This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

5d8p

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Current revision

2.35A resolution structure of iron bound BfrB (wild-type, C2221 form) from Pseudomonas aeruginosa

Structural highlights

5d8p is a 12 chain structure with sequence from Pseudomonas aeruginosa PAO1. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.35Å
Ligands:	, , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

Q9HY79_PSEAE Iron-storage protein (By similarity). Iron-storage protein, whose ferroxidase center binds Fe(2+) ions, oxidizes them by dioxygen to Fe(3+), and participates in the subsequent Fe(3+) oxide mineral core formation within the central cavity of the protein complex (By similarity).[PIRNR:PIRNR002560]

Publication Abstract from PubMed

Mobilization of iron stored in the interior cavity of BfrB requires electron transfer from the [2Fe-2S] cluster in Bfd to the core iron in BfrB. A crystal structure of the P. aeruginosa BfrB:Bfd complex revealed that BfrB can bind up to 12 Bfd molecules at 12 structurally identical binding sites, placing the [2Fe-2S] cluster of each Bfd immediately above a heme group in BfrB [Yao, H., Wang, Y., Lovell, S., Kumar, R., Ruvinsky, A. M., Battaile, K. P., Vakser, I. A., and Rivera, M. J. Am. Chem. Soc. (2012), 134, 13470-13481]. We report here a study aimed at characterizing the strength of the P. aeruginosa BfrB:Bfd association using surface plasmon resonance and isothermal titration calorimetry, as well as determining the binding energy hot spots at the protein-protein interaction interface. The results show that the 12 Bfd-binding sites on BfrB are equivalent and independent, and that the protein-protein association at each of these sites is driven entropically and is characterized by a dissociation constant (Kd) of approximately 3 muM. Determination of the binding energy hot spots was carried out by replacing certain residues that comprise the protein-protein interface with alanine, and by evaluating the effect of the mutation on Kd and on the efficiency of core iron mobilization from BfrB. The results identified hot-spot residues in both proteins [L_B^68, E_A^81 and E_A^85 in BfrB (superscript for residue number and subscript for chain) and Y2 and L5 in Bfd], which network at the interface to produce a highly complementary hot region for the interaction. The hot-spot residues are conserved in the amino acid sequences of Bfr and Bfd proteins from a number of gram negative pathogens, indicating that the BfrB:Bfd interaction is of widespread significance in bacterial iron metabolism.

Characterization of the Bacterioferritin/Bacterioferritin Associated Ferredoxin (BfrB:Bfd) Protein-Protein Interaction in Solution and Determination of Binding Energy Hot Spots.,Wang Y, Yao H, Cheng Y, Lovell SW, Battaile KP, Middaugh CR, Rivera M Biochemistry. 2015 Sep 28. PMID:26368531^[1]

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

References

↑ Wang Y, Yao H, Cheng Y, Lovell SW, Battaile KP, Middaugh CR, Rivera M. Characterization of the Bacterioferritin/Bacterioferritin Associated Ferredoxin (BfrB:Bfd) Protein-Protein Interaction in Solution and Determination of Binding Energy Hot Spots. Biochemistry. 2015 Sep 28. PMID:26368531 doi:http://dx.doi.org/10.1021/acs.biochem.5b00937

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/5d8p"

@@ Line 1: / Line 1: @@
 ==2.35A resolution structure of iron bound BfrB (wild-type, C2221 form) from Pseudomonas aeruginosa==
-<StructureSection load='5d8p' size='340' side='right' caption='[[5d8p]], [[Resolution|resolution]] 2.35&Aring;' scene=''>
+<StructureSection load='5d8p' size='340' side='right'caption='[[5d8p]], [[Resolution|resolution]] 2.35&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5d8p]] is a 12 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5D8P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5D8P FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5d8p]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_aeruginosa_PAO1 Pseudomonas aeruginosa PAO1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5D8P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5D8P FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</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]] 2.35&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5d8o|5d8o]], [[5d8q|5d8q]], [[5d8r|5d8r]], [[5d8s|5d8s]], [[5d8x|5d8x]], [[5d8y|5d8y]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ferroxidase Ferroxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.16.3.1 1.16.3.1] </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=5d8p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5d8p OCA], [https://pdbe.org/5d8p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5d8p RCSB], [https://www.ebi.ac.uk/pdbsum/5d8p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5d8p ProSAT]</span></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=5d8p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5d8p OCA], [http://pdbe.org/5d8p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5d8p RCSB], [http://www.ebi.ac.uk/pdbsum/5d8p PDBsum]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/Q9HY79_PSEAE Q9HY79_PSEAE]] Iron-storage protein (By similarity).  Iron-storage protein, whose ferroxidase center binds Fe(2+) ions, oxidizes them by dioxygen to Fe(3+), and participates in the subsequent Fe(3+) oxide mineral core formation within the central cavity of the protein complex (By similarity).[PIRNR:PIRNR002560]
+[https://www.uniprot.org/uniprot/Q9HY79_PSEAE Q9HY79_PSEAE] Iron-storage protein (By similarity).  Iron-storage protein, whose ferroxidase center binds Fe(2+) ions, oxidizes them by dioxygen to Fe(3+), and participates in the subsequent Fe(3+) oxide mineral core formation within the central cavity of the protein complex (By similarity).[PIRNR:PIRNR002560]
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 19: / Line 19: @@
 </div>
 <div class="pdbe-citations 5d8p" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Ferritin 3D structures|Ferritin 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Ferroxidase]]
+[[Category: Large Structures]]
-[[Category: Battaile, K P]]
+[[Category: Pseudomonas aeruginosa PAO1]]
-[[Category: Lovell, S]]
+[[Category: Battaile KP]]
-[[Category: Rivera, M]]
+[[Category: Lovell S]]
-[[Category: Wang, Y]]
+[[Category: Rivera M]]
-[[Category: Yao, H]]
+[[Category: Wang Y]]
-[[Category: Electron transport]]
+[[Category: Yao H]]
-[[Category: Iron binding]]
-[[Category: Iron mobilization]]
-[[Category: Iron storage]]
-[[Category: Oxidoreductase]]

5d8p

From Proteopedia

Current revision

2.35A resolution structure of iron bound BfrB (wild-type, C2221 form) from Pseudomonas aeruginosa

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox