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1tvi

From Proteopedia

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Solution structure of TM1509 from Thermotoga maritima: VT1, a NESGC target protein

Structural highlights

1tvi is a 1 chain structure with sequence from Thermotoga maritima. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Solution NMR
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT, TOPSAN

Function

YBEY_THEMA Single strand-specific metallo-endoribonuclease involved in late-stage 70S ribosome quality control and in maturation of the 3' terminus of the 16S rRNA.[HAMAP-Rule:MF_00009]

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 150-residue protein TM1509 is encoded in gene YF09_THEMA of Thermotoga maritima. TM1509 has so far no functional annotation and belongs to protein family UPF0054 (PFAM accession number: PF02130) which contains at least 146 members. The NMR structure of TM1509 reveals an alpha+beta fold comprising a four stranded beta-sheet with topology A( upward arrow), B( upward arrow), D( upward arrow), C( downward arrow) as well as five alpha-helices I-V. The structures of most members of family PF02130 can be reliably constructed using the TM1509 NMR structure, demonstrating high leverage for exploration of fold space. A multiple sequence alignment of TM1509 with homologues of family UPF0054 shows that three polypeptide segments, as well as a putative zinc-binding consensus motif HGXLHLXGYDH located at the C-terminal end of alpha-helix IV, are highly conserved. The spatial arrangement of the three His residues of this UPF0054 consensus motif is similar to the arrangement found for the His residues in the HEXXHXXGXXH zinc-binding consensus motif of matrix metallo-proteases (MMPs). Moreover, the other conserved polypeptide segments form a large cavity which encloses the putative Zn-binding pocket and might confer specificity during catalysis. However, TM1509 and the other members of the UPF0054 family do not have the crucial Glu residue in position 2 of the MMP consensus motif. Intriguingly, the TM1509 structure indicates that the Asp in the UPF0054 consensus motif (Asp 111 in TM1509) may overtake the catalytic role of the Glu. This suggests that protein family UPF0054 might contain members of a hitherto uncharacterized class of metalloproteases.

NMR solution structure of Thermotoga maritima protein TM1509 reveals a Zn-metalloprotease-like tertiary structure.,Penhoat CH, Li Z, Atreya HS, Kim S, Yee A, Xiao R, Murray D, Arrowsmith CH, Szyperski T J Struct Funct Genomics. 2005;6(1):51-62. PMID:15965736^[1]

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

References

↑ Penhoat CH, Li Z, Atreya HS, Kim S, Yee A, Xiao R, Murray D, Arrowsmith CH, Szyperski T. NMR solution structure of Thermotoga maritima protein TM1509 reveals a Zn-metalloprotease-like tertiary structure. J Struct Funct Genomics. 2005;6(1):51-62. PMID:15965736 doi:10.1007/s10969-005-5277-z

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/1tvi"

@@ Line 1: / Line 1: @@
 ==Solution structure of TM1509 from Thermotoga maritima: VT1, a NESGC target protein==
-<StructureSection load='1tvi' size='340' side='right' caption='[[1tvi]], [[NMR_Ensembles_of_Models | 20 NMR models]]' scene=''>
+<StructureSection load='1tvi' size='340' side='right'caption='[[1tvi]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1tvi]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43589 Atcc 43589]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TVI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1TVI FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1tvi]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TVI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1TVI FirstGlance]. <br>
-</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">TM1509 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2336 ATCC 43589])</td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</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=1tvi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tvi OCA], [http://pdbe.org/1tvi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1tvi RCSB], [http://www.ebi.ac.uk/pdbsum/1tvi PDBsum], [http://www.topsan.org/Proteins/NESGC/1tvi TOPSAN]</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=1tvi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tvi OCA], [https://pdbe.org/1tvi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1tvi RCSB], [https://www.ebi.ac.uk/pdbsum/1tvi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1tvi ProSAT], [https://www.topsan.org/Proteins/NESGC/1tvi TOPSAN]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/YBEY_THEMA YBEY_THEMA]] Single strand-specific metallo-endoribonuclease involved in late-stage 70S ribosome quality control and in maturation of the 3' terminus of the 16S rRNA.[HAMAP-Rule:MF_00009]
+[https://www.uniprot.org/uniprot/YBEY_THEMA YBEY_THEMA] Single strand-specific metallo-endoribonuclease involved in late-stage 70S ribosome quality control and in maturation of the 3' terminus of the 16S rRNA.[HAMAP-Rule:MF_00009]
 == 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/tv/1tvi_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/tv/1tvi_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=1tvi ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 31: / Line 32: @@
 __TOC__
 </StructureSection>
-[[Category: Atcc 43589]]
+[[Category: Large Structures]]
-[[Category: Arrowsmith, C H]]
+[[Category: Thermotoga maritima]]
-[[Category: Atreya, H S]]
+[[Category: Arrowsmith CH]]
-[[Category: Kim, S]]
+[[Category: Atreya HS]]
-[[Category: Li, Z]]
+[[Category: Kim S]]
-[[Category: Murray, D]]
+[[Category: Li Z]]
-[[Category: Structural genomic]]
+[[Category: Murray D]]
-[[Category: Penhoat, C H]]
+[[Category: Penhoat CH]]
-[[Category: Szyperski, T]]
+[[Category: Szyperski T]]
-[[Category: Xiao, R]]
+[[Category: Xiao R]]
-[[Category: Yee, A]]
+[[Category: Yee A]]
-[[Category: Alpha + beta]]
-[[Category: Four helix bundle]]
-[[Category: Mixed 4-stranded beta sheet]]
-[[Category: Nesgc]]
-[[Category: PSI, Protein structure initiative]]
-[[Category: Unknown function]]

1tvi

From Proteopedia

Current revision

Solution structure of TM1509 from Thermotoga maritima: VT1, a NESGC target protein

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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