1tm0: Difference between revisions

Latest revision as of 08:42, 1 May 2024

Crystal Structure of the putative proline racemase from Brucella melitensis, Northeast Structural Genomics Target LR31

Structural highlights

1tm0 is a 2 chain structure with sequence from Brucella melitensis bv. 1 str. 16M. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.8Å
Ligands:	MSE
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT, TOPSAN

Function

Y1586_BRUME In vitro, catalyzes the epimerization of trans-4-hydroxy-L-proline (t4LHyp) to cis-4-hydroxy-D-proline (c4DHyp) and that of trans-3-hydroxy-L-proline (t3LHyp) to cis-3-hydroxy-D-proline (c3DHyp), albeit with very low efficiency. The physiological substrate may be different (PubMed:24980702). Displays neither proline racemase activity nor t3LHyp dehydratase activity (PubMed:17849014, PubMed:24980702).^[1] ^[2] ^[3]

Evolutionary Conservation

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

References

↑ Goytia M, Chamond N, Cosson A, Coatnoan N, Hermant D, Berneman A, Minoprio P. Molecular and structural discrimination of proline racemase and hydroxyproline-2-epimerase from nosocomial and bacterial pathogens. PLoS One. 2007 Sep 12;2(9):e885. PMID:17849014 doi:https://dx.doi.org/10.1371/journal.pone.0000885
↑ Zhao S, Sakai A, Zhang X, Vetting MW, Kumar R, Hillerich B, San Francisco B, Solbiati J, Steves A, Brown S, Akiva E, Barber A, Seidel RD, Babbitt PC, Almo SC, Gerlt JA, Jacobson MP. Prediction and characterization of enzymatic activities guided by sequence similarity and genome neighborhood networks. Elife. 2014 Jun 30;3. doi: 10.7554/eLife.03275. PMID:24980702 doi:https://dx.doi.org/10.7554/eLife.03275
↑ Zhao S, Sakai A, Zhang X, Vetting MW, Kumar R, Hillerich B, San Francisco B, Solbiati J, Steves A, Brown S, Akiva E, Barber A, Seidel RD, Babbitt PC, Almo SC, Gerlt JA, Jacobson MP. Prediction and characterization of enzymatic activities guided by sequence similarity and genome neighborhood networks. Elife. 2014 Jun 30;3. doi: 10.7554/eLife.03275. PMID:24980702 doi:https://dx.doi.org/10.7554/eLife.03275

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Goytia M, Chamond N, Cosson A, Coatnoan N, Hermant D, Berneman A, Minoprio P. Molecular and structural discrimination of proline racemase and hydroxyproline-2-epimerase from nosocomial and bacterial pathogens. PLoS One. 2007 Sep 12;2(9):e885. PMID:17849014 doi:https://dx.doi.org/10.1371/journal.pone.0000885

[2] Zhao S, Sakai A, Zhang X, Vetting MW, Kumar R, Hillerich B, San Francisco B, Solbiati J, Steves A, Brown S, Akiva E, Barber A, Seidel RD, Babbitt PC, Almo SC, Gerlt JA, Jacobson MP. Prediction and characterization of enzymatic activities guided by sequence similarity and genome neighborhood networks. Elife. 2014 Jun 30;3. doi: 10.7554/eLife.03275. PMID:24980702 doi:https://dx.doi.org/10.7554/eLife.03275

[3] Zhao S, Sakai A, Zhang X, Vetting MW, Kumar R, Hillerich B, San Francisco B, Solbiati J, Steves A, Brown S, Akiva E, Barber A, Seidel RD, Babbitt PC, Almo SC, Gerlt JA, Jacobson MP. Prediction and characterization of enzymatic activities guided by sequence similarity and genome neighborhood networks. Elife. 2014 Jun 30;3. doi: 10.7554/eLife.03275. PMID:24980702 doi:https://dx.doi.org/10.7554/eLife.03275

[1]

[2]

[3]

