Periplasmic binding proteins: a versatile superfamily for protein engineering

Dwyer, Mary A.; Hellinga, Homme W.

doi:10.1016/j.sbi.2004.07.004

Cited by 326 publications

(281 citation statements)

References 55 publications

Supporting

Mentioning

280

Contrasting

Order By: Relevance

“…2. CmpA is an ␣-␤ protein and belongs to the periplasmic-binding protein superfamily (14). Similar to the related nitrate-binding protein NrtA, CmpA is composed of two domains (I and II) organized in a C-clamp shape.…”

Section: Resultsmentioning

confidence: 99%

“…Based on the order of the ␤-strands in each domain (21354), CmpA belongs to class II of the periplasmic-binding protein superfamily (14), which also includes the oxyanion-binding proteins specific for sulfate, phosphate, and molybdate (15)(16)(17)(18)(19). However, CmpA, similar to NrtA, is much larger (ϳ100 amino acids) than these oxyanionbinding proteins.…”

Section: Resultsmentioning

confidence: 99%

See 1 more Smart Citation

The Structure of a Cyanobacterial Bicarbonate Transport Protein, CmpA

Koropatkin

Koppenaal

Pakrasi

et al. 2007

Journal of Biological Chemistry

View full text Add to dashboard Cite

Cyanobacteria, blue-green algae, are the most abundant autotrophs in aquatic environments and form the base of the food chain by fixing carbon and nitrogen into cellular biomass. To compensate for the low selectivity of Rubisco for CO 2 over O 2 , cyanobacteria have developed highly efficient CO 2 -concentrating machinery of which the ABC transport system CmpABCD from Synechocystis PCC 6803 is one component. Here, we have described the structure of the bicarbonatebinding protein CmpA in the absence and presence of bicarbonate and carbonic acid. CmpA is highly homologous to the nitrate transport protein NrtA. CmpA binds carbonic acid at the entrance to the ligand-binding pocket, whereas bicarbonate binds in nearly an identical location compared with nitrate binding to NrtA. Unexpectedly, bicarbonate binding is accompanied by a metal ion, identified as Ca 2؉ via inductively coupled plasma optical emission spectrometry. The binding of bicarbonate and metal appears to be highly cooperative and suggests that CmpA may co-transport bicarbonate and calcium or that calcium acts a cofactor in bicarbonate transport.Cyanobacteria are the most abundant microorganisms in aquatic environments and play a key role in the global carbon cycle (1). It is estimated that these photosynthetic microbes are responsible for ϳ50% of carbon fixation in the oceans. Over their 2.7-billion-year existence, cyanobacteria had to adapt to a changing gaseous environment where the levels of CO 2 declined and O 2 increased (2). Because O 2 can compete with CO 2 for binding to the carbon-fixing enzyme Rubisco (3), cyanobacteria evolved the most effective CO 2 -concentrating mechanism (CCM) 2 that allows them to concentrate CO 2 levels around Rubisco up to 1000-fold. The CCM involves the import and accumulation of inorganic carbon as HCO 3 Ϫ in the cytoplasm and subsequent conversion to CO 2 in the protein microcompartment called the "carboxysome" via carbonic anhydrase.One component of this CCM machinery in Synechocystis PCC 6803 is the cmpABCD operon that encodes a high affinity bicarbonate ABC transporter that is induced under low CO 2 conditions (4). This transporter is composed of four polypeptides, a high affinity solute-binding lipoprotein (CmpA), an integral membrane permease (CmpB), a cytoplasmic ATPase (CmpD), and an ATPase/solute-binding fusion protein (CmpC) that regulates transport (Fig. 1). The CmpABCD transporter is the highest affinity bicarbonate transporter of cyanobacteria (4). This affinity is predominantly conferred by the binding of bicarbonate to CmpA (K d ϭ 5 M) (5). CmpA is anchored to the periplasmic face of the cytoplasmic membrane via a lipid anchor attached to a conserved cysteine (6). The closest known homologue of CmpA is NrtA, the solute-binding protein of the nitrate-specific NrtABCD transporter that is 48% identical and 61% similar in amino acid sequence (7). We recently published an analysis (8) of the 1.6-Å structure of NrtA complexed with nitrate to elucidate the molecular determinants of nitrate specificity. From ...

