Crystal structure of a putative short-chain dehydrogenase/reductase from Paraburkholderia xenovorans

Paraburkholderia xenovorans degrades organic wastes, including polychlorinated biphenyls. The atomic structure of a putative dehydrogenase/reductase (SDR) from P. xenovorans (PxSDR) was determined in space group P21 at a resolution of 1.45 Å. PxSDR shares less than 37% sequence identity with any known structure and assembles as a prototypical SDR tetramer. As expected, there is some conformational flexibility and difference in the substrate-binding cavity, which explains the substrate specificity. Uniquely, the cofactor-binding cavity of PxSDR is not well conserved and differs from those of other SDRs. PxSDR has an additional seven amino acids that form an additional unique loop within the cofactor-binding cavity. Further studies are required to determine how these differences affect the enzymatic functions of the SDR.

Download Full-text

Structural comparisons lead to the definition of a new superfamily of NAD(P)(H)-accepting oxidoreductases: the single-domain reductases/epimerases/dehydrogenases (the ‘RED’ family)

Biochemical Journal ◽

10.1042/bj3040095 ◽

1994 ◽

Vol 304 (1) ◽

pp. 95-99 ◽

Cited By ~ 56

Author(s):

G Labesse ◽

A Vidal-Cros ◽

J Chomilier ◽

M Gaudry ◽

J P Mornon

Keyword(s):

Amino Acids ◽

Sequence Alignment ◽

Active Site ◽

Tertiary Structure ◽

Binding Specificity ◽

Single Domain ◽

Divergent Evolution ◽

Cofactor Binding ◽

Sequence Identity ◽

Definition Of

Using both primary- and tertiary-structure comparisons, we have established new structural similarities shared by reductases, epimerases and dehydrogenases not previously known to be related. Despite the low sequence identity (down to 10%), short consensus segments are identified. We show that the sequence, the active site and the supersecondary structure are well conserved in these proteins. New homologues (the protochlorophyllide reductases) are detected, and we define a new superfamily composed of single-domain dinucleotide-binding enzymes. Rules for the cofactor-binding specificity are deduced from our sequence alignment. The involvement of some amino acids in catalysis is discussed. Comparison with two-domain dehydrogenases allows us to distinguish two general mechanisms of divergent evolution.

Download Full-text

Crystal structure of trypanosoma cruzi tyrosine aminotransferase: Substrate specificity is influenced by cofactor binding mode

Protein Science ◽

10.1110/ps.8.11.2406 ◽

2008 ◽

Vol 8 (11) ◽

pp. 2406-2417 ◽

Cited By ~ 38

Author(s):

Wulf Blankenfeldt ◽

Marisa Montemartini-Kalisz ◽

Henryk M. Kalisz ◽

Hans-Jürgen Hecht ◽

Cristina Nowicki

Keyword(s):

Crystal Structure ◽

Trypanosoma Cruzi ◽

Substrate Specificity ◽

Binding Mode ◽

Tyrosine Aminotransferase ◽

Cofactor Binding

Download Full-text

Crystal structure of ErmE - 23S rRNA methyltransferase in macrolide resistance

Scientific Reports ◽

10.1038/s41598-019-51174-0 ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 1

Author(s):

Alena Stsiapanava ◽

Maria Selmer

Keyword(s):

Crystal Structure ◽

Tertiary Structure ◽

Catalytic Domain ◽

Antibiotic Resistance Genes ◽

Macrolide Resistance ◽

Saccharopolyspora Erythraea ◽

23S Rrna ◽

Cofactor Binding ◽

Sequence Identity ◽

Adenosyl Methionine

Abstract Pathogens often receive antibiotic resistance genes through horizontal gene transfer from bacteria that produce natural antibiotics. ErmE is a methyltransferase (MTase) from Saccharopolyspora erythraea that dimethylates A2058 in 23S rRNA using S-adenosyl methionine (SAM) as methyl donor, protecting the ribosomes from macrolide binding. To gain insights into the mechanism of macrolide resistance, the crystal structure of ErmE was determined to 1.75 Å resolution. ErmE consists of an N-terminal Rossmann-like α/ß catalytic domain and a C-terminal helical domain. Comparison with ErmC’ that despite only 24% sequence identity has the same function, reveals highly similar catalytic domains. Accordingly, superposition with the catalytic domain of ErmC’ in complex with SAM suggests that the cofactor binding site is conserved. The two structures mainly differ in the C-terminal domain, which in ErmE contains a longer loop harboring an additional 310 helix that interacts with the catalytic domain to stabilize the tertiary structure. Notably, ErmE also differs from ErmC’ by having long disordered extensions at its N- and C-termini. A C-terminal disordered region rich in arginine and glycine is also a present in two other MTases, PikR1 and PikR2, which share about 30% sequence identity with ErmE and methylate the same nucleotide in 23S rRNA.

