Manganese as a Replacement for Magnesium and Zinc:  Functional Comparison of the Divalent Ions

Bock, Charles W.; Katz, Arie; Markham, and George D.; Glusker, Jenny P.

doi:10.1021/ja9906960

Cited by 249 publications

(284 citation statements)

References 56 publications

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“…Although a histidine imidazolate would be unusual as a Mg 2+ ligand, 325 examples of histidine-Mg 2+ coordination interactions are found in the Metalloprotein Database (http://metallo.scripps.edu), and 9 examples of imidazole-Mg 2+ coordination interactions are found in the Cambridge Structural Database (37), so there is ample structural precedent for such interactions. On the other hand, Zn 2+ binds more frequently to nitrogen ligands than Mg 2+ (38), and the results of the anomalous scattering experiment provide conclusive evidence for Zn 2+ E binding in the current study.…”

Section: Inferences On Substrate Bindingsupporting

confidence: 80%

Binding of Uridine 5‘-Diphosphate in the “Basic Patch” of the Zinc Deacetylase LpxC and Implications for Substrate Binding^,

Gennadios

Christianson

2006

Biochemistry

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LpxC is a zinc metalloenzyme that catalyzes the first committed step in the biosynthesis of lipid A, a vital component of the outer membrane of Gram-negative bacteria. Accordingly, the inhibition of LpxC is an attractive strategy for the treatment of Gram-negative bacterial infections. Here, we report the 2.7 Å resolution X-ray crystal structure of LpxC from Aquifex aeolicus complexed with uridine 5′-diphosphate (UDP), and the 3.1 Å resolution structure of LpxC complexed with pyrophosphate. The X-ray crystal structure of the LpxC-UDP complex provides the first view of interactions likely to be exploited by the substrate UDP group in the "basic patch" of the active site. The diphosphate group of UDP makes hydrogen bond interactions with strictly conserved residue K239 as well as solvent molecules. The ribose moiety of UDP interacts with partially conserved residue E197. The UDP uracil group hydrogen bonds with both the backbone NH group and the backbone carbonyl group of E160, and with the backbone NH group of K162 through an intervening water molecule. Finally, the α-phosphate and uracil groups of UDP interact with R143 and R262 through intervening water molecules. The structure of LpxC complexed with pyrophosphate reveals generally similar intermolecular interactions in the basic patch. Unexpectedly, diphosphate binding in both complexes is accompanied by coordination to an additional zinc ion, resulting in the identification of a new metal-binding site termed the E-site. The structures of the LpxC-UDP and LpxC-pyrophosphate complexes provide new insights regarding substrate recognition in the basic patch and metal ion coordination in the active site of LpxC.The zinc metalloenzyme UDP -{3-O-[(R)-3-hydroxymyristoyl]}-N-acetylglucosamine deacetylase (LpxC) catalyzes the first irreversible step in the biosynthesis of lipid A ( Figure 1) (1-4), which is ultimately incorporated into the outer leaflet of the outer membrane of Gramnegative bacteria as the hydrophobic anchor of lipopolysaccharide (LPS) (5-9). 1 The exterior sheath of LPS serves as a protective barrier that resists penetration by many common antibiotics such as erythromycin (8)(9)(10)(11)(12)(13)(14). Importantly, lipid A is the toxic component of LPS that triggers a severe immune response to Gram-negative bacterial infections, which can lead to septic shock accompanied by acute hypotension, multiple organ failure, and death (15-18). Accordingly, inhibitors of LpxC and lipid A biosynthesis represent a potential treatment option for Gramnegative sepsis. † This work was supported by the National Institutes of Health grant GM49758. ‡ The atomic coordinates of LpxC complexed with uridine 5′-diphosphate and pyrophosphate have been deposited in the Protein Data Bank, www.rcsb.org, with accession codes 2IER and 2IES, respectively. *To whom correspondence should be addressed: Tel: 215-898-5714. Fax: 215-573-2201. E-mail: chris@sas.upenn.edu.. 1 Abbreviations: LpxC, UDP -{3-O-[(R)-3-hydroxymyristoyl]}-N-acetylglucosamine deacetylase; LPS, lipopolysaccha...

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Section: Inferences On Substrate Bindingsupporting

confidence: 80%

Binding of Uridine 5‘-Diphosphate in the “Basic Patch” of the Zinc Deacetylase LpxC and Implications for Substrate Binding^,

Gennadios

Christianson

2006

Biochemistry

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“…Numerous studies have shown that various divalent cations affect the base selectivity of pols to different extents (13,14,(43)(44)(45)(46) …”

Section: Effect Of Metal Ions On Base Selectivitymentioning

confidence: 99%

“…Despite its ability to lower the pK a of bound water and despite having similar ionic radii to Mg 2ϩ , Zn 2ϩ is not able to activate most DNA pols. Based on its properties ( complexes, which allows less freedom for mismatched dNTPs to be accessible to the nucleotide binding pocket (44). Transition metal ions such as Mn 2ϩ bind more tightly to carboxylate groups and the triphosphate moiety of dNTPs as compared with Mg 2ϩ (9), which could explain its ability to reduce base selectivity.…”

