2.8-.ANG.-resolution crystal structure of an active-site mutant of aspartate aminotransferase from Escherichia coli

Biochemistry ◽  
1989 ◽  
Vol 28 (20) ◽  
pp. 8161-8167 ◽  
Author(s):  
Douglas L. Smith ◽  
Steven C. Almo ◽  
Michael D. Toney ◽  
Dagmar Ringe
Keyword(s):  
Crystal Structure ◽  
Escherichia Coli ◽  
Active Site ◽  
Aspartate Aminotransferase

scholarly journals Crystal structures of two monomeric triosephosphate isomerase variants identifiedviaa directed-evolution protocol selecting forL-arabinose isomerase activity

2016 ◽  
Vol 72 (6) ◽  
pp. 490-499
Author(s):  
Mirja Krause ◽  
Tiila-Riikka Kiema ◽  
Peter Neubauer ◽  
Rik K. Wierenga
Keyword(s):  
Crystal Structure ◽  
Escherichia Coli ◽  
Directed Evolution ◽  
Crystal Structures ◽  
Active Site ◽  
Triosephosphate Isomerase ◽  
Point Mutations ◽  
Van Der Waals Interactions ◽  
Side Chain ◽  
Arabinose Isomerase

The crystal structures are described of two variants of A-TIM: Ma18 (2.7 Å resolution) and Ma21 (1.55 Å resolution). A-TIM is a monomeric loop-deletion variant of triosephosphate isomerase (TIM) which has lost the TIM catalytic properties. Ma18 and Ma21 were identified after extensive directed-evolution selection experiments using anEscherichia coliL-arabinose isomerase knockout strain expressing a randomly mutated A-TIM gene. These variants facilitate better growth of theEscherichia coliselection strain in medium supplemented with 40 mML-arabinose. Ma18 and Ma21 differ from A-TIM by four and one point mutations, respectively. Ma18 and Ma21 are more stable proteins than A-TIM, as judged from CD melting experiments. Like A-TIM, both proteins are monomeric in solution. In the Ma18 crystal structure loop 6 is open and in the Ma21 crystal structure loop 6 is closed, being stabilized by a bound glycolate molecule. The crystal structures show only small differences in the active site compared with A-TIM. In the case of Ma21 it is observed that the point mutation (Q65L) contributes to small structural rearrangements near Asn11 of loop 1, which correlate with different ligand-binding properties such as a loss of citrate binding in the active site. The Ma21 structure also shows that its Leu65 side chain is involved in van der Waals interactions with neighbouring hydrophobic side-chain moieties, correlating with its increased stability. The experimental data suggest that the increased stability and solubility properties of Ma21 and Ma18 compared with A-TIM cause better growth of the selection strain when coexpressing Ma21 and Ma18 instead of A-TIM.

scholarly journals Crystal Structure of the PdxY Protein from Escherichia coli

2004 ◽  
Vol 186 (23) ◽  
pp. 8074-8082 ◽  
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.

Activity and structure of the active-site mutants R386Y and R386F of Escherichia coli aspartate aminotransferase

Biochemistry ◽  
1991 ◽  
Vol 30 (7) ◽  
pp. 1980-1985 ◽  
Author(s):  
Avis T. Danishefsky ◽  
James J. Onnufer ◽  
Gregory A. Petsko ◽  
Dagmar Ringe
Keyword(s):  
Escherichia Coli ◽  
Active Site ◽  
Aspartate Aminotransferase ◽  
Active Site Mutants

scholarly journals Crystal Structure of Pyridoxal Kinase from the Escherichia coli pdxK Gene: Implications for the Classification of Pyridoxal Kinases

2006 ◽  
Vol 188 (12) ◽  
pp. 4542-4552 ◽  
Author(s):  
Martin K. Safo ◽  
Faik N. Musayev ◽  
Martino L. di Salvo ◽  
Sharyn Hunt ◽  
Jean-Baptiste Claude ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Escherichia Coli ◽  
Active Site ◽  
Pyridoxal Phosphate ◽  
Salvage Pathway ◽  
Pyridoxal Kinase ◽  
E Coli ◽  
Binary Complexes ◽  
Significant Conformational Change

