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6vcm

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Revision as of 06:11, 22 April 2020

Crystal structure of E.coli RppH-DapF in complex with GTP, Mg2+ and F-

Structural highlights

6vcm is a 2 chain structure with sequence from Ecoli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, , ,
Related:	6vck, 6vcl
Gene:	dapF, b3809, JW5592 (ECOLI), rppH, nudH, ygdP, b2830, JW2798 (ECOLI)
Activity:	Diaminopimelate epimerase, with EC number 5.1.1.7
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

All enzymes face a challenge of discriminating cognate substrates from similar cellular compounds. Finding a correct substrate is especially difficult for the Escherichia coli Nudix hydrolase RppH, which triggers 5'-end-dependent RNA degradation by removing orthophosphate from the 5'-diphosphorylated transcripts. Here we show that RppH binds and slowly hydrolyzes NTPs, NDPs and (p)ppGpp, which each resemble the 5'-end of RNA. A series of X-ray crystal structures of RppH-nucleotide complexes, trapped in conformations either compatible or incompatible with hydrolysis, explain the low reaction rates of mononucleotides and suggest two distinct mechanisms for their hydrolysis. While RppH adopts the same catalytic arrangement with 5'-diphosphorylated nucleotides as with RNA, the enzyme hydrolyzes 5'-triphosphorylated nucleotides by extending the active site with an additional Mg2+ cation, which coordinates another reactive nucleophile. Although the average intracellular pH minimizes the hydrolysis of nucleotides by slowing their reaction with RppH, they nevertheless compete with RNA for binding and differentially inhibit the reactivity of RppH with triphosphorylated and diphosphorylated RNAs. Thus, E. coli RppH integrates various signals, such as competing non-cognate substrates and a stimulatory protein factor DapF, to achieve the differential degradation of transcripts involved in cellular processes important for the adaptation of bacteria to different growth conditions.

Principles of RNA and nucleotide discrimination by the RNA processing enzyme RppH.,Gao A, Vasilyev N, Kaushik A, Duan W, Serganov A Nucleic Acids Res. 2020 Jan 21. pii: 5710779. doi: 10.1093/nar/gkaa024. PMID:31960065^[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, Kaushik A, Duan W, Serganov A. Principles of RNA and nucleotide discrimination by the RNA processing enzyme RppH. Nucleic Acids Res. 2020 Jan 21. pii: 5710779. doi: 10.1093/nar/gkaa024. PMID:31960065 doi:http://dx.doi.org/10.1093/nar/gkaa024

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/6vcm"

@@ Line 3: / Line 3: @@
 <StructureSection load='6vcm' size='340' side='right'caption='[[6vcm]], [[Resolution|resolution]] 2.35&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6vcm]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6VCM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6VCM FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6vcm]] is a 2 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=6VCM OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6VCM 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=F:FLUORIDE+ION'>F</scene>, <scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=F:FLUORIDE+ION'>F</scene>, <scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[6vck|6vck]], [[6vcl|6vcl]]</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">dapF, b3809, JW5592 ([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='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Diaminopimelate_epimerase Diaminopimelate epimerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.1.7 5.1.1.7] </span></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=6vcm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vcm OCA], [http://pdbe.org/6vcm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6vcm RCSB], [http://www.ebi.ac.uk/pdbsum/6vcm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6vcm ProSAT]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6vcm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vcm OCA], [http://pdbe.org/6vcm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6vcm RCSB], [http://www.ebi.ac.uk/pdbsum/6vcm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6vcm ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 25: / Line 26: @@
 </StructureSection>
 [[Category: Diaminopimelate epimerase]]
+[[Category: Ecoli]]
 [[Category: Large Structures]]
 [[Category: Duan, W]]

6vcm

From Proteopedia

Revision as of 06:11, 22 April 2020

Crystal structure of E.coli RppH-DapF in complex with GTP, Mg2+ and F-

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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