Crystal Structure of SMYD2 Reveals Simultaneous Binding of PARP1 Peptides to the Active Site and an Unexpected Secondary Binding Site

Aspartate racemase (AspR) is a pyridoxal 5′-phosphate (PLP)-dependent enzyme that is responsible for D-aspartate biosynthesis in vivo. To the best of our knowledge, this is the first study to report an X-ray crystal structure of a PLP-dependent AspR, which was resolved at 1.90 Å resolution. The AspR derived from the bivalve mollusc Scapharca broughtonii (SbAspR) is a type II PLP-dependent enzyme that is similar to serine racemase (SR) in that SbAspR catalyzes both racemization and dehydration. Structural comparison of SbAspR and SR shows a similar arrangement of the active-site residues and nucleotide-binding site, but a different orientation of the metal-binding site. Superposition of the structures of SbAspR and of rat SR bound to the inhibitor malonate reveals that Arg140 recognizes the β-carboxyl group of the substrate aspartate in SbAspR. It is hypothesized that the aromatic proline interaction between the domains, which favours the closed form of SbAspR, influences the arrangement of Arg140 at the active site.

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The crystal structure of the Rv0301-Rv0300 VapBC-3 toxin-antitoxin complex from M. tuberculosis reveals a Mg2+ ion in the active site and a putative RNA-binding site

Protein Science ◽

10.1002/pro.2161 ◽

2012 ◽

Vol 21 (11) ◽

pp. 1754-1767 ◽

Cited By ~ 44

Author(s):

Andrew B. Min ◽

Linda Miallau ◽

Michael R. Sawaya ◽

Jeff Habel ◽

Duilio Cascio ◽

...

Keyword(s):

Crystal Structure ◽

Binding Site ◽

Active Site ◽

Rna Binding

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Selectivity of the surface binding site (SBS) on barley starch synthase I

Biologia ◽

10.2478/s11756-014-0418-0 ◽

2014 ◽

Vol 69 (9) ◽

Cited By ~ 10

Author(s):

Casper Wilkens ◽

Jose Cuesta-Seijo ◽

Monica Palcic ◽

Birte Svensson

Keyword(s):

Crystal Structure ◽

Surface Plasmon Resonance ◽

Binding Site ◽

Active Site ◽

Mutational Analysis ◽

Starch Synthase ◽

Surface Binding ◽

Binding Studies ◽

A Chain ◽

Surface Binding Site

AbstractStarch synthase I (SSI) from various sources has been shown to preferentially elongate branch chains of degree of polymerisation (DP) from 6–7 to produce chains of DP 8–12. In the recently determined crystal structure of barley starch synthase I (HvSSI) a so-called surface binding site (SBS) was seen, which was found by mutational analysis to be essential for the activity of HvSSI on glycogen. We now show in binding studies using surface plasmon resonance that HvSSI has no detectable affinity for malto-triose and -tetraose, but clearly binds maltopentaose, -hexaose, -heptaose (M7) and β-cyclodextrin (β-CD) albeit with a measurable K D for only β-CD and M7. Moreover, an HvSSI SBS mutant F538A lost the ability to bind β-CD and maltooligosaccharides. This behaviour suggests that a chain in the α-glucan molecule (amylopectin) that is undergoing extension attaches itself at the SBS and that the active site itself, likely working on a different end chain, has low affinity for both substrate and product.

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Identification of the site of oxidase substrate binding inScytalidium thermophilumcatalase

Acta Crystallographica Section D Structural Biology ◽

10.1107/s2059798318010628 ◽

2018 ◽

Vol 74 (10) ◽

pp. 979-985 ◽

Cited By ~ 2

Author(s):

Yonca Yuzugullu Karakus ◽

Gunce Goc ◽

Sinem Balci ◽

Briony A. Yorke ◽

Chi H. Trinh ◽

...

Keyword(s):

Crystal Structure ◽

Kinetic Analysis ◽

Binding Site ◽

Active Site ◽

Oxidase Activity ◽

Substrate Binding ◽

Binding Pocket ◽

Scytalidium Thermophilum ◽

Lateral Channel

The catalase fromScytalidium thermophilumis a homotetramer containing a hemedin each active site. Although the enzyme has a classical monofunctional catalase fold, it also possesses oxidase activity towards a number of small organics, including catechol and phenol. In order to further investigate this, the crystal structure of the complex of the catalase with the classical catalase inhibitor 3-amino-1,2,4-triazole (3TR) was determined at 1.95 Å resolution. Surprisingly, no binding to the heme site was observed; instead, 3TR occupies a binding site corresponding to the NADPH-binding pocket in mammalian catalases at the entrance to a lateral channel leading to the heme. Kinetic analysis of site-directed mutants supports the assignment of this pocket as the binding site for oxidase substrates.

