3ddr: Difference between revisions

Latest revision as of 09:05, 13 August 2026

Structure of the Serratia marcescens hemophore receptor HasR-Ile671Gly mutant in complex with its hemophore HasA and heme

Structural highlights

3ddr is a 4 chain structure with sequence from Serratia marcescens. 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:	GOL, HEM, NA
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

Q79AD2_SERMA

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

Gram-negative bacteria use specific heme uptake systems, relying on outer membrane receptors and excreted heme-binding proteins (hemophores) to scavenge and actively transport heme. To unravel the unknown molecular details involved, we present 3 structures of the Serratia marcescens receptor HasR in complex with its hemophore HasA. The transfer of heme over a distance of 9 A from its high-affinity site in HasA into a site of lower affinity in HasR is coupled with the exergonic complex formation of the 2 proteins. Upon docking to the receptor, 1 of the 2 axial heme coordinations of the hemophore is initially broken, but the position and orientation of the heme is preserved. Subsequently, steric displacement of heme by a receptor residue ruptures the other axial coordination, leading to heme transfer into the receptor.

Heme uptake across the outer membrane as revealed by crystal structures of the receptor-hemophore complex.,Krieg S, Huche F, Diederichs K, Izadi-Pruneyre N, Lecroisey A, Wandersman C, Delepelaire P, Welte W Proc Natl Acad Sci U S A. 2009 Jan 27;106(4):1045-50. Epub 2009 Jan 14. PMID:19144921^[1]

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

References

↑ Krieg S, Huche F, Diederichs K, Izadi-Pruneyre N, Lecroisey A, Wandersman C, Delepelaire P, Welte W. Heme uptake across the outer membrane as revealed by crystal structures of the receptor-hemophore complex. Proc Natl Acad Sci U S A. 2009 Jan 27;106(4):1045-50. Epub 2009 Jan 14. PMID:19144921 doi:10.1073/pnas.0809406106

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Krieg S, Huche F, Diederichs K, Izadi-Pruneyre N, Lecroisey A, Wandersman C, Delepelaire P, Welte W. Heme uptake across the outer membrane as revealed by crystal structures of the receptor-hemophore complex. Proc Natl Acad Sci U S A. 2009 Jan 27;106(4):1045-50. Epub 2009 Jan 14. PMID:19144921 doi:10.1073/pnas.0809406106

[1]

@@ Line 3: / Line 3: @@
 <StructureSection load='3ddr' size='340' side='right'caption='[[3ddr]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3ddr]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_marcescens"_(bizio_1823)_trevisan_in_de_toni_and_trevisan_1889 "bacillus marcescens" (bizio 1823) trevisan in de toni and trevisan 1889]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DDR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DDR FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3ddr]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Serratia_marcescens Serratia marcescens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DDR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DDR FirstGlance]. <br>
-</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=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</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]] 2.8&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3csl|3csl]], [[3csn|3csn]]</div></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=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">hasR ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=615 "Bacillus marcescens" (Bizio 1823) Trevisan in de Toni and Trevisan 1889]), hasA ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=615 "Bacillus marcescens" (Bizio 1823) Trevisan in de Toni and Trevisan 1889])</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=3ddr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ddr OCA], [https://pdbe.org/3ddr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ddr RCSB], [https://www.ebi.ac.uk/pdbsum/3ddr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ddr ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/HASA_SERMA HASA_SERMA]] Can bind free heme and also acquire it from hemoglobin. Conveys heme from hemoglobin to the HasR receptor which releases it into the bacterium. HasR alone can take up heme but the synergy between HasA and HasR increases heme uptake 100-fold.<ref>PMID:7937909</ref> <ref>PMID:9171402</ref>
+[https://www.uniprot.org/uniprot/Q79AD2_SERMA Q79AD2_SERMA]
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 16: / Line 15: @@
    <jmolCheckbox>
      <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dd/3ddr_consurf.spt"</scriptWhenChecked>
-     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
      <text>to colour the structure by Evolutionary Conservation</text>
    </jmolCheckbox>
@@ Line 35: / Line 34: @@
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Diederichs, K]]
+[[Category: Serratia marcescens]]
-[[Category: Krieg, S]]
+[[Category: Diederichs K]]
-[[Category: Beta-barrel]]
+[[Category: Krieg S]]
-[[Category: Heme]]
-[[Category: Hemophore receptor]]
-[[Category: Iron]]
-[[Category: Membrane]]
-[[Category: Membrane protein-heme binding protein complex]]
-[[Category: Metal-binding]]
-[[Category: Outer membrane]]
-[[Category: Outer membrane protein]]
-[[Category: Secreted]]
-[[Category: Tonb box]]

3ddr: Difference between revisions

Latest revision as of 09:05, 13 August 2026

Structure of the Serratia marcescens hemophore receptor HasR-Ile671Gly mutant in complex with its hemophore HasA and heme

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

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