Jorge C. Escalante‐Semerena

University of Georgia

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Ivan Rayment

University of Wisconsin–Madison

Paola E. Mera

University of Illinois Urbana-Champaign

C.-G. Cheong

Seoul National University

Sean A. Newmister

University of Michigan–Ann Arbor

Alexander R. Horswill

University of Colorado Denver

Thomas C. Brunold

University of Wisconsin–Madison

Vincent J. Starai

University of Georgia

R. S. Wolfe

University of Illinois Urbana-Champaign

Nicole R. Buan

University of Nebraska–Lincoln

Martin St. Maurice

Marquette University

Cooperative Institutions

University of Wisconsin–Madison

University of Georgia

University of Illinois Urbana-Champaign

Johns Hopkins University

Howard Hughes Medical Institute

University of Michigan–Ann Arbor

Johns Hopkins Medicine

Stanford University

Harvard University

University of Washington

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Structure of ATP bound RpMatB-BxBclM chimera B3

Katherine C. Rank H.A. Crosby Jorge C. Escalante‐Semerena Ivan Rayment

Chimera (genetics)

10.2210/pdb4gxr/pdb

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The three‐dimensional crystal structure of the PrpF protein of Shewanella oneidensis complexed with trans‐aconitate: Insights into its biological function

Protein Science (2007)

Graeme S. Garvey Christopher J. Rocco Jorge C. Escalante‐Semerena Ivan Rayment

In bacteria, the dehydration of 2-methylcitrate to yield 2-methylaconitate in the 2-methylcitric acid cycle is catalyzed by a cofactor-less (PrpD) enzyme or by an aconitase-like (AcnD) enzyme. Bacteria that use AcnD also require the function of the PrpF protein, whose function was previously unknown. To gain insights into the function of PrpF, the three-dimensional crystal structure of the PrpF protein from the bacterium Shewanella oneidensis was solved at 2.0 A resolution. The protein fold of PrpF is strikingly similar to those of the non-PLP-dependent diaminopimelate epimerase from Haemophilus influenzae, a putative proline racemase from Brucella melitensis, and to a recently deposited structure of a hypothetical protein from Pseudomonas aeruginosa. Results from in vitro studies show that PrpF isomerizes trans-aconitate to cis-aconitate. It is proposed that PrpF catalysis of the cis-trans isomerization proceeds through a base-catalyzed proton abstraction coupled with a rotation about C2-C3 bond of 2-methylaconitate, and that residue Lys73 is critical for PrpF function. The newly identified function of PrpF as a non-PLP-dependent isomerase, together with the fact that PrpD-containing bacteria do not require PrpF, suggest that the isomer of 2-methylaconitate that serves as a substrate of aconitase must have the same stereochemistry as that synthesized by PrpD. From this, it follows that the 2-methylaconitate isomer generated by AcnD is not a substrate of aconitase, and that PrpF is required to generate the correct isomer. As a consequence, the isomerase activity of PrpF may now be viewed as an integral part of the 2-methylcitric acid cycle.

Shewanella oneidensis

Dioxygenase

10.1110/ps.072801907

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Citations (23)

A method for the production, purification and liposome reconstitution of cobamide synthase

Methods in enzymology on CD-ROM/Methods in enzymology (2022)

Elizabeth A. Villa Jorge C. Escalante‐Semerena

Corrin

Acetyl-CoA

10.1016/bs.mie.2021.11.015

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Component A2 of the methylcoenzyme M methylreductase system from Methanobacterium thermoautotrophicum

Journal of Bacteriology (1985)

Pierre E. Rouvière Jorge C. Escalante‐Semerena R. S. Wolfe

Component A2 of the methylcoenzyme M methylreductase system of Methanobacterium thermoautotrophicum has been purified 370-fold by liquid chromatography. Homogeneity was obtained by anaerobic preparative polyacrylamide gel electrophoresis. Component A2 is a colorless, air-stable protein consisting of a single polypeptide as indicated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The relative molecular mass of the native protein was determined by high-performance, size exclusion chromatography to be Mr 52,000; on sodium dodecyl sulfate-polyacrylamide gel electrophoresis a value of Mr 59,000 was obtained. When cell extract was subjected to N6-ATP-agarose affinity chromatography the methylcoenzyme M methylreductase system was resolved into two fractions; one of them was component A2. This work provides a new operational definition for component A2, i.e., its characteristic chromatographic behavior on N6-ATP-agarose. However, its functional definition is its ability to reconstitute the methylreductase activity with components A1, A3, and C. Several attempts to assign a role to component A2 are reported.

