4j1o: Difference between revisions

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==Crystal structure of an enolase (mandelate racemase subgroup) from paracococus denitrificans pd1222 (target nysgrc-012907) with bound l-proline betaine (substrate)==
==Crystal structure of an enolase (mandelate racemase subgroup) from paracococus denitrificans pd1222 (target nysgrc-012907) with bound l-proline betaine (substrate)==
<StructureSection load='4j1o' size='340' side='right' caption='[[4j1o]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
<StructureSection load='4j1o' size='340' side='right'caption='[[4j1o]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[4j1o]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pardp Pardp]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4J1O OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4J1O FirstGlance]. <br>
<table><tr><td colspan='2'>[[4j1o]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Paracoccus_denitrificans_PD1222 Paracoccus denitrificans PD1222]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4J1O OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4J1O FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PBE:1,1-DIMETHYL-PROLINIUM'>PBE</scene></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]] 1.6&#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=4j1o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4j1o OCA], [http://pdbe.org/4j1o PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4j1o RCSB], [http://www.ebi.ac.uk/pdbsum/4j1o PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4j1o ProSAT]</span></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PBE:1,1-DIMETHYL-PROLINIUM'>PBE</scene></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=4j1o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4j1o OCA], [https://pdbe.org/4j1o PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4j1o RCSB], [https://www.ebi.ac.uk/pdbsum/4j1o PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4j1o ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://www.uniprot.org/uniprot/HPBD_PARDP HPBD_PARDP]] Catalyzes the 2-epimerization of trans-4-hydroxy-L-proline betaine (tHyp-B) to cis-4-hydroxy-D-proline betaine (cHyp-B). Is involved in a catabolic pathway that degrades tHyp-B to alpha-ketoglutarate. This pathway would permit the utilization of tHyp-B as a carbon and nitrogen source in the absence of osmotic stress, since tHyp-B functions as an osmolyte and is not catabolized when it is needed as osmoprotectant. Can also catalyze the racemization of L-proline betaine.<ref>PMID:24056934</ref>
[https://www.uniprot.org/uniprot/HPBD_PARDP HPBD_PARDP] Catalyzes the 2-epimerization of trans-4-hydroxy-L-proline betaine (tHyp-B) to cis-4-hydroxy-D-proline betaine (cHyp-B). Is involved in a catabolic pathway that degrades tHyp-B to alpha-ketoglutarate. This pathway would permit the utilization of tHyp-B as a carbon and nitrogen source in the absence of osmotic stress, since tHyp-B functions as an osmolyte and is not catabolized when it is needed as osmoprotectant. Can also catalyze the racemization of L-proline betaine.<ref>PMID:24056934</ref>  
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
UNLABELLED: Through the use of genetic, enzymatic, metabolomic, and structural analyses, we have discovered the catabolic pathway for proline betaine, an osmoprotectant, in Paracoccus denitrificans and Rhodobacter sphaeroides. Genetic and enzymatic analyses showed that several of the key enzymes of the hydroxyproline betaine degradation pathway also function in proline betaine degradation. Metabolomic analyses detected each of the metabolic intermediates of the pathway. The proline betaine catabolic pathway was repressed by osmotic stress and cold stress, and a regulatory transcription factor was identified. We also report crystal structure complexes of the P. denitrificans HpbD hydroxyproline betaine epimerase/proline betaine racemase with l-proline betaine and cis-hydroxyproline betaine. IMPORTANCE: At least half of the extant protein annotations are incorrect, and the errors propagate as the number of genome sequences increases exponentially. A large-scale, multidisciplinary sequence- and structure-based strategy for functional assignment of bacterial enzymes of unknown function has demonstrated the pathway for catabolism of the osmoprotectant proline betaine.


