scholarly journals An Open Conformation of Switch I Revealed by the Crystal Structure of a Mg2+-free Form of RHOA Complexed with GDP

2000 ◽  
Vol 275 (24) ◽  
pp. 18311-18317 ◽  
Author(s):  
Toshiyuki Shimizu ◽  
Kentaro Ihara ◽  
Ryoko Maesaki ◽  
Shinya Kuroda ◽  
Kozo Kaibuchi ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Free Form ◽  
Open Conformation

scholarly journals Crystal Structure of a ligand-bound LacY–Nanobody Complex

2018 ◽  
Vol 115 (35) ◽  
pp. 8769-8774 ◽  
Author(s):  
Hemant Kumar ◽  
Janet S. Finer-Moore ◽  
Xiaoxu Jiang ◽  
Irina Smirnova ◽  
Vladimir Kasho ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Lactose Permease ◽  
Transmembrane Helices ◽  
Helical Bundle ◽  
Flexible Loop ◽  
Sugar Binding ◽  
Open Conformation ◽  
Substrate Analog ◽  
Multiple Conformations ◽  
Alternating Access

The lactose permease of Escherichia coli (LacY), a dynamic polytopic membrane transport protein, catalyzes galactoside/H+ symport and operates by an alternating access mechanism that exhibits multiple conformations, the distribution of which is altered by sugar-binding. Camelid nanobodies were made against a double-mutant Gly46 → Trp/Gly262 → Trp (LacYWW) that produces an outward-open conformation, as opposed to the cytoplasmic open-state crystal structure of WT LacY. Nanobody 9047 (Nb9047) stabilizes WT LacY in a periplasmic-open conformation. Here, we describe the X-ray crystal structure of a complex between LacYWW, the high-affinity substrate analog 4-nitrophenyl-α-d-galactoside (NPG), and Nb9047 at 3-Å resolution. The present crystal structure demonstrates that Nb9047 binds to the periplasmic face of LacY, primarily to the C-terminal six-helical bundle, while a flexible loop of the Nb forms a bridge between the N- and C-terminal halves of LacY across the periplasmic vestibule. The bound Nb partially covers the vestibule, yet does not affect the on-rates or off-rates for the substrate binding to LacYWW, which implicates dynamic flexibility of the Nb–LacYWW complex. Nb9047-binding neither changes the overall structure of LacYWW with bound NPG, nor the positions of side chains comprising the galactoside-binding site. The current NPG-bound structure exhibits a more occluded periplasmic vestibule than seen in a previous structure of a (different Nb) apo-LacYWW/Nb9039 complex that we argue is caused by sugar-binding, with major differences located at the periplasmic ends of transmembrane helices in the N-terminal half of LacY.

scholarly journals Crystal structure of enolase fromDrosophila melanogaster

2017 ◽  
Vol 73 (4) ◽  
pp. 228-234 ◽  
Author(s):  
Congcong Sun ◽  
Baokui Xu ◽  
Xueyan Liu ◽  
Zhen Zhang ◽  
Zhongliang Su
Keyword(s):  
Crystal Structure ◽  
Catalytic Activity ◽  
Structural Basis ◽  
Molecular Replacement ◽  
Biological Processes ◽  
Conserved Residues ◽  
Dimer Interface ◽  
Open Conformation ◽  
Evolutionary Studies ◽  
Important Enzyme

Enolase is an important enzyme in glycolysis and various biological processes. Its dysfunction is closely associated with diseases. Here, the enolase fromDrosophila melanogaster(DmENO) was purified and crystallized. A crystal of DmENO diffracted to 2.0 Å resolution and belonged to space groupR32. The structure was solved by molecular replacement. Like most enolases, DmENO forms a homodimer with conserved residues in the dimer interface. DmENO possesses an open conformation in this structure and contains conserved elements for catalytic activity. This work provides a structural basis for further functional and evolutionary studies of enolase.

scholarly journals Crystal Structure ofPseudomonas aeruginosaLipase in the Open Conformation

