Sulphate ions observed in the 2.12 Å structure of a new crystal form of S. cerevisiae phosphoglycerate mutase provide insights into understanding the catalytic mechanism 1 1Edited by K. Nagai

Rigden, Daniel J.; Walter, Rebecca A.; Phillips, Simon E. V.; Fothergill‐Gilmore, Linda A.

doi:10.1006/jmbi.1999.2566

Cited by 40 publications

(51 citation statements)

References 29 publications

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“…The phosphate group is then transferred from the conserved His to the C-2 of 3PG to yield 2,3BPG as the reaction intermediate. After reorientation of the 2,3BPG intermediate in the active site, the phosphate group of C-3 is transferred back to the conserved histidine, the phosphoenzyme is regenerated, and 2PG is formed (211,220). The archaeal dPGAMs seem to form a distinct subclass clearly separated from the bacterial and eukaryotic enzymes.…”

Section: Phosphoglycerate Kinasementioning

confidence: 99%

Carbohydrate Metabolism in Archaea: Current Insights into Unusual Enzymes and Pathways and Their Regulation

Bräsen

Esser

Rauch

et al. 2014

Microbiol Mol Biol Rev

271

294

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SUMMARY The metabolism of Archaea , the third domain of life, resembles in its complexity those of Bacteria and lower Eukarya . However, this metabolic complexity in Archaea is accompanied by the absence of many “classical” pathways, particularly in central carbohydrate metabolism. Instead, Archaea are characterized by the presence of unique, modified variants of classical pathways such as the Embden-Meyerhof-Parnas (EMP) pathway and the Entner-Doudoroff (ED) pathway. The pentose phosphate pathway is only partly present (if at all), and pentose degradation also significantly differs from that known for bacterial model organisms. These modifications are accompanied by the invention of “new,” unusual enzymes which cause fundamental consequences for the underlying regulatory principles, and classical allosteric regulation sites well established in Bacteria and Eukarya are lost. The aim of this review is to present the current understanding of central carbohydrate metabolic pathways and their regulation in Archaea . In order to give an overview of their complexity, pathway modifications are discussed with respect to unusual archaeal biocatalysts, their structural and mechanistic characteristics, and their regulatory properties in comparison to their classic counterparts from Bacteria and Eukarya . Furthermore, an overview focusing on hexose metabolic, i.e., glycolytic as well as gluconeogenic, pathways identified in archaeal model organisms is given. Their energy gain is discussed, and new insights into different levels of regulation that have been observed so far, including the transcript and protein levels (e.g., gene regulation, known transcription regulators, and posttranslational modification via reversible protein phosphorylation), are presented.

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Section: Phosphoglycerate Kinasementioning

confidence: 99%

Carbohydrate Metabolism in Archaea: Current Insights into Unusual Enzymes and Pathways and Their Regulation

Bräsen

Esser

Rauch

et al. 2014

Microbiol Mol Biol Rev

271

294

View full text Add to dashboard Cite

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“…Both BPGM and dPGM can catalyze the same three overall reactions for which phosphorylation of the catalytic histidine by 2,3-bisphosphoglycerate is the first step. Previous studies of BPGM and dPGMs have provided important but so far incomplete information on the structural basis for the specific activities and molecular mechanisms (5)(6)(7)(8)(9)(10)(11)(12)(13)(14). Although a number of structures of dPGMs (9,10,12,13,(15)(16)(17)(18) and human BPGM (8) have been reported, no structure of the enzyme⅐substrate complex is available.…”

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confidence: 99%

Seeing the Process of Histidine Phosphorylation in Human Bisphosphoglycerate Mutase

Wang

Liu

Wei

et al. 2006

Journal of Biological Chemistry

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Bisphosphoglycerate mutase is an erythrocyte-specific enzyme catalyzing a series of intermolecular phosphoryl group transfer reactions. Its main function is to synthesize 2,3-bisphosphoglycerate, the allosteric effector of hemoglobin. In this paper, we directly observed real-time motion of the enzyme active site and the substrate during phosphoryl transfer. A series of high resolution crystal structures of human bisphosphoglycerate mutase co-crystallized with 2,3-bisphosphoglycerate, representing different time points in the phosphoryl transfer reaction, were solved. These structures not only clarify the argument concerning the substrate binding mode for this enzyme family but also depict the entire process of the key histidine phosphorylation as a "slow movie". It was observed that the enzyme conformation continuously changed during the different states of the reaction. These results provide direct evidence for an "in line" phosphoryl transfer mechanism, and the roles of some key residues in the phosphoryl transfer process are identified.

