Identification of Two Heme-Binding Sites in the Cytoplasmic Heme-Trafficking Protein PhuS fromPseudomonas aeruginosaand Their Relevance to Function†

Biochemistry ◽  
2007 ◽  
Vol 46 (50) ◽  
pp. 14391-14402 ◽  
Author(s):  
Darci R. Block ◽  
Gudrun S. Lukat-Rodgers ◽  
Kenton R. Rodgers ◽  
Angela Wilks ◽  
Mehul N. Bhakta ◽  
...  
Keyword(s):  
Binding Sites ◽  
Heme Binding ◽  
Heme Trafficking

scholarly journals Structure-Function Analysis of the Bifunctional CcsBA Heme Exporter and CytochromecSynthetase

mBio ◽  
2018 ◽  
Vol 9 (6) ◽  
Author(s):  
Molly C. Sutherland ◽  
Nathan L. Tran ◽  
Dustin E. Tillman ◽  
Joshua M. Jarodsky ◽  
Jason Yuan ◽  
...  
Keyword(s):  
Structure Function ◽  
Binding Site ◽  
Binding Sites ◽  
Structural Model ◽  
Function Analysis ◽  
Integral Membrane Protein ◽  
Covalent Attachment ◽  
Heme Binding ◽  
Heme Transport ◽  
Heme Trafficking

ABSTRACTAlthough intracellular heme trafficking must occur for heme protein assembly, only a few heme transporters have been unequivocally discovered and nothing is known about their structure or mechanisms. Cytochromecbiogenesis in prokaryotes requires the transport of heme from inside to outside for stereospecific attachment to cytochromecvia two thioether bonds (at CXXCH). The CcsBA integral membrane protein was shown to transport and attach heme (and thus is a cytochromecsynthetase), but the structure and mechanisms underlying these two activities are poorly understood. We employed a new cysteine/heme crosslinking tool that traps endogenous heme in heme binding sites. We combined these data with a comprehensive imidazole correction approach (for heme ligand interrogation) to map heme binding sites. Results illuminate the process of heme transfer through the membrane to an external binding site (called the WWD domain). Using meta-genomic data (GREMLIN) and Rosetta modeling programs, a structural model of the transmembrane (TM) regions in CcsBA were determined. The heme mapping data were then incorporated to model the TM heme binding site (with TM-His1 and TM-His2 as ligands) and the external heme binding WWD domain (with P-His1 and P-His2 as ligands). Other periplasmic structure/function studies facilitated modeling of the full CcsBA protein as a framework for understanding the mechanisms. Mechanisms are proposed for heme transport from TM-His to WWD/P-His and subsequent stereospecific attachment of heme. A ligand exchange of the P-His1 for histidine of CXXCH at the synthetase active site is suggested.IMPORTANCEThe movement or trafficking of heme is critical for cellular functions (e.g., oxygen transport and energy production); however, intracellular heme is tightly regulated due to its inherent cytotoxicity. These factors, combined with the transient nature of transport, have resulted in a lack of direct knowledge on the mechanisms of heme binding and trafficking. Here, we used the cytochromecbiogenesis system II pathway as a model to study heme trafficking. System II is composed of two integral membrane proteins (CcsBA) which function to transport heme across the membrane and stereospecifically position it for covalent attachment to apocytochromec. We mapped two heme binding domains in CcsBA and suggest a path for heme trafficking. These data, in combination with metagenomic coevolution data, are used to determine a structural model of CcsBA, leading to increased understanding of the mechanisms for heme transport and the cytochromecsynthetase function of CcsBA.

scholarly journals A protein with multiple heme-binding sites from rabbit serum.

