3byq

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of a duf1185 family protein (bb2672) from bordetella bronchiseptica rb50 at 1.70 A resolution

Structural highlights

3byq is a 3 chain structure with sequence from Bordetella bronchiseptica RB50. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.7Å
Ligands:	, , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT, TOPSAN

Function

A0A0H3LTD0_BORBR

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 crystal structures of BB2672 and SPO0826 were determined to resolutions of 1.7 and 2.1 A by single-wavelength anomalous dispersion and multiple-wavelength anomalous dispersion, respectively, using the semi-automated high-throughput pipeline of the Joint Center for Structural Genomics (JCSG) as part of the NIGMS Protein Structure Initiative (PSI). These proteins are the first structural representatives of the PF06684 (DUF1185) Pfam family. Structural analysis revealed that both structures adopt a variant of the Bacillus chorismate mutase fold (BCM). The biological unit of both proteins is a hexamer and analysis of homologs indicates that the oligomer interface residues are highly conserved. The conformation of the critical regions for oligomerization appears to be dependent on pH or salt concentration, suggesting that this protein might be subject to environmental regulation. Structural similarities to BCM and genome-context analysis suggest a function in amino-acid synthesis.

Structures of the first representatives of Pfam family PF06684 (DUF1185) reveal a novel variant of the Bacillus chorismate mutase fold and suggest a role in amino-acid metabolism.,Bakolitsa C, Kumar A, Jin KK, McMullan D, Krishna SS, Miller MD, Abdubek P, Acosta C, Astakhova T, Axelrod HL, Burra P, Carlton D, Chen C, Chiu HJ, Clayton T, Das D, Deller MC, Duan L, Elias Y, Ellrott K, Ernst D, Farr CL, Feuerhelm J, Grant JC, Grzechnik A, Grzechnik SK, Han GW, Jaroszewski L, Johnson HA, Klock HE, Knuth MW, Kozbial P, Marciano D, Morse AT, Murphy KD, Nigoghossian E, Nopakun A, Okach L, Paulsen J, Puckett C, Reyes R, Rife CL, Sefcovic N, Tien HJ, Trame CB, Trout CV, van den Bedem H, Weekes D, White A, Xu Q, Hodgson KO, Wooley J, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Wilson IA Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 Oct 1;66(Pt, 10):1182-9. Epub 2010 Mar 5. PMID:20944209^[1]

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

References

↑ Bakolitsa C, Kumar A, Jin KK, McMullan D, Krishna SS, Miller MD, Abdubek P, Acosta C, Astakhova T, Axelrod HL, Burra P, Carlton D, Chen C, Chiu HJ, Clayton T, Das D, Deller MC, Duan L, Elias Y, Ellrott K, Ernst D, Farr CL, Feuerhelm J, Grant JC, Grzechnik A, Grzechnik SK, Han GW, Jaroszewski L, Johnson HA, Klock HE, Knuth MW, Kozbial P, Marciano D, Morse AT, Murphy KD, Nigoghossian E, Nopakun A, Okach L, Paulsen J, Puckett C, Reyes R, Rife CL, Sefcovic N, Tien HJ, Trame CB, Trout CV, van den Bedem H, Weekes D, White A, Xu Q, Hodgson KO, Wooley J, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Wilson IA. Structures of the first representatives of Pfam family PF06684 (DUF1185) reveal a novel variant of the Bacillus chorismate mutase fold and suggest a role in amino-acid metabolism. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 Oct 1;66(Pt, 10):1182-9. Epub 2010 Mar 5. PMID:20944209 doi:10.1107/S1744309109050647

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/3byq"

