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Article: Insights into the mechanism of catalysis by the P-C bond-cleaving enzyme phosphonoacetaldehyde hydrolase derived from gene sequence analysis and mutagenesis.

Baker, A S / Ciocci, M J / Metcalf, W W / Kim, J / Babbitt, P C / Wanner, B L / Martin, B M / Dunaway-Mariano, D

1998 Volume 37, Issue 26, Page(s) 9305–9315

Abstract: ... at the imine C(1) and acyl phosphate phosphorus. ...

Abstract	Phosphonoacetaldehyde hydrolase (phosphonatase) catalyzes the hydrolysis of phosphonoacetaldehyde to acetaldehyde and inorganic phosphate. In this study, the genes encoding phosphonatase in Bacillus cereus and in Salmonella typhimurium were cloned for high-level expression in Escherichia coli. The kinetic properties of the purified, recombinant phosphonatases were determined. The Schiff base mechanism known to operate in the B. cereus enzyme was verified for the S. typhimurium enzyme by phosphonoacetaldehyde-sodium borohydride-induced inactivation and by site-directed mutagenesis of the catalytic lysine 53. The protein sequence inferred from the B. cereus phosphonatase gene was determined, and this sequence was used along with that from the S. typhimurium phosphonatase gene sequence to search the primary sequence databases for possible structural homologues. We found that phosphonatase belongs to a novel family of hydrolases which appear to use a highly conserved active site aspartate residue in covalent catalysis. On the basis of this finding and the known stereochemical course of phosphonatase-catalyzed hydrolysis at phosphorus (retention), we propose a mechanism which involves Schiff base formation with lysine 53 followed by phosphoryl transfer to aspartate (at position 11 in the S. typhimurium enzyme and position 12 in the B. cereusphosphonatase) and last hydrolysis at the imine C(1) and acyl phosphate phosphorus.
MeSH term(s)	Amino Acid Sequence ; Bacillus cereus/enzymology ; Bacillus cereus/genetics ; Binding Sites ; Carbon/metabolism ; Catalysis ; Cloning, Molecular ; Conserved Sequence/genetics ; Evolution, Molecular ; Gene Expression Regulation, Bacterial ; Hydrolases/chemistry ; Hydrolases/genetics ; Hydrolases/isolation & purification ; Hydrolases/metabolism ; Hydrolysis ; Lysine/genetics ; Lysine/metabolism ; Models, Molecular ; Molecular Sequence Data ; Multigene Family ; Mutagenesis, Site-Directed ; Phosphorus/metabolism ; Pseudomonas aeruginosa/enzymology ; Pseudomonas aeruginosa/genetics ; Salmonella typhimurium/enzymology ; Salmonella typhimurium/genetics ; Schiff Bases/metabolism ; Sequence Alignment ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid
Chemical Substances	Schiff Bases ; Phosphorus (27YLU75U4W) ; Carbon (7440-44-0) ; Hydrolases (EC 3.-) ; phosphonoacetaldehyde hydrolase (EC 3.11.1.1) ; Lysine (K3Z4F929H6)
Language	English
Publishing date	1998-06-30
Publishing country	United States
Document type	Comparative Study ; Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, U.S. Gov't, P.H.S.
ZDB-ID	1108-3
ISSN	1520-4995 ; 0006-2960
ISSN (online)	1520-4995
ISSN	0006-2960
DOI	10.1021/bi972677d
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Article ; Online: ATOMDANCE: Kernel-based denoising and choreographic analysis for protein dynamic comparison.

Babbitt, Gregory A / Rajendran, Madhusudan / Lynch, Miranda L / Asare-Bediako, Richmond / Mouli, Leora T / Ryan, Cameron J / Srivastava, Harsh / Rynkiewicz, Patrick / Phadke, Kavya / Reed, Makayla L / Moore, Nadia / Ferran, Maureen C / Fokoue, Ernest P

Biophysical journal

2024

Abstract: Comparative methods in molecular evolution and structural biology rely heavily upon the site-wise analysis of DNA sequence and protein structure, both static forms of information. However, it is widely accepted that protein function results from ... ...