@@ Line 1: / Line 1: @@
-[[Image:1tm0.gif|left|200px]]<br /><applet load="1tm0" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1tm0, resolution 2.8&Aring;" />
-'''Crystal Structure of the putative proline racemase from Brucella melitensis, Northeast Structural Genomics Target LR31'''<br />
-==About this Structure==
+==Crystal Structure of the putative proline racemase from Brucella melitensis, Northeast Structural Genomics Target LR31==
-TM0 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Brucella_melitensis_16m Brucella melitensis 16m]. Active as [http://en.wikipedia.org/wiki/Proline_racemase Proline racemase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.1.4 5.1.1.4] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1TM0 OCA].
+<StructureSection load='1tm0' size='340' side='right'caption='[[1tm0]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
-[[Category: Brucella melitensis 16m]]
+== Structural highlights ==
-[[Category: Proline racemase]]
+<table><tr><td colspan='2'>[[1tm0]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Brucella_melitensis_bv._1_str._16M Brucella melitensis bv. 1 str. 16M]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TM0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1TM0 FirstGlance]. <br>
-[[Category: Single protein]]
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.8&#8491;</td></tr>
-[[Category: Acton, T.B.]]
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-[[Category: Chen, Y.]]
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1tm0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tm0 OCA], [https://pdbe.org/1tm0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1tm0 RCSB], [https://www.ebi.ac.uk/pdbsum/1tm0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1tm0 ProSAT], [https://www.topsan.org/Proteins/NESGC/1tm0 TOPSAN]</span></td></tr>
-[[Category: Cooper, B.]]
+</table>
-[[Category: Forouhar, F.]]
+== Function ==
-[[Category: Ho, C.K.]]
+[https://www.uniprot.org/uniprot/Y1586_BRUME Y1586_BRUME] In vitro, catalyzes the epimerization of trans-4-hydroxy-L-proline (t4LHyp) to cis-4-hydroxy-D-proline (c4DHyp) and that of trans-3-hydroxy-L-proline (t3LHyp) to cis-3-hydroxy-D-proline (c3DHyp), albeit with very low efficiency. The physiological substrate may be different (PubMed:24980702). Displays neither proline racemase activity nor t3LHyp dehydratase activity (PubMed:17849014, PubMed:24980702).<ref>PMID:17849014</ref> <ref>PMID:24980702</ref> <ref>PMID:24980702</ref>
-[[Category: Hunt, J.F.]]
+== Evolutionary Conservation ==
-[[Category: Ma, L.C.]]
+[[Image:Consurf_key_small.gif|200px|right]]
-[[Category: Montelione, G.T.]]
+Check<jmol>
-[[Category: NESG, Northeast.Structural.Genomics.Consortium.]]
+  <jmolCheckbox>
-[[Category: Tong, L.]]
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/tm/1tm0_consurf.spt"</scriptWhenChecked>
-[[Category: Xiao, R.]]
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
-[[Category: alpha-beta protein that resembles double-beta barrel]]
+    <text>to colour the structure by Evolutionary Conservation</text>
-[[Category: in each of which an alpha helix is sandwiched]]
+  </jmolCheckbox>
-[[Category: nesg]]
+</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=1tm0 ConSurf].
-[[Category: northeast structural genomics consortium]]
+<div style="clear:both"></div>
-[[Category: protein structure initiative]]
+== References ==
-[[Category: psi]]
+<references/>
-[[Category: structural genomics]]
+__TOC__
+</StructureSection>
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sun Nov 25 02:23:56 2007''
+[[Category: Brucella melitensis bv. 1 str. 16M]]
+[[Category: Large Structures]]
+[[Category: Acton TB]]
+[[Category: Chen Y]]
+[[Category: Cooper B]]
+[[Category: Forouhar F]]
+[[Category: Ho CK]]
+[[Category: Hunt JF]]
+[[Category: Ma L-C]]
+[[Category: Montelione GT]]
+[[Category: Tong L]]
+[[Category: Xiao R]]

1tm0: Difference between revisions

Latest revision as of 08:42, 1 May 2024

Crystal Structure of the putative proline racemase from Brucella melitensis, Northeast Structural Genomics Target LR31

Structural highlights

Function

Evolutionary Conservation

References

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