4e8g

From Proteopedia

(Difference between revisions)

Revision as of 08:21, 6 December 2023

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

Structural highlights

4e8g 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 2Å
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]

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^[2]

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

References

↑ 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
↑ Kumar R, Zhao S, Vetting MW, Wood BM, Sakai A, Cho K, Solbiati J, Almo SC, Sweedler JV, Jacobson MP, Gerlt JA, Cronan JE. Prediction and biochemical demonstration of a catabolic pathway for the osmoprotectant proline betaine. MBio. 2014 Feb 11;5(1):e00933-13. doi: 10.1128/mBio.00933-13. PMID:24520058 doi:http://dx.doi.org/10.1128/mBio.00933-13

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4e8g"

@@ Line 4: / Line 4: @@
 == Structural highlights ==
 <table><tr><td colspan='2'>[[4e8g]] 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=4E8G OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4E8G FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=UNL:UNKNOWN+LIGAND'>UNL</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]] 2&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=UNL:UNKNOWN+LIGAND'>UNL</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=4e8g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e8g OCA], [https://pdbe.org/4e8g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4e8g RCSB], [https://www.ebi.ac.uk/pdbsum/4e8g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4e8g ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[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>
+[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 ==
@@ Line 20: / Line 21: @@
 ==See Also==
+*[[Enolase 3D structures|Enolase 3D structures]]
 *[[Mandelate racemase|Mandelate racemase]]
 *[[Mandelate racemase/muconate lactonizing enzyme 3D structures|Mandelate racemase/muconate lactonizing enzyme 3D structures]]

4e8g

From Proteopedia

Revision as of 08:21, 6 December 2023

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

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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