Abstract	Comparative methods in molecular evolution and structural biology rely heavily upon the site-wise analysis of DNA sequence and protein structure, both static forms of information. However, it is widely accepted that protein function results from nanoscale nonrandom machine-like motions induced by evolutionarily conserved molecular interactions. Comparisons of molecular dynamics (MD) simulations conducted between homologous sites representative of different functional or mutational states can potentially identify local effects on binding interaction and protein evolution. In addition, comparisons of different (i.e., nonhomologous) sites within MD simulations could be employed to identify functional shifts in local time-coordinated dynamics indicative of logic gating within proteins. However, comparative MD analysis is challenged by the large fraction of protein motion caused by random thermal noise in the surrounding solvent. Therefore, properly denoised MD comparisons could reveal functional sites involving these machine-like dynamics with good accuracy. Here, we introduce ATOMDANCE, a user-interfaced suite of comparative machine learning-based denoising tools designed for identifying functional sites and the patterns of coordinated motion they can create within MD simulations. ATOMDANCE-maxDemon4.0 employs Gaussian kernel functions to compute site-wise maximum mean discrepancy between learned features of motion, thereby assessing denoised differences in the nonrandom motions between functional or evolutionary states (e.g., ligand bound versus unbound, wild-type versus mutant). ATOMDANCE-maxDemon4.0 also employs maximum mean discrepancy to analyze potential random amino acid replacements allowing for a site-wise test of neutral versus nonneutral evolution on the divergence of dynamic function in protein homologs. Finally, ATOMDANCE-Choreograph2.0 employs mixed-model analysis of variance and graph network to detect regions where time-synchronized shifts in dynamics occur. Here, we demonstrate ATOMDANCE's utility for identifying key sites involved in dynamic responses during functional binding interactions involving DNA, small-molecule drugs, and virus-host recognition, as well as understanding shifts in global and local site coordination occurring during allosteric activation of a pathogenic protease.
Language	English
Publishing date	2024-03-21
Publishing country	United States
Document type	Journal Article
ZDB-ID	218078-9
ISSN	1542-0086 ; 0006-3495
ISSN (online)	1542-0086
ISSN	0006-3495
DOI	10.1016/j.bpj.2024.03.024
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Article: First Report of Nectria haematococca Causing Wilt of Olive Plants in Argentina.

Babbitt, S / Gally, M / Pérez, B A / Barreto, D

Plant disease

2019 Volume 86, Issue 3, Page(s) 326

Abstract: ... References: (1) C. Booth. The Genus Fusarium. CAB International, Wallingford, UK, 1971. (2) R. L. Munjal et ... Symposium Proceedings. Indian Society of Tree Scientists. P. K. Kosla, ed. Sdan, India, 1982. (3) B ...

Abstract	Death of 8- to 12-month-old olive plants (Olea europaea L. 'Arbequina', 'Arauco', and 'Picual') has been observed since 1998 in northwestern Argentina. No mycelium or perithecium was observed when examining rotting roots of greenhouse-collected plants. Root segments of diseased plants were plated on potato dextrose agar. Cultures developed a white mycelium after 2 to 3 days, producing microconidia, macroconidia, and chlamydospores identified as Fusarium solani (1). After 15 days of incubation at 23 ± 2°C, reddish perithecia developed infrequently on root segments and adjacent substratum. Single-septate ascospores were hyaline and turned light brown with longitudinal striations at maturity. Microscopic measurements agreed with Nectria haematococca (1). To conduct Koch's postulates (two experiments, two treatments including inoculated and controls, 10 replicates per treatment), young rooted cuttings (6- to 12-month-old) were transferred to pots with a soilless mix and F. solani-colonized oat grains (10:1 vol/vol) and placed in growth chamber (25 to 28°C). First symptoms of the disease were leaf drooping and apex bending after 5 days. At approximately 9 days, leaves turned brownish, developed wilting from the tip downward, and plant death. Controls remained healthy. The fungus was reisolated, and perithecia of N. haematococca developed. F. solani has been reported causing wilt and sudden death in olive previously (2,3). To our knowledge, this is the first report of perithecial development associated with F. solani on olive. References: (1) C. Booth. The Genus Fusarium. CAB International, Wallingford, UK, 1971. (2) R. L. Munjal et al. Studies on diseases of olive in himachal pradesh. Pages 437-440 In: Improvement of Forest Biomass. Symposium Proceedings. Indian Society of Tree Scientists. P. K. Kosla, ed. Sdan, India, 1982. (3) B. A. Pérez et al. (Abstr.) Phytopathology 91 (suppl):S71, 2001.
Language	English
Publishing date	2019-02-28
Publishing country	United States
Document type	Journal Article
ZDB-ID	754182-x
ISSN	0191-2917
ISSN	0191-2917
DOI	10.1094/PDIS.2002.86.3.326A
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Article ; Online: Structural Basis for the Asymmetry of a 4-Oxalocrotonate Tautomerase Trimer.