Download Full-text

Physiology and Substrate Specificity of Two Closely Related Amino Acid Transporters, SerP1 and SerP2, of Lactococcus lactis

Journal of Bacteriology ◽

10.1128/jb.02471-14 ◽

2014 ◽

Vol 197 (5) ◽

pp. 951-958 ◽

Cited By ~ 4

Author(s):

Elke E. E. Noens ◽

Juke S. Lolkema

Keyword(s):

Amino Acids ◽

Amino Acid ◽

Substrate Specificity ◽

Lactococcus Lactis ◽

Main Function ◽

Content Type ◽

High Affinity ◽

Sequence Identity ◽

Peptidoglycan Synthesis ◽

Affinity Constants

TheserP1andserP2genes found adjacently on the chromosome ofLactococcus lactisstrains encode two members of the amino acid-polyamine-organocation (APC) superfamily of secondary transporters that share 61% sequence identity. SerP1 transportsl-serine,l-threonine, andl-cysteine with high affinity. Affinity constants (Km) are in the 20 to 40 μM range. SerP2 is adl-alanine/dl-serine/glycine transporter. The preferred substrate appears to bedl-alanine for which the affinities were found to be 38 and 20 μM for thedandlisomers, respectively. The common substratel-serine is a high-affinity substrate of SerP1 and a low-affinity substrate of SerP2 with affinity constants of 18 and 356 μM, respectively. Growth experiments demonstrate that SerP1 is the mainl-serine transporter responsible for optimal growth in media containing free amino acids as the sole source of amino acids. SerP2 is able to replace SerP1 in this role only in medium lacking the high-affinity substratesl-alanine and glycine. SerP2 plays an adverse role for the cell by being solely responsible for the uptake of toxicd-serine. The main function of SerP2 is in cell wall biosynthesis through the uptake ofd-alanine, an essential precursor in peptidoglycan synthesis. SerP2 has overlapping substrate specificity and shares 42% sequence identity with CycA ofEscherichia coli, a transporter whose involvement in peptidoglycan synthesis is well established. No evidence was obtained for a role of SerP1 and SerP2 in the excretion of excess amino acids during growth ofL. lactison protein/peptide-rich media.

Download Full-text

Improved ionic conductivity of Na3+Sc Zr2-Si2PO12 (x=0.2, 0.3, 0.4, 0.5) NASICON via optimized sintering conditions: Investigation of crystal structure, local atomic structure, and microstructure

Chemical Physics Letters ◽

10.1016/j.cplett.2021.138706 ◽

2021 ◽

pp. 138706

Author(s):

B. Santhoshkumar ◽

D.L.R. Khanna ◽

M.B. Choudhary ◽

P. Lokeswara Rao ◽

K.V. Ramanathan ◽

...

Keyword(s):

Crystal Structure ◽

Ionic Conductivity ◽

Atomic Structure ◽

Local Atomic Structure ◽

Sintering Conditions ◽

Structure And Microstructure

Download Full-text

Analysis of Sequence Divergence in Mammalian ABCGs Predicts a Structural Network of Residues That Underlies Functional Divergence

International Journal of Molecular Sciences ◽

10.3390/ijms22063012 ◽

2021 ◽

Vol 22 (6) ◽

pp. 3012

Author(s):

James I. Mitchell-White ◽

Thomas Stockner ◽

Nicholas Holliday ◽

Stephen J. Briddon ◽

Ian D. Kerr

Keyword(s):

Substrate Specificity ◽

Functional Divergence ◽

3D Structure ◽

Sequence Divergence ◽

Conformational Flexibility ◽

Substrate Selectivity ◽

Multiple Sequence ◽

Atp Binding Cassette Transporters ◽

Structural Network ◽

Wide Substrate Specificity

The five members of the mammalian G subfamily of ATP-binding cassette transporters differ greatly in their substrate specificity. Four members of the subfamily are important in lipid transport and the wide substrate specificity of one of the members, ABCG2, is of significance due to its role in multidrug resistance. To explore the origin of substrate selectivity in members 1, 2, 4, 5 and 8 of this subfamily, we have analysed the differences in conservation between members in a multiple sequence alignment of ABCG sequences from mammals. Mapping sets of residues with similar patterns of conservation onto the resolved 3D structure of ABCG2 reveals possible explanations for differences in function, via a connected network of residues from the cytoplasmic to transmembrane domains. In ABCG2, this network of residues may confer extra conformational flexibility, enabling it to transport a wider array of substrates.

Download Full-text

Crystal structure of steroid reductase SRD5A reveals conserved steroid reduction mechanism

Nature Communications ◽

10.1038/s41467-020-20675-2 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Yufei Han ◽

Qian Zhuang ◽

Bo Sun ◽

Wenping Lv ◽

Sheng Wang ◽

...

Keyword(s):

Crystal Structure ◽

Biochemical Characterization ◽

Substrate Binding ◽

Binding Pocket ◽

Substrate Binding Pocket ◽

Transmembrane Segments ◽

Therapeutic Molecules ◽

Binding Cavity ◽

Immune System Regulation ◽

Mediated Reduction

AbstractSteroid hormones are essential in stress response, immune system regulation, and reproduction in mammals. Steroids with 3-oxo-Δ4 structure, such as testosterone or progesterone, are catalyzed by steroid 5α-reductases (SRD5As) to generate their corresponding 3-oxo-5α steroids, which are essential for multiple physiological and pathological processes. SRD5A2 is already a target of clinically relevant drugs. However, the detailed mechanism of SRD5A-mediated reduction remains elusive. Here we report the crystal structure of PbSRD5A from Proteobacteria bacterium, a homolog of both SRD5A1 and SRD5A2, in complex with the cofactor NADPH at 2.0 Å resolution. PbSRD5A exists as a monomer comprised of seven transmembrane segments (TMs). The TM1-4 enclose a hydrophobic substrate binding cavity, whereas TM5-7 coordinate cofactor NADPH through extensive hydrogen bonds network. Homology-based structural models of HsSRD5A1 and -2, together with biochemical characterization, define the substrate binding pocket of SRD5As, explain the properties of disease-related mutants and provide an important framework for further understanding of the mechanism of NADPH mediated steroids 3-oxo-Δ4 reduction. Based on these analyses, the design of therapeutic molecules targeting SRD5As with improved specificity and therapeutic efficacy would be possible.

Download Full-text