Agarose

Sodium dodecyl sulfate

Polyacrylamide

Methanobacterium

Molecular mass

Gel permeation chromatography

10.1128/jb.162.1.61-66.1985

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Citations (53)

Biochemical and Mutational Analyses of AcuA, the Acetyltransferase Enzyme That Controls the Activity of the Acetyl Coenzyme A Synthetase (AcsA) in Bacillus subtilis

Journal of Bacteriology (2008)

Jeffrey G. Gardner Jorge C. Escalante‐Semerena

The acuABC genes of Bacillus subtilis comprise a putative posttranslational modification system. The AcuA protein is a member of the Gcn5-related N-acetyltransferase (GNAT) superfamily, the AcuC protein is a class I histone deacetylase, and the role of the AcuB protein is not known. AcuA controls the activity of acetyl coenzyme A synthetase (AcsA; EC 6.2.1.1) in this bacterium by acetylating residue Lys549. Here we report the kinetic analysis of wild-type and variant AcuA proteins. We contrived a genetic scheme for the identification of AcuA residues critical for activity. Changes at residues H177 and G187 completely inactivated AcuA and led to its rapid turnover. Changes at residues R42 and T169 were less severe. In vitro assay conditions were optimized, and an effective means of inactivating the enzyme was found. The basic kinetic parameters of wild-type and variant AcuA proteins were obtained and compared to those of eukaryotic GNATs. Insights into how the isolated mutations may exert their deleterious effect were investigated by using the crystal structure of an AcuA homolog.

Acetyltransferases

Coenzyme A

Acetyl-CoA

10.1128/jb.00340-08

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Citations (43)

The last step in coenzyme B12 synthesis is localized to the cell membrane in bacteria and archaea

Microbiology (2004)

Lori A. Maggio‐Hall Kathy R. Claas Jorge C. Escalante‐Semerena

In Salmonella enterica, the last step of the synthesis of adenosylcobamide is catalysed by the cobalamin synthase enzyme encoded by the cobS gene of this bacterium. Overexpression of the S. enterica cobS gene in Escherichia coli elicited the accumulation of the phage shock protein PspA, a protein whose expression has been linked to membrane stress. Resolution of inner and outer membranes of S. enterica by isopycnic density ultracentrifugation showed CobS activity associated with the inner membrane, a result that was confirmed using antibodies against CobS. Computer analysis of the predicted amino acid sequence of CobS suggested it was an integral membrane protein. Results of experiments performed with strains carrying plasmids encoding CobS-alkaline phosphatase or CobS-beta-galactosidase protein fusions were consistent with the membrane localization of the CobS protein. Modifications to the predicted model were made based on data obtained from experiments using protein fusions. The function encoded by the cobS orthologue in the methanogenic archaeon Methanobacterium thermoautotrophicum strain deltaH compensated for the lack of CobS during cobalamin synthesis in cobS strains of S. enterica. Cobalamin synthase activity was also detected in a membrane preparation of M. thermoautotrophicum. It was concluded that the assembly of the nucleotide loop of adenosylcobamides in archaea and bacteria is a membrane-associated process. Possible reasons for the association of adenosylcobamide biosynthetic enzymes with the cell membrane are discussed.

Methanobacterium

Salmonella enterica

10.1099/mic.0.26952-0

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Citations (40)

Structural studies of the phosphoribosyltransferase involved in cobamide biosynthesis in methanogenic archaea and cyanobacteria

Scientific Reports (2022)