Medellin, Brenda P / Lancaster, Emily B / Brown, Shoshana D / Rakhade, Swanand / Babbitt, Patricia C / Whitman, Christian P / Zhang, Yan Jessie

Biochemistry

2020 Volume 59, Issue 16, Page(s) 1592–1603

Abstract: Tautomerase superfamily (TSF) members are constructed from a single β-α-β unit or two consecutively joined β-α-β units. This pattern prevails throughout the superfamily consisting of more than 11000 members where homo- or heterohexamers are localized in ... ...

Abstract	Tautomerase superfamily (TSF) members are constructed from a single β-α-β unit or two consecutively joined β-α-β units. This pattern prevails throughout the superfamily consisting of more than 11000 members where homo- or heterohexamers are localized in the 4-oxalocrotonate tautomerase (4-OT) subgroup and trimers are found in the other four subgroups. One exception is a subset of sequences that are double the length of the short 4-OTs in the 4-OT subgroup, where the coded proteins form trimers. Characterization of two members revealed an interesting dichotomy. One is a symmetric trimer, whereas the other is an asymmetric trimer. One monomer is flipped 180° relative to the other two monomers so that three unique protein-protein interfaces are created that are composed of different residues. A bioinformatics analysis of the fused 4-OT subset shows a further division into two clusters with a total of 133 sequences. The analysis showed that members of one cluster (86 sequences) have more salt bridges if the asymmetric trimer forms, whereas the members of the other cluster (47 sequences) have more salt bridges if the symmetric trimer forms. This hypothesis was examined by the kinetic and structural characterization of two proteins within each cluster. As predicted, all four proteins function as 4-OTs, where two assemble into asymmetric trimers (designated R7 and F6) and two form symmetric trimers (designated W0 and Q0). These findings can be extended to the other sequences in the two clusters in the fused 4-OT subset, thereby annotating their oligomer properties and activities.
MeSH term(s)	Alcaligenaceae/enzymology ; Amino Acid Sequence ; Bacterial Proteins/chemistry ; Binding Sites ; Bordetella/enzymology ; Burkholderia/enzymology ; Burkholderiaceae/enzymology ; Computational Biology ; Isomerases/chemistry ; Kinetics ; Protein Structure, Quaternary ; Sequence Alignment
Chemical Substances	Bacterial Proteins ; 4-oxalocrotonate tautomerase (EC 5.-) ; Isomerases (EC 5.-)
Language	English
Publishing date	2020-04-13
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	1108-3
ISSN	1520-4995 ; 0006-2960
ISSN (online)	1520-4995
ISSN	0006-2960
DOI	10.1021/acs.biochem.0c00211
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Article ; Online: Kinetic and Structural Analysis of Two Linkers in the Tautomerase Superfamily: Analysis and Implications.

Baas, Bert-Jan / Medellin, Brenda P / LeVieux, Jake A / Erwin, Kaci / Lancaster, Emily B / Johnson, William H / Kaoud, Tamer S / Moreno, R Yvette / de Ruijter, Marieke / Babbitt, Patricia C / Zhang, Yan Jessie / Whitman, Christian P

Biochemistry

2021 Volume 60, Issue 22, Page(s) 1776–1786

Abstract: The tautomerase superfamily (TSF) is a collection of enzymes and proteins that share a simple β-α-β structural scaffold. Most members are constructed from a single-core β-α-β motif or two consecutively fused β-α-β motifs in which the N-terminal proline ( ... ...