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A Novel Adenylate Binding Site Confers Phosphopantetheine Adenylyltransferase Interactions with Coenzyme A

Journal of Bacteriology ◽

10.1128/jb.185.14.4074-4080.2003 ◽

2003 ◽

Vol 185 (14) ◽

pp. 4074-4080 ◽

Cited By ~ 32

Author(s):

Tina Izard

Keyword(s):

Crystal Structure ◽

High Resolution ◽

Binding Site ◽

Active Site ◽

Binding Sites ◽

Biosynthetic Pathway ◽

Coenzyme A ◽

Asymmetric Unit ◽

Phosphate Moiety ◽

Reversible Transfer

ABSTRACT Phosphopantetheine adenylyltransferase (PPAT) regulates the key penultimate step in the essential coenzyme A (CoA) biosynthetic pathway. PPAT catalyzes the reversible transfer of an adenylyl group from Mg2+:ATP to 4′-phosphopantetheine to form 3′-dephospho-CoA (dPCoA) and pyrophosphate. The high-resolution crystal structure of PPAT complexed with CoA has been determined. Remarkably, CoA and the product dPCoA bind to the active site in distinct ways. Although the phosphate moiety within the phosphopantetheine arm overlaps, the pantetheine arm binds to the same pocket in two distinct conformations, and the adenylyl moieties of these two ligands have distinct binding sites. Moreover, the PPAT:CoA crystal structure confirms the asymmetry of binding to the two trimers within the hexameric enzyme. Specifically, the pantetheine arm of CoA bound to one protomer within the asymmetric unit displays the dPCoA-like conformation with the adenylyl moiety disordered, whereas CoA binds the twofold-related protomer in an ordered and unique fashion.

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Crystal Structure of the PdxY Protein from Escherichia coli

Journal of Bacteriology ◽

10.1128/jb.186.23.8074-8082.2004 ◽

2004 ◽

Vol 186 (23) ◽

pp. 8074-8082 ◽

Cited By ~ 25

Author(s):

Martin K. Safo ◽

Faik N. Musayev ◽

Sharyn Hunt ◽

Martino L. di Salvo ◽

Neel Scarsdale ◽

...

Keyword(s):

Crystal Structure ◽

Escherichia Coli ◽

Binding Site ◽

Sequence Homology ◽

Active Site ◽

Pyridoxal Phosphate ◽

Protein A ◽

Detailed Comparison ◽

Protein Product ◽

Atp Binding Site

ABSTRACT The crystal structure of Escherichia coli PdxY, the protein product of the pdxY gene, has been determined to a 2.2-Å resolution. PdxY is a member of the ribokinase superfamily of enzymes and has sequence homology with pyridoxal kinases that phosphorylate pyridoxal at the C-5′ hydroxyl. The protein is a homodimer with an active site on each monomer composed of residues that come exclusively from each respective subunit. The active site is filled with a density that fits that of pyridoxal. In monomer A, the ligand appears to be covalently attached to Cys122 as a thiohemiacetal, while in monomer B it is not covalently attached but appears to be partially present as pyridoxal 5′-phosphate. The presence of pyridoxal phosphate and pyridoxal as ligands was confirmed by the activation of aposerine hydroxymethyltransferase after release of the ligand by the denaturation of PdxY. The ligand, which appears to be covalently attached to Cys122, does not dissociate after denaturation of the protein. A detailed comparison (of functional properties, sequence homology, active site and ATP-binding-site residues, and active site flap types) of PdxY with other pyridoxal kinases as well as the ribokinase superfamily in general suggested that PdxY is a member of a new subclass of the ribokinase superfamily. The structure of PdxY also permitted an interpretation of work that was previously published about this enzyme.

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The Active Site of O-Acetylserine Sulfhydrylase Is the Anchor Point for Bienzyme Complex Formation with Serine Acetyltransferase

Journal of Bacteriology ◽

10.1128/jb.187.9.3201-3205.2005 ◽

2005 ◽

Vol 187 (9) ◽

pp. 3201-3205 ◽

Cited By ~ 62

Author(s):

Bin Huang ◽

Matthew W. Vetting ◽

Steven L. Roderick

Keyword(s):

Crystal Structure ◽

Complex Formation ◽

Binding Site ◽

Active Site ◽

Binding Pocket ◽

Anion Binding ◽

Carboxyl Group ◽

Serine Acetyltransferase ◽

Cysteine Synthase

ABSTRACT The biosynthesis of cysteine in bacteria and plants is carried out by a two-step pathway, catalyzed by serine acetyltransferase (SAT) and O-acetylserine sulfhydrylase (OASS; O-acetylserine [thiol] lyase). The aerobic form of OASS forms a tight bienzyme complex with SAT in vivo, termed cysteine synthase. We have determined the crystal structure of OASS in complex with a C-terminal peptide of SAT required for bienzyme complex formation. The binding site of the peptide is at the active site of OASS, and its C-terminal carboxyl group occupies the same anion binding pocket as the α-carboxylate of the O-acetylserine substrate of OASS. These results explain the partial inhibition of OASS by SAT on complex formation as well as the competitive dissociation of the complex by O-acetylserine.

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