2000 ◽  
Vol 275 (40) ◽  
pp. 31219-31225 ◽  
Author(s):  
Marco Nardini ◽  
Dietmar A. Lang ◽  
Klaus Liebeton ◽  
Karl-Erich Jaeger ◽  
Bauke W. Dijkstra
Keyword(s):  
Crystal Structure ◽  
Open Conformation

scholarly journals Crystal structure of ribonuclease F1 ofFusarium moniliformein its free form and in complex with 2 GMP

1993 ◽  
Vol 49 (s1) ◽  
pp. c102-c103
Author(s):  
D. G. Vassylev ◽  
K. Katayanagi ◽  
K. Ishikawa ◽  
M. Tsujimoto-Hirano ◽  
M. Danno ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Free Form

scholarly journals Induced-fitting and electrostatic potential change of PcyA upon substrate binding demonstrated by the crystal structure of the substrate-free form

FEBS Letters ◽  
2006 ◽  
Vol 580 (16) ◽  
pp. 3823-3828 ◽  
Author(s):  
Yoshinori Hagiwara ◽  
Masakazu Sugishima ◽  
Yasuhiro Takahashi ◽  
Keiichi Fukuyama
Keyword(s):  
Crystal Structure ◽  
Electrostatic Potential ◽  
Substrate Binding ◽  
Potential Change ◽  
Free Form

Crystal Structure of Inhibitor-Bound P450BM-3 Reveals Open Conformation of Substrate Access Channel†,‡

Biochemistry ◽  
2008 ◽  
Vol 47 (12) ◽  
pp. 3662-3670 ◽  
Author(s):  
Donovan C. Haines ◽  
Baozhi Chen ◽  
Diana R. Tomchick ◽  
Muralidhar Bondlela ◽  
Amita Hegde ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Open Conformation ◽  
Access Channel

scholarly journals Recognition of the 3′ splice site RNA by the U2AF heterodimer involves a dynamic population shift

2016 ◽  
Vol 113 (46) ◽  
pp. E7169-E7175 ◽  
Author(s):  
Lena Voith von Voithenberg ◽  
Carolina Sánchez-Rico ◽  
Hyun-Seo Kang ◽  
Tobias Madl ◽  
Katia Zanier ◽  
...  
Keyword(s):  
Splice Site ◽  
Rna Binding ◽  
Free Form ◽  
Rna Recognition Motif ◽  
Single Pair ◽  
Open Conformation ◽  
Population Shift ◽  
Rna Ligands ◽  
U2 Auxiliary Factor ◽  
Dynamic Population

An essential early step in the assembly of human spliceosomes onto pre-mRNA involves the recognition of regulatory RNA cis elements in the 3′ splice site by the U2 auxiliary factor (U2AF). The large (U2AF65) and small (U2AF35) subunits of the U2AF heterodimer contact the polypyrimidine tract (Py-tract) and the AG-dinucleotide, respectively. The tandem RNA recognition motif domains (RRM1,2) of U2AF65 adopt closed/inactive and open/active conformations in the free form and when bound to bona fide Py-tract RNA ligands. To investigate the molecular mechanism and dynamics of 3′ splice site recognition by U2AF65 and the role of U2AF35 in the U2AF heterodimer, we have combined single-pair FRET and NMR experiments. In the absence of RNA, the RRM1,2 domain arrangement is highly dynamic on a submillisecond time scale, switching between closed and open conformations. The addition of Py-tract RNA ligands with increasing binding affinity (strength) gradually shifts the equilibrium toward an open conformation. Notably, the protein–RNA complex is rigid in the presence of a strong Py-tract but exhibits internal motion with weak Py-tracts. Surprisingly, the presence of U2AF35, whose UHM domain interacts with U2AF65 RRM1, increases the population of the open arrangement of U2AF65 RRM1,2 in the absence and presence of a weak Py-tract. These data indicate that the U2AF heterodimer promotes spliceosome assembly by a dynamic population shift toward the open conformation of U2AF65 to facilitate the recognition of weak Py-tracts at the 3′ splice site. The structure and RNA binding of the heterodimer was unaffected by cancer-linked myelodysplastic syndrome mutants.

Sign in / Sign up

Export Citation Format

Share Document