Abstract	The tautomerase superfamily (TSF) is a collection of enzymes and proteins that share a simple β-α-β structural scaffold. Most members are constructed from a single-core β-α-β motif or two consecutively fused β-α-β motifs in which the N-terminal proline (Pro-1) plays a key and unusual role as a catalytic residue. The cumulative evidence suggests that a gene fusion event took place in the evolution of the TSF followed by duplication (of the newly fused gene) to result in the diversification of activity that is seen today. Analysis of the sequence similarity network (SSN) for the TSF identified several linking proteins ("linkers") whose similarity links subgroups of these contemporary proteins that might hold clues about structure-function relationship changes accompanying the emergence of new activities. A previously uncharacterized pair of linkers (designated N1 and N2) was identified in the SSN that connected the 4-oxalocrotonate tautomerase (4-OT) and
MeSH term(s)	Amino Acid Sequence ; Binding Sites/physiology ; Catalysis ; Catalytic Domain/physiology ; Evolution, Molecular ; Hydrolases/chemistry ; Isomerases/chemistry ; Kinetics ; Magnetic Resonance Spectroscopy/methods ; Models, Chemical
Chemical Substances	Hydrolases (EC 3.-) ; cis-3-chloroacrylic acid dehalogenase (EC 3.8.1.-) ; 4-oxalocrotonate tautomerase (EC 5.-) ; Isomerases (EC 5.-)
Language	English
Publishing date	2021-05-21
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	1108-3
ISSN	1520-4995 ; 0006-2960
ISSN (online)	1520-4995
ISSN	0006-2960
DOI	10.1021/acs.biochem.1c00220
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Article ; Online: Evolutionary Variation in MADS Box Dimerization Affects Floral Development and Protein Abundance in Maize.

Abraham-Juárez, María Jazmín / Schrager-Lavelle, Amanda / Man, Jarrett / Whipple, Clinton / Handakumbura, Pubudu / Babbitt, Courtney / Bartlett, Madelaine

The Plant cell

2020 Volume 32, Issue 11, Page(s) 3408–3424

Abstract: Interactions between MADS box transcription factors are critical in the regulation of floral development, and shifting MADS box protein-protein interactions are predicted to have influenced floral evolution. However, precisely how evolutionary variation ... ...

Abstract	Interactions between MADS box transcription factors are critical in the regulation of floral development, and shifting MADS box protein-protein interactions are predicted to have influenced floral evolution. However, precisely how evolutionary variation in protein-protein interactions affects MADS box protein function remains unknown. To assess the impact of changing MADS box protein-protein interactions on transcription factor function, we turned to the grasses, where interactions between B-class MADS box proteins vary. We tested the functional consequences of this evolutionary variability using maize (
MeSH term(s)	Chromatin Assembly and Disassembly ; Evolution, Molecular ; Flowers/genetics ; Flowers/growth & development ; Gene Expression Regulation, Plant ; Genetic Pleiotropy ; MADS Domain Proteins/genetics ; MADS Domain Proteins/metabolism ; Mutation ; Plant Proteins/genetics ; Plant Proteins/metabolism ; Plants, Genetically Modified ; Protein Multimerization ; Protein Processing, Post-Translational ; Ubiquitination ; Zea mays/genetics ; Zea mays/growth & development ; Zea mays/metabolism
Chemical Substances	MADS Domain Proteins ; Plant Proteins
Language	English
Publishing date	2020-09-01
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	623171-8
ISSN	1532-298X ; 1040-4651
ISSN (online)	1532-298X
ISSN	1040-4651
DOI	10.1105/tpc.20.00300
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Article: Comparative Molecular Dynamics Simulations Provide Insight Into Antibiotic Interactions: A Case Study Using the Enzyme L,L-Diaminopimelate Aminotransferase (DapL).

Adams, Lily E / Rynkiewicz, Patrick / Babbitt, Gregory A / Mortensen, Jamie S / North, Rachel A / Dobson, Renwick C J / Hudson, André O

Frontiers in molecular biosciences

2020 Volume 7, Page(s) 46

Abstract: The L,L-diaminopimelate aminotransferase (DapL) pathway, a recently discovered variant of the lysine biosynthetic pathway, is an attractive pipeline to identify targets for the development of novel antibiotic compounds. DapL is a homodimer that catalyzes ...

Abstract	The L,L-diaminopimelate aminotransferase (DapL) pathway, a recently discovered variant of the lysine biosynthetic pathway, is an attractive pipeline to identify targets for the development of novel antibiotic compounds. DapL is a homodimer that catalyzes the conversion of tetrahydrodipicolinate to L,L-diaminopimelate in a single transamination reaction. The penultimate and ultimate products of the lysine biosynthesis pathway,
Language	English
Publishing date	2020-03-24
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2814330-9
ISSN	2296-889X
ISSN	2296-889X
DOI	10.3389/fmolb.2020.00046
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Article ; Online: New computational approaches to understanding molecular protein function.

Jacquelyn S Fetrow / Patricia C Babbitt

PLoS Computational Biology, Vol 14, Iss 4, p e

2018 Volume 1005756

Keywords	Biology (General) ; QH301-705.5
Language	English
Publishing date	2018-04-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
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Article: Reengineering the glutathione S-transferase scaffold: a rational design strategy pays off.

