5cx7

From Proteopedia

(Difference between revisions)

Current revision

Crystal Structure of PduOC:Heme Complex

Structural highlights

5cx7 is a 16 chain structure with sequence from Salmonella enterica subsp. enterica serovar Livingstone. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.97Å
Ligands:	, , , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PDUO_SALTY Converts cob(I)alamin to adenosylcobalamin (adenosylcob(III)alamin), the cofactor for propanediol dehydratase. Found in the bacterial microcompartment (BMC) dedicated to 1,2-propanediol (1,2-PD) degradation (PubMed:11160088, PubMed:15547259, PubMed:27446048, PubMed:15817784, PubMed:20656910). For adenosylcobalamin synthesis dATP can replace ATP, but no other nucleotides will substitute (PubMed:15547259). PduS and PduO allow regeneration of the adenosylcobalamin cofactor within the BMC (Probable).^[1] ^[2] ^[3] ^[4] ^[5] The 1,2-PD-specific bacterial microcompartment (BMC) concentrates low levels of 1,2-PD catabolic enzymes, concentrates volatile reaction intermediates thus enhancing pathway flux and keeps the level of toxic, mutagenic propionaldehyde low.^[6]

Publication Abstract from PubMed

The two-domain protein PduO, involved in 1,2-propanediol utilization in the pathogenic Gram-negative bacterium Salmonella enterica is an ATP:Cob(I)alamin adenosyltransferase, but this is a function of the N-terminal domain alone. The role of its C-terminal domain (PduOC) is, however, unknown. In this study, comparative growth assays with a set of Salmonella mutant strains showed that this domain is necessary for effective in vivo catabolism of 1,2-propanediol. It was also shown that isolated, recombinantly-expressed PduOC binds heme in vivo. The structure of PduOC co-crystallized with heme was solved (1.9 A resolution) showing an octameric assembly with four heme moieities. The four heme groups are highly solvent-exposed and the heme iron is hexa-coordinated with bis-His ligation by histidines from different monomers. Static light scattering confirmed the octameric assembly in solution, but a mutation of the heme-coordinating histidine caused dissociation into dimers. Isothermal titration calorimetry using the PduOC apoprotein showed strong heme binding (K d = 1.6 x 10(-7) M). Biochemical experiments showed that the absence of the C-terminal domain in PduO did not affect adenosyltransferase activity in vitro. The evidence suggests that PduOC:heme plays an important role in the set of cobalamin transformations required for effective catabolism of 1,2-propanediol. Salmonella PduO is one of the rare proteins which binds the redox-active metabolites heme and cobalamin, and the heme-binding mode of the C-terminal domain differs from that in other members of this protein family.

The Crystal Structure of the C-Terminal Domain of the Salmonella enterica PduO Protein: An Old Fold with a New Heme-Binding Mode.,Ortiz de Orue Lucana D, Hickey N, Hensel M, Klare JP, Geremia S, Tiufiakova T, Torda AE Front Microbiol. 2016 Jun 28;7:1010. doi: 10.3389/fmicb.2016.01010. eCollection, 2016. PMID:27446048^[7]

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

References

↑ Johnson CL, Pechonick E, Park SD, Havemann GD, Leal NA, Bobik TA. Functional genomic, biochemical, and genetic characterization of the Salmonella pduO gene, an ATP:cob(I)alamin adenosyltransferase gene. J Bacteriol. 2001 Mar;183(5):1577-84. PMID:11160088 doi:10.1128/JB.183.5.1577-1584.2001
↑ Johnson CL, Buszko ML, Bobik TA. Purification and initial characterization of the Salmonella enterica PduO ATP:Cob(I)alamin adenosyltransferase. J Bacteriol. 2004 Dec;186(23):7881-7. PMID:15547259 doi:10.1128/JB.186.23.7881-7887.2004
↑ Sampson EM, Johnson CLV, Bobik TA. Biochemical evidence that the pduS gene encodes a bifunctional cobalamin reductase. Microbiology (Reading). 2005 Apr;151(Pt 4):1169-1177. PMID:15817784 doi:10.1099/mic.0.27755-0
↑ Cheng S, Bobik TA. Characterization of the PduS cobalamin reductase of Salmonella enterica and its role in the Pdu microcompartment. J Bacteriol. 2010 Oct;192(19):5071-80. PMID:20656910 doi:10.1128/JB.00575-10
↑ Ortiz de Orue Lucana D, Hickey N, Hensel M, Klare JP, Geremia S, Tiufiakova T, Torda AE. The Crystal Structure of the C-Terminal Domain of the Salmonella enterica PduO Protein: An Old Fold with a New Heme-Binding Mode. Front Microbiol. 2016 Jun 28;7:1010. doi: 10.3389/fmicb.2016.01010. eCollection, 2016. PMID:27446048 doi:http://dx.doi.org/10.3389/fmicb.2016.01010
↑ Jakobson CM, Tullman-Ercek D, Slininger MF, Mangan NM. A systems-level model reveals that 1,2-Propanediol utilization microcompartments enhance pathway flux through intermediate sequestration. PLoS Comput Biol. 2017 May 5;13(5):e1005525. doi: 10.1371/journal.pcbi.1005525., eCollection 2017 May. PMID:28475631 doi:http://dx.doi.org/10.1371/journal.pcbi.1005525
↑ Ortiz de Orue Lucana D, Hickey N, Hensel M, Klare JP, Geremia S, Tiufiakova T, Torda AE. The Crystal Structure of the C-Terminal Domain of the Salmonella enterica PduO Protein: An Old Fold with a New Heme-Binding Mode. Front Microbiol. 2016 Jun 28;7:1010. doi: 10.3389/fmicb.2016.01010. eCollection, 2016. PMID:27446048 doi:http://dx.doi.org/10.3389/fmicb.2016.01010

