The structure of human ubiquitin in 2-methyl-2,4-pentanediol: a new conformational switch.

PubWeight™: 1.00‹?› | Rank: Top 15%

🔗 View Article (PMC 3064841)

Published in Protein Sci on March 01, 2011

Authors

Kuo Ying Huang1, Gabriele A Amodeo, Liang Tong, Ann McDermott

Author Affiliations

1: Department of Chemistry, Columbia University, New York, New York 10027, USA.

Articles citing this

Protein backbone and sidechain torsion angles predicted from NMR chemical shifts using artificial neural networks. J Biomol NMR (2013) 2.75

Atomic-level description of ubiquitin folding. Proc Natl Acad Sci U S A (2013) 1.65

Site-resolved measurement of microsecond-to-millisecond conformational-exchange processes in proteins by solid-state NMR spectroscopy. J Am Chem Soc (2012) 0.97

Observing the overall rocking motion of a protein in a crystal. Nat Commun (2015) 0.89

Allosteric switch regulates protein-protein binding through collective motion. Proc Natl Acad Sci U S A (2016) 0.83

Ensemble MD simulations restrained via crystallographic data: accurate structure leads to accurate dynamics. Protein Sci (2014) 0.82

Motional timescale predictions by molecular dynamics simulations: case study using proline and hydroxyproline sidechain dynamics. Proteins (2013) 0.80

Practical considerations over spectral quality in solid state NMR spectroscopy of soluble proteins. J Biomol NMR (2013) 0.78

Structural heterogeneity in microcrystalline ubiquitin studied by solid-state NMR. Protein Sci (2015) 0.78

Enhancing the quality of protein conformation ensembles with relative populations. J Biomol NMR (2014) 0.77

Ensembles of a small number of conformations with relative populations. J Biomol NMR (2015) 0.76

Flexibility and Design: Conformational Heterogeneity along the Evolutionary Trajectory of a Redesigned Ubiquitin. Structure (2017) 0.75

Accelerating proton spin diffusion in perdeuterated proteins at 100 kHz MAS. J Biomol NMR (2016) 0.75

Protein conformational dynamics studied by (15)N and (1)H R1ρ relaxation dispersion: Application to wild-type and G53A ubiquitin crystals. Solid State Nucl Magn Reson (2017) 0.75

Slow conformational exchange and overall rocking motion in ubiquitin protein crystals. Nat Commun (2017) 0.75

Articles cited by this

Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr D Biol Crystallogr (1998) 169.28

Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr A (1991) 119.63

Structure of ubiquitin refined at 1.8 A resolution. J Mol Biol (1987) 9.19

Recognition dynamics up to microseconds revealed from an RDC-derived ubiquitin ensemble in solution. Science (2008) 8.04

The role of dynamic conformational ensembles in biomolecular recognition. Nat Chem Biol (2009) 7.36

Crystal structure of a UBP-family deubiquitinating enzyme in isolation and in complex with ubiquitin aldehyde. Cell (2002) 4.33

The ubiquitin binding domain ZnF UBP recognizes the C-terminal diglycine motif of unanchored ubiquitin. Cell (2006) 3.46

Protein backbone chemical shifts predicted from searching a database for torsion angle and sequence homology. J Biomol NMR (2007) 3.20

Conformational selection or induced fit: a flux description of reaction mechanism. Proc Natl Acad Sci U S A (2009) 3.03

Structural basis for specific cleavage of Lys 63-linked polyubiquitin chains. Nature (2008) 2.94

Structure of the ubiquitin hydrolase UCH-L3 complexed with a suicide substrate. J Biol Chem (2004) 2.75

Structural properties of polyubiquitin chains in solution. J Mol Biol (2002) 2.72

Backbone and side-chain 13C and 15N signal assignments of the alpha-spectrin SH3 domain by magic angle spinning solid-state NMR at 17.6 Tesla. Chembiochem (2001) 2.08

Structural basis of ubiquitin recognition by the deubiquitinating protease USP2. Structure (2006) 1.92

Internal dynamics of human ubiquitin revealed by 13C-relaxation studies of randomly fractionally labeled protein. Biochemistry (1996) 1.92

COMO: a program for combined molecular replacement. Acta Crystallogr D Biol Crystallogr (2001) 1.91

Structural insights into the assembly and function of the SAGA deubiquitinating module. Science (2010) 1.74

Assignments of carbon NMR resonances for microcrystalline ubiquitin. J Am Chem Soc (2004) 1.70

De novo design of the hydrophobic core of ubiquitin. Protein Sci (1997) 1.69

Protein structure determination by high-resolution solid-state NMR spectroscopy: application to microcrystalline ubiquitin. J Am Chem Soc (2005) 1.66

Structural basis for ubiquitin-mediated dimerization and activation of the ubiquitin protein ligase Cbl-b. Mol Cell (2007) 1.60

Structural insights into endosomal sorting complex required for transport (ESCRT-I) recognition of ubiquitinated proteins. J Biol Chem (2004) 1.57

Crystal polymorphism of protein GB1 examined by solid-state NMR spectroscopy and X-ray diffraction. J Phys Chem B (2007) 1.46

Protein structure determination from 13C spin-diffusion solid-state NMR spectroscopy. J Am Chem Soc (2008) 1.39

Synthetic, structural and biological studies of the ubiquitin system: the total chemical synthesis of ubiquitin. Biochem J (1994) 1.38

Assignment of the backbone resonances for microcrystalline ubiquitin. J Am Chem Soc (2004) 1.33

Conformational flexibility of a microcrystalline globular protein: order parameters by solid-state NMR spectroscopy. J Am Chem Soc (2006) 1.24

Microsecond timescale backbone conformational dynamics in ubiquitin studied with NMR R1rho relaxation experiments. Protein Sci (2005) 1.22

Alcohol-induced conformational changes of ubiquitin. Arch Biochem Biophys (1986) 1.11

High-resolution solid-state NMR studies on uniformly [13C,15N]-labeled ubiquitin. Chembiochem (2005) 1.11

Temperature dependence of protein backbone motion from carbonyl 13C and amide 15N NMR relaxation. J Magn Reson (2005) 1.09

Structural basis of ubiquitin recognition by the ubiquitin-associated (UBA) domain of the ubiquitin ligase EDD. J Biol Chem (2007) 0.97

Computational identification of slow conformational fluctuations in proteins. J Phys Chem B (2009) 0.96

Solid-state NMR spectroscopy of 10% 13C labeled ubiquitin: spectral simplification and stereospecific assignment of isopropyl groups. J Biomol NMR (2006) 0.91

1H-15N correlation spectroscopy of nanocrystalline proteins. J Biomol NMR (2005) 0.91

Conformational dynamics and structural plasticity play critical roles in the ubiquitin recognition of a UIM domain. J Mol Biol (2010) 0.89

Probing slow backbone dynamics in proteins using TROSY-based experiments to detect cross-correlated time-modulation of isotropic chemical shifts. J Biomol NMR (2004) 0.87

Probing molecular motion by double-quantum (13C,13C) solid-state NMR spectroscopy: application to ubiquitin. J Am Chem Soc (2010) 0.84

Articles by these authors

The RIP1/RIP3 necrosome forms a functional amyloid signaling complex required for programmed necrosis. Cell (2012) 4.29

Protein production and purification. Nat Methods (2008) 3.97

Inhibition of p38 MAP kinase by utilizing a novel allosteric binding site. Nat Struct Biol (2002) 3.92

Polyadenylation factor CPSF-73 is the pre-mRNA 3'-end-processing endonuclease. Nature (2006) 2.95

UNC119 is required for G protein trafficking in sensory neurons. Nat Neurosci (2011) 2.38

Structural basis of the alpha1-beta subunit interaction of voltage-gated Ca2+ channels. Nature (2004) 2.38

Molecular basis for the inhibition of human NMPRTase, a novel target for anticancer agents. Nat Struct Mol Biol (2006) 2.21

Crystal structure of human DJ-1, a protein associated with early onset Parkinson's disease. J Biol Chem (2003) 2.15

Crystal structure of the heterotrimer core of Saccharomyces cerevisiae AMPK homologue SNF1. Nature (2007) 1.94

Structural and molecular basis of the assembly of the TRPP2/PKD1 complex. Proc Natl Acad Sci U S A (2009) 1.84

Structure and function of the 5'-->3' exoribonuclease Rat1 and its activating partner Rai1. Nature (2009) 1.83

Structural and biochemical studies identify tobacco SABP2 as a methyl salicylate esterase and implicate it in plant innate immunity. Proc Natl Acad Sci U S A (2005) 1.73

Crystal structure of the carboxyltransferase domain of acetyl-coenzyme A carboxylase. Science (2003) 1.63

Identification of a quality-control mechanism for mRNA 5'-end capping. Nature (2010) 1.58

Crystal structure of the human symplekin-Ssu72-CTD phosphopeptide complex. Nature (2010) 1.58

Pyrazole urea-based inhibitors of p38 MAP kinase: from lead compound to clinical candidate. J Med Chem (2002) 1.56

Bacterial neuraminidase facilitates mucosal infection by participating in biofilm production. J Clin Invest (2006) 1.54

