scholarly journals Transition metal binding selectivity in proteins and its correlation with the phylogenomic classification of the cation diffusion facilitator protein family

2017 ◽  
Author(s):  
Shiran Barber-Zucker ◽  
Boaz Shaanan ◽  
Raz Zarivach
Keyword(s):  
Binding Site ◽  
De Novo ◽  
Specific Binding ◽  
Protein Family ◽  
Cation Diffusion ◽  
Binding Selectivity ◽  
Cation Diffusion Facilitator ◽  
Conserved Sequence ◽  
Metal Selectivity

AbstractDivalent d-block metal cations (DDMCs), such as Fe, Zn and Mn, participate in many biological processes. Understanding how specific DDMCs are transported to and within the cell and what controls their binding selectivity to different proteins is crucial for defining the mechanisms of metalloproteins. To better understand such processes, we scanned the RCSB Protein Data Bank, performed a de novo structural-based comprehensive analysis of seven DDMCs and found their amino acid binding and coordination geometry propensities. We then utilized these results to characterize the correlation between metal selectivity, specific binding site composition and phylogenetic classification of the cation diffusion facilitator (CDF) protein family, a family of DDMC transporters found throughout evolution and sharing a conserved structure, yet with different members displaying distinct metal selectivity. Our analysis shows that DDMCs differ, at times significantly, in terms of their binding propensities, and that in each CDF clade, the metal selectivity-related binding site has a unique and conserved sequence signature. However, only limited correlation exists between the composition of the DDMC binding site in each clade and the metal selectivity shown by its proteins.

scholarly journals Functional Determinants of Metal Ion Transport and Selectivity in Paralogous Cation Diffusion Facilitator Transporters CzcD and MntE in Streptococcus pneumoniae

2016 ◽  
Vol 198 (7) ◽  
pp. 1066-1076 ◽  
Author(s):  
Julia E. Martin ◽  
David P. Giedroc
Keyword(s):  
Streptococcus Pneumoniae ◽  
Metal Ion ◽  
Transmembrane Domain ◽  
Divalent Metal ◽  
Cation Diffusion ◽  
Metal Specificity ◽  
Cation Diffusion Facilitator ◽  
Content Type ◽  
Metal Selectivity ◽  
A Site

ABSTRACTCation diffusion facilitators (CDFs) are a large family of divalent metal transporters that collectively possess broad metal specificity and contribute to intracellular metal homeostasis and virulence in bacterial pathogens.Streptococcus pneumoniaeexpresses two homologous CDF efflux transporters, MntE and CzcD. Cells lackingmntEorczcDare sensitive to manganese (Mn) or zinc (Zn) toxicity, respectively, and specifically accumulate Mn or Zn, respectively, thus suggesting that MntE selectively transports Mn, while CzcD transports Zn. Here, we probe the origin of this metal specificity using a phenotypic growth analysis of pneumococcal variants. Structural homology toEscherichia coliYiiP predicts that both MntE and CzcD are dimeric and each protomer harbors four pairs of conserved metal-binding sites, termed the A site, the B site, and the C1/C2 binuclear site. We find that single amino acid mutations within both the transmembrane domain A site and the B site in both CDFs result in a cellular metal sensitivity similar to that of the corresponding null mutants. However, multiple mutations in the predicted cytoplasmic C1/C2 cluster of MntE have no impact on cellular Mn resistance, in contrast to the analogous substitutions in CzcD, which do have on impact on cellular Zn resistance. Deletion of the MntE-specific C-terminal tail, present only in Mn-specific bacterial CDFs, resulted in only a modest growth phenotype. Further analysis of MntE-CzcD functional chimeric transporters showed that Asn and Asp in theND-DD A-site motif of MntE and the most N-terminal His in theHD-HD site A of CzcD (the specified amino acids are underlined) play key roles in transporter metal selectivity.IMPORTANCECation diffusion facilitator (CDF) proteins are divalent metal ion transporters that are conserved in organisms ranging from bacteria to humans and that play important roles in cellular physiology, from metal homeostasis and resistance to type I diabetes in vertebrates. The respiratory pathogenStreptococcus pneumoniaeexpresses two metal CDF transporters, CzcD and MntE. How CDFs achieve metal selectivity is unclear. We show here that CzcD and MntE are true paralogs, as CzcD transports zinc, while MntE selectively transports manganese. Through the use of an extensive collection of pneumococcal variants, we show that a primary determinant for metal selectivity is the A site within the transmembrane domain. This extends our understanding of how CDFs discriminate among transition metals.

scholarly journals The cation diffusion facilitator protein MamM's cytoplasmic domain exhibits metal-type dependent binding modes and discriminates against Mn2+

2020 ◽  
Vol 295 (49) ◽  
pp. 16614-16629
Author(s):  
Shiran Barber-Zucker ◽  
Jenny Hall ◽  
Afonso Froes ◽  
Sofiya Kolusheva ◽  
Fraser MacMillan ◽  
...  
Keyword(s):  
Transmembrane Domain ◽  
Magnetotactic Bacteria ◽  
Crystal Form ◽  
Binding Modes ◽  
Cation Diffusion ◽  
Cation Diffusion Facilitator ◽  
Metal Type ◽  
Metal Selectivity ◽  
Functional Discrimination ◽  
Metal Recognition

