2k78

From Proteopedia

(Difference between revisions)

Current revision

Solution Structure of the IsdC NEAT domain bound to Zinc Protoporphyrin

Structural highlights

2k78 is a 1 chain structure with sequence from Staphylococcus aureus subsp. aureus MW2. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Solution NMR
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

ISDC_STAAW Involved in heme (porphyrin) scavenging. Binds hemoglobin and almost exclusively free-base protoporphyrin IX. Probably has a role as the central conduit of the isd heme uptake system, i.e. mediates the transfer of the iron-containing nutrient from IsdABH to the membrane translocation system IsdDEF (By similarity). Hemin-free IsdC (apo-IsdC) acquires hemin from hemin-containing IsdA (holo-IsdA) probably through the activated holo-IsdA-apo-IsdC complex and due to the higher affinity of apo-IsdC for the cofactor. The reaction is reversible.^[1]

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

Staphylococcus aureus scavenges heme-iron from host hemoproteins using iron-regulated surface determinant (Isd) proteins. IsdC is the central conduit through which heme is passed across the cell wall and binds this molecule using a NEAr Transporter (NEAT) domain. NMR spectroscopy was used to determine the structure of IsdC in complex with a heme analog, zinc-substituted protoporphyrin IX (ZnPPIX). The backbone coordinates of the ensemble of conformers representing the structure exhibit a root mean square deviation to the mean structure of 0.53 +/- 0.11 angstroms. IsdC partially buries protoporphyrin within a large hydrophobic pocket that is located at the end of its beta-barrel structure. The central metal ion of the analog adopts a pentacoordinate geometry in which a highly conserved tyrosine residue serves as a proximal ligand. Consistent with the structure and its role in heme transfer across the cell wall, we show that IsdC weakly binds heme (K(D) = 0.34 +/- 0.12 microm) and that ZnPPIX rapidly dissociates from the protein at a rate of 126 +/- 30 s(-1). NMR studies of the apo-form of IsdC reveal that a 3(10) helix within the binding pocket undergoes a flexible to rigid transition as heme is captured. This structural plasticity may increase the efficiency of heme transfer across the cell wall by facilitating protein-protein interactions between apoIsdC and upstream hemoproteins.

The IsdC protein from Staphylococcus aureus uses a flexible binding pocket to capture heme.,Villareal VA, Pilpa RM, Robson SA, Fadeev EA, Clubb RT J Biol Chem. 2008 Nov 14;283(46):31591-600. Epub 2008 Aug 20. PMID:18715872^[2]

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

References

↑ Liu M, Tanaka WN, Zhu H, Xie G, Dooley DM, Lei B. Direct hemin transfer from IsdA to IsdC in the iron-regulated surface determinant (Isd) heme acquisition system of Staphylococcus aureus. J Biol Chem. 2008 Mar 14;283(11):6668-76. doi: 10.1074/jbc.M708372200. Epub 2008 , Jan 9. PMID:18184657 doi:http://dx.doi.org/10.1074/jbc.M708372200
↑ Villareal VA, Pilpa RM, Robson SA, Fadeev EA, Clubb RT. The IsdC protein from Staphylococcus aureus uses a flexible binding pocket to capture heme. J Biol Chem. 2008 Nov 14;283(46):31591-600. Epub 2008 Aug 20. PMID:18715872 doi:10.1074/jbc.M801126200

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2k78"

@@ Line 1: / Line 1: @@
 ==Solution Structure of the IsdC NEAT domain bound to Zinc Protoporphyrin==
-<StructureSection load='2k78' size='340' side='right' caption='[[2k78]], [[NMR_Ensembles_of_Models | 30 NMR models]]' scene=''>
+<StructureSection load='2k78' size='340' side='right'caption='[[2k78]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2k78]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Staaw Staaw]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2K78 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2K78 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2k78]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_aureus_subsp._aureus_MW2 Staphylococcus aureus subsp. aureus MW2]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2K78 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2K78 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZNH:PROTOPORPHYRIN+IX+CONTAINING+ZN'>ZNH</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">isdC, sirD, MW1013 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=196620 STAAW])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZNH:PROTOPORPHYRIN+IX+CONTAINING+ZN'>ZNH</scene></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=2k78 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2k78 OCA], [http://pdbe.org/2k78 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2k78 RCSB], [http://www.ebi.ac.uk/pdbsum/2k78 PDBsum]</span></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=2k78 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2k78 OCA], [https://pdbe.org/2k78 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2k78 RCSB], [https://www.ebi.ac.uk/pdbsum/2k78 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2k78 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/ISDC_STAAW ISDC_STAAW]] Involved in heme (porphyrin) scavenging. Binds hemoglobin and almost exclusively free-base protoporphyrin IX. Probably has a role as the central conduit of the isd heme uptake system, i.e. mediates the transfer of the iron-containing nutrient from IsdABH to the membrane translocation system IsdDEF (By similarity). Hemin-free IsdC (apo-IsdC) acquires hemin from hemin-containing IsdA (holo-IsdA) probably through the activated holo-IsdA-apo-IsdC complex and due to the higher affinity of apo-IsdC for the cofactor. The reaction is reversible.<ref>PMID:18184657</ref>
+[https://www.uniprot.org/uniprot/ISDC_STAAW ISDC_STAAW] Involved in heme (porphyrin) scavenging. Binds hemoglobin and almost exclusively free-base protoporphyrin IX. Probably has a role as the central conduit of the isd heme uptake system, i.e. mediates the transfer of the iron-containing nutrient from IsdABH to the membrane translocation system IsdDEF (By similarity). Hemin-free IsdC (apo-IsdC) acquires hemin from hemin-containing IsdA (holo-IsdA) probably through the activated holo-IsdA-apo-IsdC complex and due to the higher affinity of apo-IsdC for the cofactor. The reaction is reversible.<ref>PMID:18184657</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/k7/2k78_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/k7/2k78_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 32: / Line 33: @@
 __TOC__
 </StructureSection>
-[[Category: Staaw]]
+[[Category: Large Structures]]
-[[Category: Clubb, R T]]
+[[Category: Staphylococcus aureus subsp. aureus MW2]]
-[[Category: Fadeev, E A]]
+[[Category: Clubb RT]]
-[[Category: Pilpa, R M]]
+[[Category: Fadeev EA]]
-[[Category: Robson, S A]]
+[[Category: Pilpa RM]]
-[[Category: Villareal, V A]]
+[[Category: Robson SA]]
-[[Category: Cell wall]]
+[[Category: Villareal VA]]
-[[Category: Heme]]
-[[Category: Heme-binding protein]]
-[[Category: Iron]]
-[[Category: Isd]]
-[[Category: Isdc]]
-[[Category: Metal-binding]]
-[[Category: Neat domain]]
-[[Category: Nmr complex]]
-[[Category: Peptidoglycan-anchor]]
-[[Category: Secreted]]
-[[Category: Transport protein]]

2k78

From Proteopedia

Current revision

Solution Structure of the IsdC NEAT domain bound to Zinc Protoporphyrin

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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