Categories: Bordetella bronchiseptica RB50 | Large Structures

@@ Line 1: / Line 1: @@
-[[Image:3byq.jpg|left|200px]]<br /><applet load="3byq" size="350" color="white" frame="true" align="right" spinBox="true"
-caption="3byq, resolution 1.700&Aring;" />
-'''Crystal structure of protein of unknown function (DUF1185) (NP_889209.1) from Bordetella bronchiseptica at 1.70 A resolution'''<br />
-==About this Structure==
+==Crystal structure of a duf1185 family protein (bb2672) from bordetella bronchiseptica rb50 at 1.70 A resolution==
-BYQ is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bordetella_bronchiseptica_rb50 Bordetella bronchiseptica rb50] with <scene name='pdbligand=CL:'>CL</scene>, <scene name='pdbligand=PG4:'>PG4</scene> and <scene name='pdbligand=EDO:'>EDO</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Known structural/functional Sites: <scene name='pdbsite=AC1:Cl+Binding+Site+For+Residue+A+193'>AC1</scene>, <scene name='pdbsite=AC2:Cl+Binding+Site+For+Residue+B+193'>AC2</scene>, <scene name='pdbsite=AC3:Cl+Binding+Site+For+Residue+C+194'>AC3</scene>, <scene name='pdbsite=AC4:Pg4+Binding+Site+For+Residue+A+194'>AC4</scene>, <scene name='pdbsite=AC5:Pg4+Binding+Site+For+Residue+C+195'>AC5</scene>, <scene name='pdbsite=AC6:Edo+Binding+Site+For+Residue+C+196'>AC6</scene>, <scene name='pdbsite=AC7:Edo+Binding+Site+For+Residue+B+194'>AC7</scene>, <scene name='pdbsite=AC8:Edo+Binding+Site+For+Residue+A+195'>AC8</scene>, <scene name='pdbsite=AC9:Edo+Binding+Site+For+Residue+A+196'>AC9</scene>, <scene name='pdbsite=BC1:Edo+Binding+Site+For+Residue+A+197'>BC1</scene>, <scene name='pdbsite=BC2:Edo+Binding+Site+For+Residue+B+195'>BC2</scene>, <scene name='pdbsite=BC3:Edo+Binding+Site+For+Residue+B+196'>BC3</scene>, <scene name='pdbsite=BC4:Edo+Binding+Site+For+Residue+B+197'>BC4</scene>, <scene name='pdbsite=BC5:Edo+Binding+Site+For+Residue+B+198'>BC5</scene>, <scene name='pdbsite=BC6:Edo+Binding+Site+For+Residue+C+198'>BC6</scene>, <scene name='pdbsite=BC7:Edo+Binding+Site+For+Residue+C+199'>BC7</scene>, <scene name='pdbsite=BC8:Edo+Binding+Site+For+Residue+A+198'>BC8</scene>, <scene name='pdbsite=BC9:Edo+Binding+Site+For+Residue+A+199'>BC9</scene>, <scene name='pdbsite=CC1:Edo+Binding+Site+For+Residue+C+200'>CC1</scene>, <scene name='pdbsite=CC2:Edo+Binding+Site+For+Residue+B+199'>CC2</scene>, <scene name='pdbsite=CC3:Edo+Binding+Site+For+Residue+C+201'>CC3</scene>, <scene name='pdbsite=CC4:Edo+Binding+Site+For+Residue+C+202'>CC4</scene>, <scene name='pdbsite=CC5:Edo+Binding+Site+For+Residue+C+203'>CC5</scene>, <scene name='pdbsite=CC6:Edo+Binding+Site+For+Residue+B+200'>CC6</scene>, <scene name='pdbsite=CC7:Edo+Binding+Site+For+Residue+B+201'>CC7</scene>, <scene name='pdbsite=CC8:Edo+Binding+Site+For+Residue+B+202'>CC8</scene>, <scene name='pdbsite=CC9:Edo+Binding+Site+For+Residue+A+200'>CC9</scene>, <scene name='pdbsite=DC1:Edo+Binding+Site+For+Residue+A+201'>DC1</scene>, <scene name='pdbsite=DC2:Edo+Binding+Site+For+Residue+A+202'>DC2</scene>, <scene name='pdbsite=DC3:Edo+Binding+Site+For+Residue+B+203'>DC3</scene> and <scene name='pdbsite=DC4:Edo+Binding+Site+For+Residue+B+204'>DC4</scene>. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BYQ OCA].
+<StructureSection load='3byq' size='340' side='right'caption='[[3byq]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
-[[Category: Bordetella bronchiseptica rb50]]
+== Structural highlights ==
-[[Category: Single protein]]
+<table><tr><td colspan='2'>[[3byq]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Bordetella_bronchiseptica_RB50 Bordetella bronchiseptica RB50]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BYQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3BYQ FirstGlance]. <br>
-[[Category: JCSG, Joint Center for Structural Genomics.]]