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“…Although the hydrogen bonding is less clear in molecule B, because the oxygen positions are less defined, the positions of the sulfate ions differ by only 0.5 Å when the two molecules are superimposed. This sulfate ion is likely to model the position of a substrate phosphate group, as appears to occur in the structures of other dPGM family members, for example, the dPGM from S. cerevisiae (39). Also present in the active site are a number of very well defined water molecules which make multiple hydrogen bonds and whose positions correspond extremely closely between the two independent Rv3214 molecules.…”

Section: Downloaded Frommentioning

confidence: 92%

“…In this context, threedimensional structure should provide a more reliable guide. Structures are available for a number of dPGM family enzymes, including the monomeric Schizosaccharomyces pombe dPGM (45), the dimeric human (47) and E. coli (1) dPGMs, and the tetrameric dPGMs from Saccharomyces cerevisiae (5,36,39) and M. tuberculosis (Rv0489) (25). In contrast, the structure of the Bacillus subtilis protein Sfp (35), the first for an EntD-like 4Ј-phosphopantetheinyl transferase, has an ␣/␤ fold completely different from that of the dPGMs and is monomeric but with a twofold internal repeat.…”

mentioning

confidence: 99%

Structural and Functional Analysis of Rv3214 from Mycobacterium tuberculosis , a Protein with Conflicting Functional Annotations, Leads to Its Characterization as a Phosphatase

Watkins

Baker

2006

J Bacteriol

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The availability of complete genome sequences has highlighted the problems of functional annotation of the many gene products that have only limited sequence similarity with proteins of known function. The predicted protein encoded by open reading frame Rv3214 from the Mycobacterium tuberculosis H37Rv genome was originally annotated as EntD through sequence similarity with the Escherichia coli EntD, a 4-phosphopantetheinyl transferase implicated in siderophore biosynthesis. An alternative annotation, based on slightly higher sequence identity, grouped Rv3214 with proteins of the cofactor-dependent phosphoglycerate mutase (dPGM) family. The crystal structure of this protein has been solved by single-wavelength anomalous dispersion methods and refined at 2.07-Å resolution (R ‫؍‬ 0.229; R free ‫؍‬ 0.245). The protein is dimeric, with a monomer fold corresponding to the classical dPGM ␣/␤ structure, albeit with some variations. Closer comparisons of structure and sequence indicate that it most closely corresponds with a broad-spectrum phosphatase subfamily within the dPGM superfamily. This functional annotation has been confirmed by biochemical assays which show negligible mutase activity but acid phosphatase activity with a pH optimum of 5.4 and suggests that Rv3214 may be important for mycobacterial phosphate metabolism in vivo. Despite its weak sequence similarity with the 4-phosphopantetheinyl transferases (EntD homologues), there is little evidence to support this function.

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Sulphate ions observed in the 2.12 Å structure of a new crystal form of S. cerevisiae phosphoglycerate mutase provide insights into understanding the catalytic mechanism 1 1Edited by K. Nagai

Cited by 40 publications

References 29 publications

Carbohydrate Metabolism in Archaea: Current Insights into Unusual Enzymes and Pathways and Their Regulation

Carbohydrate Metabolism in Archaea: Current Insights into Unusual Enzymes and Pathways and Their Regulation

Seeing the Process of Histidine Phosphorylation in Human Bisphosphoglycerate Mutase

Structural and Functional Analysis of Rv3214 from Mycobacterium tuberculosis , a Protein with Conflicting Functional Annotations, Leads to Its Characterization as a Phosphatase

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