Cation diffusion facilitator (CDF) proteins are a conserved family of divalent transition metal cation transporters. CDF proteins are usually composed of two domains: the transmembrane domain, in which the metal cations are transported through, and a regulatory cytoplasmic C-terminal domain (CTD). Each CDF protein transports either one specific metal or multiple metals from the cytoplasm, and it is not known whether the CTD takes an active regulatory role in metal recognition and discrimination during cation transport. Here, the model CDF protein MamM, an iron transporter from magnetotactic bacteria, was used to probe the role of the CTD in metal recognition and selectivity. Using a combination of biophysical and structural approaches, the binding of different metals to MamM CTD was characterized. Results reveal that different metals bind distinctively to MamM CTD in terms of their binding sites, thermodynamics, and binding-dependent conformations, both in crystal form and in solution, which suggests a varying level of functional discrimination between CDF domains. Furthermore, these results provide the first direct evidence that CDF CTDs play a role in metal selectivity. We demonstrate that MamM's CTD can discriminate against Mn2+, supporting its postulated role in preventing magnetite formation poisoning in magnetotactic bacteria via Mn2+ incorporation.

scholarly journals The cation diffusion facilitator protein MamM’s cytoplasmic domain exhibits metal-type dependent binding modes and discriminates against Mn2+

2020 ◽  
Author(s):  
Shiran Barber-Zucker ◽  
Jenny Hall ◽  
Afonso Froes ◽  
Sofiya Kolusheva ◽  
Fraser MacMillan ◽  
...  
Keyword(s):  
Direct Evidence ◽  
Transmembrane Domain ◽  
Crystal Form ◽  
Binding Modes ◽  
Cation Diffusion ◽  
Cation Diffusion Facilitator ◽  
Metal Type ◽  
Metal Selectivity ◽  
Specific Metal

SummaryCation diffusion facilitator (CDF) proteins are a conserved family of divalent transition metal cation transporters. CDF proteins are usually composed of two domains: the transmembrane domain (TMD), in which the metal cations are transported through, and a regulatory cytoplasmic C-terminal domain (CTD). Each CDF protein transports either one specific metal, or multiple metals, from the cytoplasm. Here, the model CDF protein MamM, from magnetotactic bacteria, was used to probe the role of the CTD in metal selectivity. Using a combination of biophysical and structural approaches, the binding of different metals to MamM CTD was characterized. Results reveal that different metals bind distinctively to MamM CTD in terms of; their binding sites, thermodynamics and binding-dependent conformation, both in crystal form and in solution. Furthermore, the results indicate that the CTD discriminates against Mn2+ and provides the first direct evidence that CDF CTD’s play a role in metal selectivity.

scholarly journals Putative metal binding site in the transmembrane domain of the manganese transporter SLC30A10 is different from that of related zinc transporters

Metallomics ◽  
2018 ◽  
Vol 10 (8) ◽  
pp. 1053-1064 ◽  
Author(s):  
Charles E. Zogzas ◽  
Somshuvra Mukhopadhyay
Keyword(s):  
Binding Site ◽  
Metal Binding ◽  
Transmembrane Domain ◽  
Zinc Transporters ◽  
Cation Diffusion ◽  
Metal Binding Site ◽  
Cation Diffusion Facilitator

Mechanism by which the cation diffusion facilitator SLC30A10 transports manganese is fundamentally different from that of previously-studied proteins in this superfamily.

scholarly journals FunFam protein families improve residue level molecular function prediction

2019 ◽  
Author(s):  
Linus Mathias Scheibenreif ◽  
Maria Littmann ◽  
Christine Orengo ◽  
Burkhard Rost
Keyword(s):  
Protein Binding ◽  
Binding Site ◽  
De Novo ◽  
Prediction Method ◽  
Fold Increase ◽  
Residue Level ◽  
Protein Domain ◽  
Enzymatic Function ◽  
Binding Residues

Abstract Background The CATH database provides a hierarchical classification of protein domain structures including a sub-classification of superfamilies into functional families (FunFams). We analyzed the similarity of binding site annotations in these FunFams and incorporated FunFams into the prediction of protein binding residues. Results FunFam members agreed, on average, in 36.9±0.6% of their binding residue annotations. This constituted a 6.7-fold increase over randomly grouped proteins and a 1.2-fold increase (1.1-fold on the same dataset) over proteins with the same enzymatic function (identical Enzyme Commission, EC, number). Mapping de novo binding site prediction methods (BindPredict-CCS, BindPredict-CC) onto FunFam resulted in consensus predictions for those residues that were aligned and predicted alike (binding/non-binding) within a FunFam. This simple consensus increased the F1-score (for binding) 1.5-fold over the original prediction method. Variation of the threshold for how many proteins in the consensus prediction had to agree provided a convenient control of accuracy/precision and coverage/recall, e.g. reaching a precision as high as 60.8±0.4% for a stringent threshold. Conclusions The FunFams outperformed even the carefully curated EC numbers in terms of agreement of binding site residues. Additionally, we assume that our proof-of-principle through the prediction of protein binding residues will be relevant for many other solutions profiting from FunFams to infer functional information at the residue level.