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5cx7"

Categories: Large Structures | Salmonella enterica subsp. enterica serovar Livingstone | Geremia S | Hickey N | Ortiz de Orue Lucana D

@@ Line 1: / Line 1: @@
 ==Crystal Structure of PduOC:Heme Complex==
-<StructureSection load='5cx7' size='340' side='right' caption='[[5cx7]], [[Resolution|resolution]] 1.97&Aring;' scene=''>
+<StructureSection load='5cx7' size='340' side='right'caption='[[5cx7]], [[Resolution|resolution]] 1.97&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5cx7]] is a 16 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5CX7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5CX7 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5cx7]] is a 16 chain structure with sequence from [https://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_Livingstone Salmonella enterica subsp. enterica serovar Livingstone]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5CX7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5CX7 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 1.97&#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=5cx7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5cx7 OCA], [http://pdbe.org/5cx7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5cx7 RCSB], [http://www.ebi.ac.uk/pdbsum/5cx7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5cx7 ProSAT]</span></td></tr>
+<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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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=5cx7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5cx7 OCA], [https://pdbe.org/5cx7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5cx7 RCSB], [https://www.ebi.ac.uk/pdbsum/5cx7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5cx7 ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/PDUO_SALTY PDUO_SALTY] Converts cob(I)alamin to adenosylcobalamin (adenosylcob(III)alamin), the cofactor for propanediol dehydratase. Found in the bacterial microcompartment (BMC) dedicated to 1,2-propanediol (1,2-PD) degradation (PubMed:11160088, PubMed:15547259, PubMed:27446048, PubMed:15817784, PubMed:20656910). For adenosylcobalamin synthesis dATP can replace ATP, but no other nucleotides will substitute (PubMed:15547259). PduS and PduO allow regeneration of the adenosylcobalamin cofactor within the BMC (Probable).<ref>PMID:11160088</ref> <ref>PMID:15547259</ref> <ref>PMID:15817784</ref> <ref>PMID:20656910</ref> <ref>PMID:27446048</ref>   The 1,2-PD-specific bacterial microcompartment (BMC) concentrates low levels of 1,2-PD catabolic enzymes, concentrates volatile reaction intermediates thus enhancing pathway flux and keeps the level of toxic, mutagenic propionaldehyde low.<ref>PMID:28475631</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The two-domain protein PduO, involved in 1,2-propanediol utilization in the pathogenic Gram-negative bacterium Salmonella enterica is an ATP:Cob(I)alamin adenosyltransferase, but this is a function of the N-terminal domain alone. The role of its C-terminal domain (PduOC) is, however, unknown. In this study, comparative growth assays with a set of Salmonella mutant strains showed that this domain is necessary for effective in vivo catabolism of 1,2-propanediol. It was also shown that isolated, recombinantly-expressed PduOC binds heme in vivo. The structure of PduOC co-crystallized with heme was solved (1.9 A resolution) showing an octameric assembly with four heme moieities. The four heme groups are highly solvent-exposed and the heme iron is hexa-coordinated with bis-His ligation by histidines from different monomers. Static light scattering confirmed the octameric assembly in solution, but a mutation of the heme-coordinating histidine caused dissociation into dimers. Isothermal titration calorimetry using the PduOC apoprotein showed strong heme binding (K d = 1.6 x 10(-7) M). Biochemical experiments showed that the absence of the C-terminal domain in PduO did not affect adenosyltransferase activity in vitro. The evidence suggests that PduOC:heme plays an important role in the set of cobalamin transformations required for effective catabolism of 1,2-propanediol. Salmonella PduO is one of the rare proteins which binds the redox-active metabolites heme and cobalamin, and the heme-binding mode of the C-terminal domain differs from that in other members of this protein family.
+The Crystal Structure of the C-Terminal Domain of the Salmonella enterica PduO Protein: An Old Fold with a New Heme-Binding Mode.,Ortiz de Orue Lucana D, Hickey N, Hensel M, Klare JP, Geremia S, Tiufiakova T, Torda AE Front Microbiol. 2016 Jun 28;7:1010. doi: 10.3389/fmicb.2016.01010. eCollection, 2016. PMID:27446048<ref>PMID:27446048</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 5cx7" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
 __TOC__
 </StructureSection>
-[[Category: Geremia, S]]
+[[Category: Large Structures]]
-[[Category: Hickey, N]]
+[[Category: Salmonella enterica subsp. enterica serovar Livingstone]]
-[[Category: Lucana, D Ortiz de Orue]]
+[[Category: Geremia S]]
-[[Category: Bis-hi]]
+[[Category: Hickey N]]
-[[Category: Heme binding domain]]
+[[Category: Ortiz de Orue Lucana D]]
-[[Category: Pduoc]]
-[[Category: Unknown function]]

5cx7

From Proteopedia

Current revision

Crystal Structure of PduOC:Heme Complex

Structural highlights

Function

Publication Abstract from PubMed

References

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