ABSTRACT The pdxK and pdxY genes have been found to code for pyridoxal kinases, enzymes involved in the pyridoxal phosphate salvage pathway. Two pyridoxal kinase structures have recently been published, including Escherichia coli pyridoxal kinase 2 (ePL kinase 2) and sheep pyridoxal kinase, products of the pdxY and pdxK genes, respectively. We now report the crystal structure of E. coli pyridoxal kinase 1 (ePL kinase 1), encoded by a pdxK gene, and an isoform of ePL kinase 2. The structures were determined in the unliganded and binary complexes with either MgATP or pyridoxal to 2.1-, 2.6-, and 3.2-Å resolutions, respectively. The active site of ePL kinase 1 does not show significant conformational change upon binding of either pyridoxal or MgATP. Like sheep PL kinase, ePL kinase 1 exhibits a sequential random mechanism. Unlike sheep pyridoxal kinase, ePL kinase 1 may not tolerate wide variation in the size and chemical nature of the 4′ substituent on the substrate. This is the result of differences in a key residue at position 59 on a loop (loop II) that partially forms the active site. Residue 59, which is His in ePL kinase 1, interacts with the formyl group at C-4′ of pyridoxal and may also determine if residues from another loop (loop I) can fill the active site in the absence of the substrate. Both loop I and loop II are suggested to play significant roles in the functions of PL kinases.

Molecular aspects of β-ketoacyl synthase (KAS) catalysis

2000 ◽  
Vol 28 (6) ◽  
pp. 601-607 ◽  
Author(s):  
P. von Wettstein-Knowles ◽  
J. Gotthardt Olsen ◽  
K. Arnvig McGuire ◽  
S. Larsen
Keyword(s):  
Crystal Structure ◽  
Escherichia Coli ◽  
Active Site ◽  
Chalcone Synthase ◽  
Crystal Structure Data ◽  
The Other ◽  
Ketoacyl Synthase ◽  
Chain Length Specificity ◽  
Catalytic Mechanisms ◽  
Molecular Aspects

Crystal structure data for Escherichia coli β-ketoacyl synthase (KAS) I with C10 and C12 fatty acid substrates bound in conjunction with results from mutagenizing residues in the active site leads to a model for catalysis. Differences from and similarities to the other Claisen enzymes carrying out decarboxylations reveal two catalytic mechanisms, one for KAS I and KAS II, the other for KAS III and chalcone synthase. A comparison of the structures of KAS I and KAS II does not reveal the basis of chain-length specificity. The structures of the Arabidopsis thaliana KAS family are compared.

scholarly journals Structural evidence for a latch mechanism regulating access to the active site of SufS-family cysteine desulfurases

2020 ◽  
Vol 76 (3) ◽  
pp. 291-301 ◽  
Author(s):  
Jack A. Dunkle ◽  
Michael R. Bruno ◽  
Patrick A. Frantom
Keyword(s):  
Crystal Structure ◽  
Escherichia Coli ◽  
Sequence Analysis ◽  
Active Site ◽  
Resting State ◽  
Sulfur Source ◽  
Structural Elements ◽  
Cysteine Desulfurase ◽  
X Ray

Cysteine serves as the sulfur source for the biosynthesis of Fe–S clusters and thio-cofactors, molecules that are required for core metabolic processes in all organisms. Therefore, cysteine desulfurases, which mobilize sulfur for its incorporation into thio-cofactors by cleaving the Cα—S bond of cysteine, are ubiquitous in nature. SufS, a type 2 cysteine desulfurase that is present in plants and microorganisms, mobilizes sulfur from cysteine to the transpersulfurase SufE to initiate Fe–S biosynthesis. Here, a 1.5 Å resolution X-ray crystal structure of the Escherichia coli SufS homodimer is reported which adopts a state in which the two monomers are rotated relative to their resting state, displacing a β-hairpin from its typical position blocking transpersulfurase access to the SufS active site. A global structure and sequence analysis of SufS family members indicates that the active-site β-hairpin is likely to require adjacent structural elements to function as a β-latch regulating access to the SufS active site.

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