show abstract

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

The Structure of a Cyanobacterial Bicarbonate Transport Protein, CmpA

Koropatkin

Koppenaal

Pakrasi

et al. 2007

Journal of Biological Chemistry

View full text Add to dashboard Cite

show abstract

“…The members of the periplasmic-binding protein superfold are typified by a ligand-mediated hinge-bending motion interconverting open (apo-protein) and closed (protein-ligand complex) conformations 36 , which may contribute to scaffold-imposed limitations. In maltose-binding protein the free energy of formation of the closed state, ΔG C , has been estimated to be 8.4±0.2 kcal/mol 37 ; the corresponding values for ecRBP or tteRBP are not known.…”

Section: Discussionmentioning

confidence: 99%

RETRACTED: Local Encoding of Computationally Designed Enzyme Activity

Allert

Dwyer

Hellinga

2007

Journal of Molecular Biology

View full text Add to dashboard Cite

One aim of computational protein design is to introduce novel enzyme activity into proteins of known structure by predicting mutations that stabilize transition states. Previously we have shown that it is possible to introduce triose phosphate isomerase activity into the ribose-binding protein of Escherichia coli by constructing 17 mutations in the first two layers of residues that surround the wild-type ligand-binding site. Here we report that these mutations can be "transplanted" into a homologous ribose-binding protein, isolated from the hyperthermophilic bacterium Thermoanaerobacter tengcongensis, with retention of catalytic activity, substrate affinity, and reaction pH dependence. The observed 10 5 -10 6 -fold rate enhancement corresponds to 70% of the maximally known transition-state binding energy. The wild-type sequences in these two homologues are almost perfectly conserved in the vicinity of their ribose-binding sites, but diverge significantly at increasing distance from these sites. The results demonstrate that the computationally designed mutations are sufficient to encode the observed enzyme activity, that all the observed activity is locally encoded within the layer of residues directly in contact with the substrate, and that in this case at least 70% of transition state stabilization energy can be achieved using straightforward considerations of stereochemical complementarity between enzyme and reactants.

show abstract

“…[51]. Notably, it interacts with AI-2 molecules in conjugation with a two-component sensor kinase, LuxQ with a hybrid of a periplasmic sensor domain and cytoplasmic histidine domains [52]. Irrespective of LuxP interaction with AI-2 or not, the unliganded apoform hold open to have specific interaction through the PAS domain with the LuxQ (LuxQp) [53].…”

Section: Luxpqmentioning

confidence: 99%

Meddling Vibrio cholerae Murmurs: A Neoteric Advancement in Cholera Research

2015

View full text Add to dashboard Cite

Cholera, a known diarrheal disease is associated with various risk factors like hypovolemic shock, rice watery stools, and death in developing countries. The overuse of antibiotics to treat cholera imposed a selective pressure for the emergence and spread of multi-drug resistant Vibrio cholerae strains. The failure of conventional antimicrobial therapy urged the researchers to find an alternative therapy that could meddle the cholera murmurs (Quorum Sensing). It seems to effectively overcome the conventional cholera therapies in parallel to decrease the morbidity and mortality rate in the developing countries. The paramount objective of this review essentially focuses on the different Quorum Sensing (QS) regulatory switches governing virulence and pathogenicity of Vibrio cholerae. This review also provides an insight into the plausible QS targets that could be exploited to bring about a breakthrough to the prevailing cholera therapy.

show abstract

Periplasmic binding proteins: a versatile superfamily for protein engineering

Cited by 326 publications

References 55 publications

The Structure of a Cyanobacterial Bicarbonate Transport Protein, CmpA

The Structure of a Cyanobacterial Bicarbonate Transport Protein, CmpA

RETRACTED: Local Encoding of Computationally Designed Enzyme Activity

Meddling Vibrio cholerae Murmurs: A Neoteric Advancement in Cholera Research

Contact Info

Product

Resources

About