Victoria L. Jeter Anne H. Schwarzwalder Ivan Rayment Jorge C. Escalante‐Semerena

Abstract Cobamides (Cbas) are coenzymes used by cells across all domains of life, but de novo synthesis is only found in some bacteria and archaea. Five enzymes assemble the nucleotide loop in the alpha phase of the corrin ring. Condensation of the activated ring and nucleobase yields adenosyl-Cba 5′-phosphate, which upon dephosphorylation yields the biologically active coenzyme (AdoCba). Base activation is catalyzed by a phosphoribosyltransferase (PRTase). The structure of the Salmonella enterica PRTase enzyme (i.e., Se CobT) is well-characterized, but archaeal PRTases are not. To gain insights into the mechanism of base activation by the PRTase from Methanocaldococcus jannaschii ( Mj CobT), we solved crystal structures of the enzyme in complex with substrate and products. We determined several structures: (i) a 2.2 Å structure of Mj CobT in the absence of ligand (apo), (ii) structures of Mj CobT bound to nicotinate mononucleotide (NaMN) and α-ribazole 5′-phosphate (α-RP) or α-adenylyl-5′-phosphate (α-AMP) at 2.3 and 1.4 Å, respectively. In Mj CobT the general base that triggers the reaction is an aspartate residue (Asp 52) rather than a glutamate residue (E317) as in Se CobT. Notably, the dimer interface in Mj CobT is completely different from that observed in Se CobT. Finally, entry PDB 3L0Z does not reflect the correct structure of Mj CobT.

Phosphoribosyltransferase

Residue (chemistry)

Transferase

Dephosphorylation

10.1038/s41598-022-21765-5

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Citations (2)

The poc locus is required for 1,2-propanediol-dependent transcription of the cobalamin biosynthetic (cob) and propanediol utilization (pdu) genes of Salmonella typhimurium

Journal of Bacteriology (1992)

Michelle R. Rondon Jorge C. Escalante‐Semerena

In this communication we present evidence that indicates that 1,2-propanediol (1,2-PDL) is a positive effector of the transcription of the cobalamin (vitamin B12) biosynthetic (cob) operon and of the 1,2-PDL utilization (pdu) genes. The stimulatory effects of 1,2-PDL were demonstrated using Mu d-lac transcriptional fusions to cob and pdu. Significantly increased levels of transcription of the cob and pdu operon fusions were measured in cultures grown under both anoxic and highly aerated conditions when 1,2-PDL was present in the culture medium. We have isolated mutants that carry lesions that render both pdu and cob transcription unresponsive to 1,2-PDL. These mutations were mapped to the region between cob and pdu (41 min), and they define the poc locus PDL and cobalamin). The poc locus is required for the positive regulatory effects of 1,2-PDL to be exerted. Complementation of Poc function was achieved in trans by an F' plasmid carrying the poc+ locus, suggesting that at least one diffusible product regulates the expression of cob and pdu in S. typhimurium.

Propanediol

Transcription

10.1128/jb.174.7.2267-2272.1992

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Citations (89)

cobB function is required for catabolism of propionate in Salmonella typhimurium LT2: evidence for existence of a substitute function for CobB within the 1,2-propanediol utilization (pdu) operon

Journal of Bacteriology (1996)

Allen W. Tsang Jorge C. Escalante‐Semerena

The cobB function of Salmonella typhimurium LT2 was defined in vivo as an alternative activity for the nicotinic acid mononucleotide:5,6-dimethylbenzimidazole phosphoribosyltransferase enzyme (CobT), which is involved in the assembly of the nucleotide loop of cobalamin in this bacterium (J. R. Trzebiatowski, G. A. O'Toole, and J. C. Escalante-Semerena, J. Bacteriol. 176:3568-3575, 1994). In this paper we document that, independent of their inability to substitute for CobT function, cobB mutants are unable to use propionate as a carbon and energy source. A plasmid carrying only a wild-type copy of cobB complemented the cobalamin biosynthesis and propionate catabolism phenotypes of cobB mutants, indicating that a lack of CobB was responsible for both phenotypes. We demonstrate the existence of a function encoded by the 1,2-propanediol utilization (pdu) operon, which when induced by 1,2-propanediol compensated for the lack of CobB during propionate catabolism but failed to compensate for CobT in the assembly of the nucleotide loop of cobalamin in a cobB cobT double mutant.

Catabolism

CobB

Auxotrophy

10.1128/jb.178.23.7016-7019.1996

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Citations (21)

Crystal Structure of L-Threonine-O-3-phosphate Decarboxylase from S. enterica complexed with a substrate

C.-G. Cheong Jorge C. Escalante‐Semerena Ivan Rayment

10.2210/pdb1lc7/pdb

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Citations (0)