganov A Nucleic Acids Res. 2018 May 4. pii: 4992646. doi: 10.1093/nar/gky327. PMID:29733359^[6]

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

References

↑ Wiseman JS, Nichols JS. Purification and properties of diaminopimelic acid epimerase from Escherichia coli. J Biol Chem. 1984 Jul 25;259(14):8907-14. PMID:6378903
↑ Richaud C, Higgins W, Mengin-Lecreulx D, Stragier P. Molecular cloning, characterization, and chromosomal localization of dapF, the Escherichia coli gene for diaminopimelate epimerase. J Bacteriol. 1987 Apr;169(4):1454-9. PMID:3031013
↑ Lam LK, Arnold LD, Kalantar TH, Kelland JG, Lane-Bell PM, Palcic MM, Pickard MA, Vederas JC. Analogs of diaminopimelic acid as inhibitors of meso-diaminopimelate dehydrogenase and LL-diaminopimelate epimerase. J Biol Chem. 1988 Aug 25;263(24):11814-9. PMID:3042781
↑ Badger JL, Wass CA, Kim KS. Identification of Escherichia coli K1 genes contributing to human brain microvascular endothelial cell invasion by differential fluorescence induction. Mol Microbiol. 2000 Apr;36(1):174-82. PMID:10760174
↑ Deana A, Celesnik H, Belasco JG. The bacterial enzyme RppH triggers messenger RNA degradation by 5' pyrophosphate removal. Nature. 2008 Jan 17;451(7176):355-8. PMID:18202662 doi:http://dx.doi.org/nature06475
↑ Gao A, Vasilyev N, Luciano DJ, Levenson-Palmer R, Richards J, Marsiglia WM, Traaseth NJ, Belasco JG, Serganov A. Structural and kinetic insights into stimulation of RppH-dependent RNA degradation by the metabolic enzyme DapF. Nucleic Acids Res. 2018 May 4. pii: 4992646. doi: 10.1093/nar/gky327. PMID:29733359 doi:http://dx.doi.org/10.1093/nar/gky327

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/6d1v"

@@ Line 1: / Line 1: @@
 ==Crystal structure of E. coli RppH-DapF complex, monomer bound to RNA==
-<StructureSection load='6d1v' size='340' side='right' caption='[[6d1v]], [[Resolution|resolution]] 1.81&Aring;' scene=''>
+<StructureSection load='6d1v' size='340' side='right'caption='[[6d1v]], [[Resolution|resolution]] 1.81&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6d1v]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Eco24 Eco24]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6D1V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6D1V FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6d1v]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6D1V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6D1V FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
 <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=APC:DIPHOSPHOMETHYLPHOSPHONIC+ACID+ADENOSYL+ESTER'>APC</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">dapF ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=331111 ECO24]), rppH, nudH, ygdP, b2830, JW2798 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=331111 ECO24])</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">dapF ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI]), rppH, nudH, ygdP, b2830, JW2798 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>
 <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6d1v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6d1v OCA], [http://pdbe.org/6d1v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6d1v RCSB], [http://www.ebi.ac.uk/pdbsum/6d1v PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6d1v ProSAT]</span></td></tr>
 </table>
@@ Line 24: / Line 24: @@
 __TOC__
 </StructureSection>
-[[Category: Eco24]]
+[[Category: Ecoli]]
+[[Category: Large Structures]]
 [[Category: Gao, A]]
 [[Category: Serganov, A]]

6d1v

From Proteopedia

Revision as of 10:02, 4 December 2019

Crystal structure of E. coli RppH-DapF complex, monomer bound to RNA

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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