New structural insights into bacterial sulfoacetaldehyde and taurine metabolism

In last year's issue 4 of Biochemical Journal, Zhou et al. (Biochem J. 476, 733–746) kinetically and structurally characterized the reductase IsfD from Klebsiella oxytoca that catalyzes the reversible reduction in sulfoacetaldehyde to the corresponding alcohol isethionate. This is a key step in detoxification of the carbonyl intermediate formed in bacterial nitrogen assimilation from the α-aminoalkanesulfonic acid taurine. In 2019, the work on sulfoacetaldehyde reductase IsfD was the exciting start to a quite remarkable series of articles dealing with structural elucidation of proteins involved in taurine metabolism as well as the discovery of novel degradation pathways in bacteria.

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Biochemical and structural investigation of sulfoacetaldehyde reductase from Klebsiella oxytoca

Biochemical Journal ◽

10.1042/bcj20190005 ◽

2019 ◽

Vol 476 (4) ◽

pp. 733-746 ◽

Cited By ~ 6

Author(s):

Yan Zhou ◽

Yifeng Wei ◽

Lianyun Lin ◽

Tong Xu ◽

Ee Lui Ang ◽

...

Keyword(s):

Nitrogen Assimilation ◽

Structural Investigation ◽

Bioinformatics Analysis ◽

Substrate Binding ◽

Klebsiella Oxytoca ◽

Waste Product ◽

Sulfonate Group ◽

Metabolic Functions ◽

Bond Network ◽

Β Sheet

Abstract Sulfoacetaldehyde reductase (IsfD) is a member of the short-chain dehydrogenase/reductase (SDR) family, involved in nitrogen assimilation from aminoethylsulfonate (taurine) in certain environmental and human commensal bacteria. IsfD catalyzes the reversible NADPH-dependent reduction of sulfoacetaldehyde, which is generated by transamination of taurine, forming hydroxyethylsulfonate (isethionate) as a waste product. In the present study, the crystal structure of Klebsiella oxytoca IsfD in a ternary complex with NADPH and isethionate was solved at 2.8 Å, revealing residues important for substrate binding. IsfD forms a homotetramer in both crystal and solution states, with the C-terminal tail of each subunit interacting with the C-terminal tail of the diagonally opposite subunit, forming an antiparallel β sheet that constitutes part of the substrate-binding site. The sulfonate group of isethionate is stabilized by a hydrogen bond network formed by the residues Y148, R195, Q244 and a water molecule. In addition, F249 from the diagonal subunit restrains the conformation of Y148 to further stabilize the orientation of the sulfonate group. Mutation of any of these four residues into alanine resulted in a complete loss of catalytic activity for isethionate oxidation. Biochemical investigations of the substrate scope of IsfD, and bioinformatics analysis of IsfD homologs, suggest that IsfD is related to the promiscuous 3-hydroxyacid dehydrogenases with diverse metabolic functions.

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Final Technical Report: Genetic Control of Nitrogen Assimilation in Klebsiella oxytoca.

10.2172/900350 ◽

2007 ◽

Author(s):

Valley Stewart

Keyword(s):

Genetic Control ◽

Nitrogen Assimilation ◽

Klebsiella Oxytoca ◽

Technical Report

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Structural Insights Into the Initiation and Elongation of Ubiquitination by Ubr1

10.1101/2021.04.12.439291 ◽

2021 ◽

Author(s):

Man Pan ◽

Qingyun Zheng ◽

Tian Wang ◽

Lujun Liang ◽

Junxiong Mao ◽

...

Keyword(s):

Electron Microscopy ◽

E3 Ligase ◽

Degradation Pathways ◽

Single Chain ◽

Cryo Electron Microscopy ◽

N Terminus ◽

Specific Manner ◽

Ubiquitin Conjugating Enzyme ◽

Structural Insights ◽

Conjugating Enzyme

The N-end rule pathway was one of the first ubiquitin (Ub)-dependent degradation pathways to be identified. Ubr1, a single-chain E3 ligase, targets proteins bearing a destabilizing residue at the N-terminus (N-degron) for rapid K48-linked ubiquitination and proteasome-dependent degradation. How Ubr1 catalyses the initiation of ubiquitination on the substrate and elongation of the Ub chain in a linkage-specific manner through a single E2 ubiquitin-conjugating enzyme (Ubc2) remains unknown. Here, we report the cryo-electron microscopy structures of two complexes representing the initiation and elongation intermediates of Ubr1 captured using chemical approaches. In these two structures, Ubr1 adopts different conformations to facilitate the transfer of Ub from Ubc2 to either an N-degron peptide or a monoubiquitinated degron. These structures not only reveal the architecture of the Ubr1 complex but also provide mechanistic insights into the initiation and elongation steps of ubiquitination catalyzed by Ubr1.

