2gem

From Proteopedia

(Difference between revisions)

Current revision

2.1A crystal structure of Salmonella tyhpimurium YeaZ, a putative Gram-negative RPF, form-A

Structural highlights

2gem is a 2 chain structure with sequence from Salmonella enterica subsp. enterica serovar Typhimurium. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.1Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

TSAB_SALTY Required for the formation of a threonylcarbamoyl group on adenosine at position 37 (t(6)A37) in tRNAs that read codons beginning with adenine. Is involved in the transfer of the threonylcarbamoyl moiety of threonylcarbamoyl-AMP (TC-AMP) to the N6 group of A37, together with TsaD and TsaE; this reaction does not require ATP in vitro. TsaB seems to play an indirect role in the t(6)A biosynthesis pathway, possibly in regulating the core enzymatic function of TsaD (By similarity). Neither binds polyphosphates nor a wide range of nucleotides on its own. Does not show O-sialoglycoprotein endopeptidase activity. Has been identified as the first Gram-negative bacterial RPF (Resuscitation-Promoting Factor) capable of reviving VNC (viable but non-culturable) cells when added externally, but the million-fold lower activity as compared to Gram-positive bacterial RPFs may indicate a lack of physiological relevance.^[1]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

The Salmonella typhimurium "yeaZ" gene (StyeaZ) encodes an essential protein of unknown function (StYeaZ), which has previously been annotated as a putative homolog of the Pasteurella haemolytica M22 O-sialoglycoprotein endopeptidase Gcp. YeaZ has also recently been reported as the first example of an RPF from a gram-negative bacterial species. To further characterize the properties of StYeaZ and the widely occurring MK-M22 family, we describe the purification, biochemical analysis, crystallization, and structure determination of StYeaZ. The crystal structure of StYeaZ reveals a classic two-lobed actin-like fold with structural features consistent with nucleotide binding. However, microcalorimetry experiments indicated that StYeaZ neither binds polyphosphates nor a wide range of nucleotides. Additionally, biochemical assays show that YeaZ is not an active O-sialoglycoprotein endopeptidase, consistent with the lack of the critical zinc binding motif. We present a detailed comparison of YeaZ with available structural homologs, the first reported structural analysis of an MK-M22 family member. The analysis indicates that StYeaZ has an unusual orientation of the A and B lobes which may require substantial relative movement or interaction with a partner protein in order to bind ligands. Comparison of the fold of YeaZ with that of a known RPF domain from a gram-positive species shows significant structural differences and therefore potentially distinctive RPF mechanisms for these two bacterial classes.

Structural characterization of Salmonella typhimurium YeaZ, an M22 O-sialoglycoprotein endopeptidase homolog.,Nichols CE, Johnson C, Lockyer M, Charles IG, Lamb HK, Hawkins AR, Stammers DK Proteins. 2006 Jul 1;64(1):111-23. PMID:16617437^[2]

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

References

↑ Panutdaporn N, Kawamoto K, Asakura H, Makino SI. Resuscitation of the viable but non-culturable state of Salmonella enterica serovar Oranienburg by recombinant resuscitation-promoting factor derived from Salmonella Typhimurium strain LT2. Int J Food Microbiol. 2006 Feb 15;106(3):241-7. Epub 2005 Oct 5. PMID:16213054 doi:http://dx.doi.org/S0168-1605(05)00435-6
↑ Nichols CE, Johnson C, Lockyer M, Charles IG, Lamb HK, Hawkins AR, Stammers DK. Structural characterization of Salmonella typhimurium YeaZ, an M22 O-sialoglycoprotein endopeptidase homolog. Proteins. 2006 Jul 1;64(1):111-23. PMID:16617437 doi:http://dx.doi.org/10.1002/prot.20982

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2gem"

Categories: Large Structures | Salmonella enterica subsp. enterica serovar Typhimurium | Nichols CE | Stammers DK

@@ Line 1: / Line 1: @@
 ==2.1A crystal structure of Salmonella tyhpimurium YeaZ, a putative Gram-negative RPF, form-A==
-<StructureSection load='2gem' size='340' side='right' caption='[[2gem]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
+<StructureSection load='2gem' size='340' side='right'caption='[[2gem]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2gem]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GEM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2GEM FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2gem]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_Typhimurium Salmonella enterica subsp. enterica serovar Typhimurium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GEM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2GEM FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2gel|2gel]]</td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.1&#8491;</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=2gem FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gem OCA], [http://pdbe.org/2gem PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2gem RCSB], [http://www.ebi.ac.uk/pdbsum/2gem PDBsum]</span></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=2gem FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gem OCA], [https://pdbe.org/2gem PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2gem RCSB], [https://www.ebi.ac.uk/pdbsum/2gem PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2gem ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/TSAB_SALTY TSAB_SALTY]] Required for the formation of a threonylcarbamoyl group on adenosine at position 37 (t(6)A37) in tRNAs that read codons beginning with adenine. Is involved in the transfer of the threonylcarbamoyl moiety of threonylcarbamoyl-AMP (TC-AMP) to the N6 group of A37, together with TsaD and TsaE; this reaction does not require ATP in vitro. TsaB seems to play an indirect role in the t(6)A biosynthesis pathway, possibly in regulating the core enzymatic function of TsaD (By similarity). Neither binds polyphosphates nor a wide range of nucleotides on its own. Does not show O-sialoglycoprotein endopeptidase activity.  Has been identified as the first Gram-negative bacterial RPF (Resuscitation-Promoting Factor) capable of reviving VNC (viable but non-culturable) cells when added externally, but the million-fold lower activity as compared to Gram-positive bacterial RPFs may indicate a lack of physiological relevance.<ref>PMID:16213054</ref>
+[https://www.uniprot.org/uniprot/TSAB_SALTY TSAB_SALTY] Required for the formation of a threonylcarbamoyl group on adenosine at position 37 (t(6)A37) in tRNAs that read codons beginning with adenine. Is involved in the transfer of the threonylcarbamoyl moiety of threonylcarbamoyl-AMP (TC-AMP) to the N6 group of A37, together with TsaD and TsaE; this reaction does not require ATP in vitro. TsaB seems to play an indirect role in the t(6)A biosynthesis pathway, possibly in regulating the core enzymatic function of TsaD (By similarity). Neither binds polyphosphates nor a wide range of nucleotides on its own. Does not show O-sialoglycoprotein endopeptidase activity.  Has been identified as the first Gram-negative bacterial RPF (Resuscitation-Promoting Factor) capable of reviving VNC (viable but non-culturable) cells when added externally, but the million-fold lower activity as compared to Gram-positive bacterial RPFs may indicate a lack of physiological relevance.<ref>PMID:16213054</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ge/2gem_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ge/2gem_consurf.spt"</scriptWhenChecked>
-    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
-</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2gem ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 31: / Line 32: @@
 __TOC__
 </StructureSection>
-[[Category: Nichols, C E]]
+[[Category: Large Structures]]
-[[Category: Stammers, D K]]
+[[Category: Salmonella enterica subsp. enterica serovar Typhimurium]]
-[[Category: Actin-like-fold]]
+[[Category: Nichols CE]]
-[[Category: Chaperone]]
+[[Category: Stammers DK]]
-[[Category: Glycoprotease]]
-[[Category: M22]]
-[[Category: Yeaz]]

2gem

From Proteopedia

Current revision

2.1A crystal structure of Salmonella tyhpimurium YeaZ, a putative Gram-negative RPF, form-A

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox