Crystal structure of Thermus caldophilus phosphoglycerate kinase in the open conformation

2006 ◽  
Vol 350 (4) ◽  
pp. 1044-1049 ◽  
Author(s):  
Jun Hyuck Lee ◽  
Young Jun Im ◽  
Jungdon Bae ◽  
Dooil Kim ◽  
Mun-Kyoung Kim ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Phosphoglycerate Kinase ◽  
Open Conformation ◽  
Thermus Caldophilus

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

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 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

Structure of the Ca2+-saturated C-terminal domain of scallop troponin C in complex with a troponin I fragment

2013 ◽  
Vol 394 (1) ◽  
pp. 55-68 ◽  
Author(s):  
Yusuke S. Kato ◽  
Fumiaki Yumoto ◽  
Hiroyuki Tanaka ◽  
Takuya Miyakawa ◽  
Yumiko Miyauchi ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Structural Change ◽  
Troponin I ◽  
Adductor Muscle ◽  
Troponin C ◽  
Striated Muscles ◽  
Terminal Domain ◽  
Open Conformation ◽  
Ef Hands ◽  
Contractile Forces

Abstract Troponin C (TnC) is the Ca2+-sensing subunit of troponin that triggers the contraction of striated muscles. In scallops, the striated muscles consume little ATP energy in sustaining strong contractile forces. The N-terminal domain of TnC works as the Ca2+ sensor in vertebrates, whereas scallop TnC uses the C-terminal domain as the Ca2+ sensor, suggesting that there are differences in the mechanism of the Ca2+-dependent regulation of muscles between invertebrates and vertebrates. Here, we report the crystal structure of Akazara scallop (Chlamys nipponensis akazara) adductor muscle TnC C-terminal domain (asTnCC) complexed with a short troponin I fragment (asTnIS) and Ca2+. The electron density of a Ca2+ ion is observed in only one of the two EF-hands. The EF-hands of asTnCC can only be in the fully open conformation with the assistance of asTnIS. The number of hydrogen bonds between asTnCC and asTnIS is markedly lower than the number in the vertebrate counterparts. The Ca2+ modulation on the binding between asTnCC and asTnIS is weaker, but structural change of the complex depending on Ca2+ concentration was observed. Together, these findings provide a detailed description of the distinct molecular mechanism of contractile regulation in the scallop adductor muscle from that of vertebrates.

scholarly journals Crystal structure of the RNA 2′,3′-cyclic phosphodiesterase fromDeinococcus radiodurans

2017 ◽  
Vol 73 (5) ◽  
pp. 276-280 ◽  
Author(s):  
Wanchun Han ◽  
Jiahui Cheng ◽  
Congli Zhou ◽  
Yuejin Hua ◽  
Ye Zhao
Keyword(s):  
Crystal Structure ◽  
Active Site ◽  
Catalytic Mechanism ◽  
Deinococcus Radiodurans ◽  
Sulfate Ion ◽  
Open Conformation ◽  
Domains Of Life

2′,3′-Cyclic phosphodiesterase (CPDase) homologues have been found in all domains of life and are involved in diverse RNA and nucleotide metabolisms. The CPDase fromDeinococcus radioduranswas crystallized and the crystals diffracted to 1.6 Å resolution, which is the highest resolution currently known for a CPDase structure. Structural comparisons revealed that the enzyme is in an open conformation in the absence of substrate. Nevertheless, the active site is well formed, and the representative motifs interact with sulfate ion, which suggests a conserved catalytic mechanism.

Sign in / Sign up

Export Citation Format

Share Document