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.7&#8491;</td></tr>
-[[Category: CL]]
+<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=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene></td></tr>
-[[Category: EDO]]
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3byq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3byq OCA], [https://pdbe.org/3byq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3byq RCSB], [https://www.ebi.ac.uk/pdbsum/3byq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3byq ProSAT], [https://www.topsan.org/Proteins/JCSG/3byq TOPSAN]</span></td></tr>
-[[Category: PG4]]
+</table>
-[[Category: jcsg]]
+== Function ==
-[[Category: joint center for structural genomics]]
+[https://www.uniprot.org/uniprot/A0A0H3LTD0_BORBR A0A0H3LTD0_BORBR]
-[[Category: np_889209 1]]
+== Evolutionary Conservation ==
-[[Category: protein of unknown function (duf1185)]]
+[[Image:Consurf_key_small.gif|200px|right]]
-[[Category: protein structure initiative]]
+Check<jmol>
-[[Category: psi-2]]
+  <jmolCheckbox>
-[[Category: structural genomics]]
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/by/3byq_consurf.spt"</scriptWhenChecked>
-[[Category: unknown function]]
+    <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/main_output.php?pdb_ID=3byq ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The crystal structures of BB2672 and SPO0826 were determined to resolutions of 1.7 and 2.1 A by single-wavelength anomalous dispersion and multiple-wavelength anomalous dispersion, respectively, using the semi-automated high-throughput pipeline of the Joint Center for Structural Genomics (JCSG) as part of the NIGMS Protein Structure Initiative (PSI). These proteins are the first structural representatives of the PF06684 (DUF1185) Pfam family. Structural analysis revealed that both structures adopt a variant of the Bacillus chorismate mutase fold (BCM). The biological unit of both proteins is a hexamer and analysis of homologs indicates that the oligomer interface residues are highly conserved. The conformation of the critical regions for oligomerization appears to be dependent on pH or salt concentration, suggesting that this protein might be subject to environmental regulation. Structural similarities to BCM and genome-context analysis suggest a function in amino-acid synthesis.
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 19:07:51 2008''
+Structures of the first representatives of Pfam family PF06684 (DUF1185) reveal a novel variant of the Bacillus chorismate mutase fold and suggest a role in amino-acid metabolism.,Bakolitsa C, Kumar A, Jin KK, McMullan D, Krishna SS, Miller MD, Abdubek P, Acosta C, Astakhova T, Axelrod HL, Burra P, Carlton D, Chen C, Chiu HJ, Clayton T, Das D, Deller MC, Duan L, Elias Y, Ellrott K, Ernst D, Farr CL, Feuerhelm J, Grant JC, Grzechnik A, Grzechnik SK, Han GW, Jaroszewski L, Johnson HA, Klock HE, Knuth MW, Kozbial P, Marciano D, Morse AT, Murphy KD, Nigoghossian E, Nopakun A, Okach L, Paulsen J, Puckett C, Reyes R, Rife CL, Sefcovic N, Tien HJ, Trame CB, Trout CV, van den Bedem H, Weekes D, White A, Xu Q, Hodgson KO, Wooley J, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Wilson IA Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 Oct 1;66(Pt, 10):1182-9. Epub 2010 Mar 5. PMID:20944209<ref>PMID:20944209</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3byq" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Bordetella bronchiseptica RB50]]
+[[Category: Large Structures]]

3byq

From Proteopedia

Current revision

Crystal structure of a duf1185 family protein (bb2672) from bordetella bronchiseptica rb50 at 1.70 A resolution

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

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