scholarly journals The metal binding site composition of the cation diffusion facilitator protein MamM cytoplasmic domain impacts its metal responsivity

2020 ◽  
Author(s):  
Shiran Barber-Zucker ◽  
Anat Shahar ◽  
Sofiya Kolusheva ◽  
Raz Zarivach
Keyword(s):  
Metal Binding ◽  
Binding Sites ◽  
Transmembrane Domain ◽  
Metal Cations ◽  
Data Bank ◽  
Cation Diffusion ◽  
Cation Diffusion Facilitator ◽  
Metal Selectivity ◽  
The Impact

AbstractThe cation diffusion facilitator (CDF) is a conserved family of divalent d-block metal cation transporters that extrude these cations selectively from the cytoplasm. CDF proteins are composed of two domains: the transmembrane domain, through which the cations are transported, and a regulatory cytoplasmic C-terminal domain (CTD). Metal binding to the CTD leads to its tighter conformation, and this sequentially promotes conformational change of the transmembrane domain which allows the actual transport of specific metal cations. It was recently shown that the magnetotactic bacterial CDF protein MamM CTD has a role in metal selectivity, as binding of different metal cations exhibits distinctive affinities and conformations. It is yet unclear whether the composition of the CTD binding sites can impact metal selectivity. Here we performed a mutational study of MamM CTD, where we exchanged the metal binding residues with different metal-binding amino acids. Using X-ray crystallography and Trp-fluorescence spectrometry, we studied the impact of the mutations on the CTD conformation in the presence of different metals. Our results reveal that the incorporation of such mutations alters the domain response to metals in vitro, as mutant forms of the CTD bind metals differently in terms of the composition of the binding sites and the CTD conformation.CoordinatesMamM CTD structures have been deposited in the Protein Data Bank under the following accession codes: 6H5V, 6H5M, 6H5U, 6H8G, 6HAO, 6H88, 6H87, 6H8A, 6H89, 6H8D, 6H5K, 6H9Q, 6H84, 6H83, 6HA2, 6H8I, 6H9T, 6H81, 6HAN, 6H85, 6H9P, 6HHS.

scholarly journals FunFam protein families improve residue level molecular function prediction

2019 ◽  
Author(s):  
Linus Mathias Scheibenreif ◽  
Maria Littmann ◽  
Christine Orengo ◽  
Burkhard Rost
Keyword(s):  
Protein Binding ◽  
Binding Site ◽  
De Novo ◽  
Prediction Method ◽  
Fold Increase ◽  
Residue Level ◽  
Protein Domain ◽  
Enzymatic Function ◽  
Binding Residues

Abstract Background The CATH database provides a hierarchical classification of protein domain structures including a sub-classification of superfamilies into functional families (FunFams). We analyzed the similarity of binding site annotations in these FunFams and incorporated FunFams into the prediction of protein binding residues. Results FunFam members agreed, on average, in 36.9±0.6% of their binding residue annotations. This constituted a 6.7-fold increase over randomly grouped proteins and a 1.2-fold increase (1.1-fold on the same dataset) over proteins with the same enzymatic function (identical Enzyme Commission, EC, number). Mapping de novo binding site prediction methods (BindPredict-CCS, BindPredict-CC) onto FunFam resulted in consensus predictions for those residues that were aligned and predicted alike (binding/non-binding) within a FunFam. This simple consensus increased the F1-score (for binding) 1.5-fold over the original prediction method. Variation of the threshold for how many proteins in the consensus prediction had to agree provided a convenient control of accuracy/precision and coverage/recall, e.g. reaching a precision as high as 60.8±0.4% for a stringent threshold. Conclusions The FunFams outperformed even the carefully curated EC numbers in terms of agreement of binding site residues. Additionally, we assume that our proof-of-principle through the prediction of protein binding residues will be relevant for many other solutions profiting from FunFams to infer functional information at the residue level.

scholarly journals Metal transport mechanism of the cation diffusion facilitator (CDF) protein family – a structural perspective on human CDF (ZnT)-related diseases

2021 ◽  
Author(s):  
Shiran Barber-Zucker ◽  
Arie Moran ◽  
Raz Zarivach
Keyword(s):  
Transport Mechanism ◽  
Metal Transport ◽  
Protein Family ◽  
Cation Diffusion ◽  
Cation Diffusion Facilitator ◽  
Mechanistic Analysis ◽  
Structural Perspective

A mechanistic analysis and structural perspective of cation diffusion facilitator (human ZnT) related diseases.

Sign in / Sign up

Export Citation Format

Share Document