1982 ◽  
Vol 257 (7) ◽  
pp. 3925-3931 ◽  
Author(s):  
K Tsutsui ◽  
G C Mueller
Keyword(s):  
Binding Sites ◽  
Rabbit Serum ◽  
Heme Binding

scholarly journals BionoiNet: ligand-binding site classification with off-the-shelf deep neural network

2020 ◽  
Vol 36 (10) ◽  
pp. 3077-3083
Author(s):  
Wentao Shi ◽  
Jeffrey M Lemoine ◽  
Abd-El-Monsif A Shawky ◽  
Manali Singha ◽  
Limeng Pu ◽  
...  
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Ligand Binding ◽  
Binding Sites ◽  
Protein Structures ◽  
Supplementary Information ◽  
Heme Binding ◽  
Unseen Data ◽  
Ligand Binding Sites ◽  
Binding Pockets

Abstract Motivation Fast and accurate classification of ligand-binding sites in proteins with respect to the class of binding molecules is invaluable not only to the automatic functional annotation of large datasets of protein structures but also to projects in protein evolution, protein engineering and drug development. Deep learning techniques, which have already been successfully applied to address challenging problems across various fields, are inherently suitable to classify ligand-binding pockets. Our goal is to demonstrate that off-the-shelf deep learning models can be employed with minimum development effort to recognize nucleotide- and heme-binding sites with a comparable accuracy to highly specialized, voxel-based methods. Results We developed BionoiNet, a new deep learning-based framework implementing a popular ResNet model for image classification. BionoiNet first transforms the molecular structures of ligand-binding sites to 2D Voronoi diagrams, which are then used as the input to a pretrained convolutional neural network classifier. The ResNet model generalizes well to unseen data achieving the accuracy of 85.6% for nucleotide- and 91.3% for heme-binding pockets. BionoiNet also computes significance scores of pocket atoms, called BionoiScores, to provide meaningful insights into their interactions with ligand molecules. BionoiNet is a lightweight alternative to computationally expensive 3D architectures. Availability and implementation BionoiNet is implemented in Python with the source code freely available at: https://github.com/CSBG-LSU/BionoiNet. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Bach1, a heme-dependent transcription factor, reveals presence of multiple heme binding sites with distinct coordination structure

IUBMB Life ◽  
2007 ◽  
Vol 59 (8) ◽  
pp. 542-551 ◽  
Author(s):  
Shusuke Hira ◽  
Takeshi Tomita ◽  
Toshitaka Matsui ◽  
Kazuhiko Igarashi ◽  
Masao Ikeda-Saito
Keyword(s):  
Transcription Factor ◽  
Binding Sites ◽  
Heme Binding ◽  
Coordination Structure

Preferred heme binding sites of histidine-rich glycoprotein

Biochemistry ◽  
1985 ◽  
Vol 24 (21) ◽  
pp. 5919-5924 ◽  
Author(s):  
Mary Kappel Burch ◽  
William T. Morgan
Keyword(s):  
Binding Sites ◽  
Heme Binding

scholarly journals The Cytoplasmic Heme-binding Protein (PhuS) from the Heme Uptake System ofPseudomonas aeruginosaIs an Intracellular Heme-trafficking Protein to the δ-Regioselective Heme Oxygenase

2006 ◽  
Vol 281 (19) ◽  
pp. 13652-13662 ◽  
Author(s):  
Ila B. Lansky ◽  
Gudrun S. Lukat-Rodgers ◽  
Darci Block ◽  
Kenton R. Rodgers ◽  
Melanie Ratliff ◽  
...  
Keyword(s):  
Heme Oxygenase ◽  
Binding Protein ◽  
Uptake System ◽  
Heme Binding ◽  
Heme Uptake ◽  
Heme Trafficking ◽  
Heme Binding Protein

scholarly journals Quantification of Active Apohemoglobin Heme-Binding Sites via Dicyanohemin Incorporation

Biochemistry ◽  
2017 ◽  
Vol 56 (40) ◽  
pp. 5245-5259 ◽  
Author(s):  
Ivan S. Pires ◽  
Donald A. Belcher ◽  
Andre F. Palmer
Keyword(s):  
Binding Sites ◽  
Heme Binding
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