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Structural insights into the broadened substrate profile of the extended-spectrum β-lactamase OXY-1-1 fromKlebsiella oxytoca

Acta Crystallographica Section D Biological Crystallography ◽

10.1107/s090744491203466x ◽

2012 ◽

Vol 68 (11) ◽

pp. 1460-1467 ◽

Cited By ~ 1

Author(s):

Yu-He Liang ◽

Rong Gao ◽

Xiao-Dong Su

Keyword(s):

Klebsiella Oxytoca ◽

Binding Pocket ◽

Structural Basis ◽

Substrate Binding Pocket ◽

Class A ◽

Serious Infections ◽

Hospital Patients ◽

Surface Electrostatic Potential ◽

Structural Insights ◽

Positive Half

Klebsiella oxytocais a pathogen that causes serious infections in hospital patients. It shows resistance to many clinically used β-lactam antibiotics by producing chromosomally encoded OXY-family β-lactamases. Here, the crystal structure of an OXY-family β-lactamase, OXY-1-1, determined at 1.93 Å resolution is reported. The structure shows that the OXY-1-1 β-lactamase has a typical class A β-lactamase fold and exhibits greater similarity to CTX-M-type β-lactamases than to TEM-family or SHV-family β-lactamases. It is also shown that the enzyme provides more space around the active cavity for theR1andR2substituents of β-lactam antibiotics. The half-positive/half-negative distribution of surface electrostatic potential in the substrate-binding pocket indicates the preferred properties of substrates or inhibitors of the enzyme. The results reported here provide a structural basis for the broadened substrate profile of the OXY-family β-lactamases.

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Reading the phosphorylation code: binding of the 14-3-3 protein to multivalent client phosphoproteins

Biochemical Journal ◽

10.1042/bcj20200084 ◽

2020 ◽

Vol 477 (7) ◽

pp. 1219-1225 ◽

Cited By ~ 4

Author(s):

Nikolai N. Sluchanko

Keyword(s):

Protein Function ◽

Intrinsically Disordered Protein ◽

Structural Basis ◽

Major Protein ◽

Post Translational Modifications ◽

Protein Protein Interaction ◽

Intrinsically Disordered ◽

Biochemical Journal ◽

Multiple Binding ◽

And Control

Many major protein–protein interaction networks are maintained by ‘hub’ proteins with multiple binding partners, where interactions are often facilitated by intrinsically disordered protein regions that undergo post-translational modifications, such as phosphorylation. Phosphorylation can directly affect protein function and control recognition by proteins that ‘read’ the phosphorylation code, re-wiring the interactome. The eukaryotic 14-3-3 proteins recognizing multiple phosphoproteins nicely exemplify these concepts. Although recent studies established the biochemical and structural basis for the interaction of the 14-3-3 dimers with several phosphorylated clients, understanding their assembly with partners phosphorylated at multiple sites represents a challenge. Suboptimal sequence context around the phosphorylated residue may reduce binding affinity, resulting in quantitative differences for distinct phosphorylation sites, making hierarchy and priority in their binding rather uncertain. Recently, Stevers et al. [Biochemical Journal (2017) 474: 1273–1287] undertook a remarkable attempt to untangle the mechanism of 14-3-3 dimer binding to leucine-rich repeat kinase 2 (LRRK2) that contains multiple candidate 14-3-3-binding sites and is mutated in Parkinson's disease. By using the protein-peptide binding approach, the authors systematically analyzed affinities for a set of LRRK2 phosphopeptides, alone or in combination, to a 14-3-3 protein and determined crystal structures for 14-3-3 complexes with selected phosphopeptides. This study addresses a long-standing question in the 14-3-3 biology, unearthing a range of important details that are relevant for understanding binding mechanisms of other polyvalent proteins.

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