Prediction and biochemical demonstration of a catabolic pathway for the osmoprotectant proline betaine.,Kumar R, Zhao S, Vetting MW, Wood BM, Sakai A, Cho K, Solbiati J, Almo SC, Sweedler JV, Jacobson MP, Gerlt JA, Cronan JE MBio. 2014 Feb 11;5(1):e00933-13. doi: 10.1128/mBio.00933-13. PMID:24520058<ref>PMID:24520058</ref>
==See Also==
 
*[[Mandelate racemase/muconate lactonizing enzyme 3D structures|Mandelate racemase/muconate lactonizing enzyme 3D structures]]
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 4j1o" style="background-color:#fffaf0;"></div>
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Pardp]]
[[Category: Large Structures]]
[[Category: Almo, S C]]
[[Category: Paracoccus denitrificans PD1222]]
[[Category: Bhosle, R]]
[[Category: Almo SC]]
[[Category: Bonanno, J B]]
[[Category: Bhosle R]]
[[Category: Chamala, S]]
[[Category: Bonanno JB]]
[[Category: Evans, B]]
[[Category: Chamala S]]
[[Category: Gerlt, J A]]
[[Category: Evans B]]
[[Category: Gizzi, A]]
[[Category: Gerlt JA]]
[[Category: Hammonds, J]]
[[Category: Gizzi A]]
[[Category: Hillerich, B]]
[[Category: Hammonds J]]
[[Category: Kar, A]]
[[Category: Hillerich B]]
[[Category: LaFleur, J]]
[[Category: Kar A]]
[[Category: Love, J]]
[[Category: LaFleur J]]
[[Category: Morisco, L L]]
[[Category: Love J]]
[[Category: Structural genomic]]
[[Category: Morisco LL]]
[[Category: Seidel, R D]]
[[Category: Seidel RD]]
[[Category: Sojitra, S]]
[[Category: Sojitra S]]
[[Category: Stead, M]]
[[Category: Stead M]]
[[Category: Toro, R]]
[[Category: Toro R]]
[[Category: Vetting, M W]]
[[Category: Vetting MW]]
[[Category: Villigas, G]]
[[Category: Villigas G]]
[[Category: Wasserman, S R]]
[[Category: Wasserman SR]]
[[Category: Betaine racemase]]
[[Category: Enolase]]
[[Category: Isomerase]]
[[Category: Nysgrc]]
[[Category: Proline betaine racemease]]
[[Category: Psi-biology]]

Latest revision as of 15:00, 1 March 2024

Crystal structure of an enolase (mandelate racemase subgroup) from paracococus denitrificans pd1222 (target nysgrc-012907) with bound l-proline betaine (substrate)Crystal structure of an enolase (mandelate racemase subgroup) from paracococus denitrificans pd1222 (target nysgrc-012907) with bound l-proline betaine (substrate)

Structural highlights

4j1o is a 2 chain structure with sequence from Paracoccus denitrificans PD1222. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.6Å
Ligands:, , ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

HPBD_PARDP Catalyzes the 2-epimerization of trans-4-hydroxy-L-proline betaine (tHyp-B) to cis-4-hydroxy-D-proline betaine (cHyp-B). Is involved in a catabolic pathway that degrades tHyp-B to alpha-ketoglutarate. This pathway would permit the utilization of tHyp-B as a carbon and nitrogen source in the absence of osmotic stress, since tHyp-B functions as an osmolyte and is not catabolized when it is needed as osmoprotectant. Can also catalyze the racemization of L-proline betaine.[1]

See Also

References

  1. ↑ Zhao S, Kumar R, Sakai A, Vetting MW, Wood BM, Brown S, Bonanno JB, Hillerich BS, Seidel RD, Babbitt PC, Almo SC, Sweedler JV, Gerlt JA, Cronan JE, Jacobson MP. Discovery of new enzymes and metabolic pathways by using structure and genome context. Nature. 2013 Sep 22. doi: 10.1038/nature12576. PMID:24056934 doi:http://dx.doi.org/10.1038/nature12576

4j1o, resolution 1.60Å

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