Section: Properties Of Divalent Cations That Can Activate Dna Polymermentioning

confidence: 99%

Different Divalent Cations Alter the Kinetics and Fidelity of DNA Polymerases

Vashishtha

Wang

Konigsberg

2016

Journal of Biological Chemistry

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Divalent metal ions are essential components of DNA polymerases both for catalysis of the nucleotidyl transfer reaction and for base excision. They occupy two sites, A and B, for DNA synthesis. Recently, a third metal ion was shown to be essential for phosphoryl transfer reaction. The metal ion in the A site is coordinated by the carboxylate of two highly conserved acidic residues, water molecules, and the 3-hydroxyl group of the primer so that the A metal is in an octahedral complex. Its catalytic function is to lower the pK a of the hydroxyl group, making it a highly effective nucleophile that can attack the ␣ phosphorous atom of the incoming dNTP. The metal ion in the B site is coordinated by the same two carboxylates that are affixed to the A metal ion as well as the non-bridging oxygen atoms of the incoming dNTP. The carboxyl oxygen of an adjacent peptide bond serves as the sixth ligand that completes the octahedral coordination geometry of the B metal ion. Similarly, two metal ions are required for proofreading; one helps to lower the pK a of the attacking water molecule, and the other helps to stabilize the transition state for nucleotide excision. The role of different divalent cations are discussed in relation to these two activities as well as their influence on base selectivity and misincorporation by DNA polymerases. Some, but not all, of the effects of these different metal ions can be rationalized based on their intrinsic properties, which are tabulated in this review.All DNA polymerases (DNA pols) 2 require Mg 2ϩ or Mn 2ϩ for primer extension and for excision of incorrectly incorporated dNTPs via intrinsic 3Ј35Ј exonuclease activity (1-5). A two-metal-ion mechanism is used by all DNA pols to catalyze nucleotide addition to a growing primer strand (6). Although DNA polymerases employ the physiologically relevant Mg 2ϩ , other divalent metal ions can substitute for Mg 2ϩ , although they tend to reduce the fidelity of DNA replication (7-10). The effect of metal ion cofactors on the fidelity of DNA replication has been studied for various DNA pols including E. coli DNA pol I (11), AMV DNA pol (12), Klenow fragment of E. coli DNA pol I (13), T4 pol (7), T7 pol (7), human pol ␣ (7), pol ␤ (7), and Dpo4 (8). Some metal ions have been shown to be mutagens and carcinogens probably because they reduce the base selectivity of DNA pols (7,8,(11)(12)(13)(14)(15). Different divalent cations influence fidelity check points in the minimal kinetic scheme for the nucleotidyl transfer reaction (Scheme 1). Cations that can substitute for Mg 2ϩ affect DNA pols by: 1) altering the groundstate binding affinity of incoming dNTPs to pol⅐DNA binary complexes (16); 2) decreasing base selectivity by promoting misincorporation during primer extension (8); 3) decreasing the rate of base excision (17); 4) altering primer extension past a mismatch at the primer-template (P/T) terminus (17). This review will address the way various metal ions increase misincorporation based on their physical properties. Our emphasis will be on th...

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“…[14][15][16][17][18][19][20] In this study, we studied geometrical structures, charge distributions, and bond structures of hydrated and hydrolysis complexes of Zn 2+ , as well as the mechanisms of hydration, dehydration, and hydrolysis.…”

Section: Introductionmentioning

confidence: 99%

Quantum Chemical Studies of Mononuclear Zinc Species of Hydration and Hydrolysis

Zhu

Pan

2005

J. Phys. Chem. A

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Optimal geometries, charge distributions, bond analysis, changes of Gibbs free energy, entropies and enthalpies of hydration, and hydrolysis reactions for mononuclear species of Zn 2+ including hydrated and hydrolysis complexes were investigated using quantum chemical calculations in the gas phase. Optimized geometrical structures showed that the stable hydrated and hydrolysis zinc species without outer-sphere water molecules . Results of NPA (Natural Population Analysis) indicated that the charge on the Zn atom of the hydrated ions decreased but the charge on the zinc atom of the hydrolysis species increased with the increase of inner-sphere water molecules. NBO (Natural Bond Orbital) analyses demonstrated that hydrated and hydrolysis species of zinc were mainly electrostatic bonding compounds. Calculations of reaction energies indicated that inner-sphere water molecules became more unfavorable as the hydrolysis increased. Stepwise hydrolysis equilibrium constants decreased successively and the order remained unchanged when the inner-sphere dehydration occurred.

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Manganese as a Replacement for Magnesium and Zinc: Functional Comparison of the Divalent Ions

Cited by 249 publications

References 56 publications

Binding of Uridine 5‘-Diphosphate in the “Basic Patch” of the Zinc Deacetylase LpxC and Implications for Substrate Binding^,

Binding of Uridine 5‘-Diphosphate in the “Basic Patch” of the Zinc Deacetylase LpxC and Implications for Substrate Binding^,

Different Divalent Cations Alter the Kinetics and Fidelity of DNA Polymerases

Quantum Chemical Studies of Mononuclear Zinc Species of Hydration and Hydrolysis

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Manganese as a Replacement for Magnesium and Zinc: Functional Comparison of the Divalent Ions

Cited by 249 publications

References 56 publications

Binding of Uridine 5‘-Diphosphate in the “Basic Patch” of the Zinc Deacetylase LpxC and Implications for Substrate Binding,

Binding of Uridine 5‘-Diphosphate in the “Basic Patch” of the Zinc Deacetylase LpxC and Implications for Substrate Binding,

Different Divalent Cations Alter the Kinetics and Fidelity of DNA Polymerases

Quantum Chemical Studies of Mononuclear Zinc Species of Hydration and Hydrolysis

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Resources

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Binding of Uridine 5‘-Diphosphate in the “Basic Patch” of the Zinc Deacetylase LpxC and Implications for Substrate Binding^,

Binding of Uridine 5‘-Diphosphate in the “Basic Patch” of the Zinc Deacetylase LpxC and Implications for Substrate Binding^,