Babbitt, P C

Proceedings of the National Academy of Sciences of the United States of America

2000 Volume 97, Issue 19, Page(s) 10298–10300

MeSH term(s)	Glutathione/metabolism ; Glutathione Transferase/chemistry ; Glutathione Transferase/metabolism ; Models, Molecular ; Protein Conformation ; Protein Engineering
Chemical Substances	Glutathione Transferase (EC 2.5.1.18) ; Glutathione (GAN16C9B8O)
Language	English
Publishing date	2000-03-21
Publishing country	United States
Document type	Comment ; Journal Article ; Research Support, U.S. Gov't, P.H.S.
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.97.19.10298
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Article ; Online: Risk Factors for Multisystem Inflammatory Syndrome in Children: A Case-control Investigation.

Zambrano, Laura D / Wu, Michael J / Martin, Lora / Malloch, Lacy / Chen, Sabrina / Newhams, Margaret M / Kucukak, Suden / Son, Mary Beth / Sanders, Cameron / Patterson, Kayla / Halasa, Natasha / Fitzgerald, Julie C / Leroue, Matthew K / Hall, Mark / Irby, Katherine / Rowan, Courtney M / Wellnitz, Kari / Sahni, Leila C / Loftis, Laura /

Bradford, Tamara T / Staat, Mary / Babbitt, Christopher / Carroll, Christopher L / Pannaraj, Pia S / Kong, Michele / Schuster, Jennifer E / Chou, Janet / Patel, Manish M / Randolph, Adrienne G / Campbell, Angela P / Hobbs, Charlotte V

The Pediatric infectious disease journal

2023 Volume 42, Issue 6, Page(s) e190–e196

Abstract: ... Hispanic Black children were more likely to develop multisystem inflammatory syndrome in children (MIS-C ... interviews, we investigated patient, household, and community factors underlying MIS-C likelihood.: Methods ... MIS-C case patients hospitalized in 2021 across 14 US pediatric hospitals were matched by age and site ...

Abstract	Background: In a 2020 pilot case-control study using medical records, we reported that non-Hispanic Black children were more likely to develop multisystem inflammatory syndrome in children (MIS-C) after adjustment for sociodemographic factors and underlying medical conditions. Using structured interviews, we investigated patient, household, and community factors underlying MIS-C likelihood. Methods: MIS-C case patients hospitalized in 2021 across 14 US pediatric hospitals were matched by age and site to outpatient controls testing positive for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) within 3 months of the admission date. Caregiver interviews queried race/ethnicity, medical history, and household and potential community exposures 1 month before MIS-C hospitalization (case-patients) or after SARS-CoV-2 infection (controls). We calculated adjusted odds ratios (aOR) using mixed-effects multivariable logistic regression. Results: Among 275 case patients and 496 controls, race/ethnicity, social vulnerability and patient or family history of autoimmune/rheumatologic disease were not associated with MIS-C. In previously healthy children, MIS-C was associated with a history of hospitalization for an infection [aOR: 4.8; 95% confidence interval (CI): 2.1-11.0]. Household crowding (aOR: 1.7; 95% CI: 1.2-2.6), large event attendance (aOR: 1.7; 95% CI: 1.3-2.1), school attendance with limited masking (aOR: 2.6; 95% CI: 1.1-6.6), public transit use (aOR: 1.8; 95% CI: 1.4-2.4) and co-resident testing positive for SARS-CoV-2 (aOR: 2.2; 95% CI: 1.3-3.7) were associated with increased MIS-C likelihood, with risk increasing with the number of these factors. Conclusions: From caregiver interviews, we clarify household and community exposures associated with MIS-C; however, we did not confirm prior associations between sociodemographic factors and MIS-C.
MeSH term(s)	Child ; Humans ; COVID-19/epidemiology ; SARS-CoV-2 ; Case-Control Studies ; Crowding ; Family Characteristics ; Systemic Inflammatory Response Syndrome/epidemiology ; Risk Factors
Language	English
Publishing date	2023-03-16
Publishing country	United States
Document type	Journal Article ; Research Support, U.S. Gov't, P.H.S.
ZDB-ID	392481-6
ISSN	1532-0987 ; 0891-3668
ISSN (online)	1532-0987
ISSN	0891-3668
DOI	10.1097/INF.0000000000003900
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