Targeting the human cancer pathway protein interaction network by structural genomics. Mol Cell Proteomics (2008) 1.54

Optimal alignment for enzymatic proton transfer: structure of the Michaelis complex of triosephosphate isomerase at 1.2-A resolution. Proc Natl Acad Sci U S A (2002) 1.53

Crystal structure of 1-deoxy-D-xylulose 5-phosphate synthase, a crucial enzyme for isoprenoids biosynthesis. J Biol Chem (2006) 1.53

Crystal structures of human and Staphylococcus aureus pyruvate carboxylase and molecular insights into the carboxyltransfer reaction. Nat Struct Mol Biol (2008) 1.51

Crystal structure of the Toll/interleukin-1 receptor domain of human IL-1RAPL. J Biol Chem (2004) 1.50

Molecular insights into substrate recognition and catalysis by tryptophan 2,3-dioxygenase. Proc Natl Acad Sci U S A (2006) 1.50

Quantum chemical 13C(alpha) chemical shift calculations for protein NMR structure determination, refinement, and validation. Proc Natl Acad Sci U S A (2008) 1.50

An extensively associated dimer in the structure of the C713S mutant of the TIR domain of human TLR2. Biochem Biophys Res Commun (2002) 1.45

Crystal structure of yeast acetyl-coenzyme A synthetase in complex with AMP. Biochemistry (2004) 1.44

Molecular basis for the inhibition of the carboxyltransferase domain of acetyl-coenzyme-A carboxylase by haloxyfop and diclofop. Proc Natl Acad Sci U S A (2004) 1.41

Conserved surface features form the double-stranded RNA binding site of non-structural protein 1 (NS1) from influenza A and B viruses. J Biol Chem (2007) 1.40

Crystal structure of murine CstF-77: dimeric association and implications for polyadenylation of mRNA precursors. Mol Cell (2007) 1.38

Active site loop motion in triosephosphate isomerase: T-jump relaxation spectroscopy of thermal activation. Biochemistry (2003) 1.38

Structure and function of malic enzymes, a new class of oxidative decarboxylases. Biochemistry (2003) 1.37

Computational modeling of the catalytic reaction in triosephosphate isomerase. J Mol Biol (2004) 1.36

Crystal structure of carnitine acetyltransferase and implications for the catalytic mechanism and fatty acid transport. Cell (2003) 1.32

A mechanism for the potent inhibition of eukaryotic acetyl-coenzyme A carboxylase by soraphen A, a macrocyclic polyketide natural product. Mol Cell (2004) 1.32

Crystal structure of the carboxyltransferase domain of acetyl-coenzyme A carboxylase in complex with CP-640186. Structure (2004) 1.30

Crystal structures of the BAR-PH and PTB domains of human APPL1. Structure (2007) 1.30

A serendipitous discovery that in situ proteolysis is essential for the crystallization of yeast CPSF-100 (Ydh1p). Acta Crystallogr Sect F Struct Biol Cryst Commun (2006) 1.27

A symmetrical tetramer for S. aureus pyruvate carboxylase in complex with coenzyme A. Structure (2009) 1.26

A mammalian pre-mRNA 5' end capping quality control mechanism and an unexpected link of capping to pre-mRNA processing. Mol Cell (2013) 1.25

Crystal structure of human Taspase1, a crucial protease regulating the function of MLL. Structure (2005) 1.24

Huntingtin-associated protein-1 is a modifier of the age-at-onset of Huntington's disease. Hum Mol Genet (2008) 1.23

Structural and biochemical studies of the 5'→3' exoribonuclease Xrn1. Nat Struct Mol Biol (2011) 1.22

Novel homozygous p.E64D mutation in DJ1 in early onset Parkinson disease (PARK7). Hum Mutat (2004) 1.22

Magic angle spinning solid-state NMR spectroscopy for structural studies of protein interfaces. resonance assignments of differentially enriched Escherichia coli thioredoxin reassembled by fragment complementation. J Am Chem Soc (2004) 1.21

Nicotinamide adenine dinucleotide metabolism as an attractive target for drug discovery. Expert Opin Ther Targets (2007) 1.19

Crystal structure of the alpha(6)beta(6) holoenzyme of propionyl-coenzyme A carboxylase. Nature (2010) 1.18

Crystal structure of the BEACH domain reveals an unusual fold and extensive association with a novel PH domain. EMBO J (2002) 1.17

Crystal structure of biotin carboxylase in complex with substrates and implications for its catalytic mechanism. J Biol Chem (2009) 1.15

The use of in situ proteolysis in the crystallization of murine CstF-77. Acta Crystallogr Sect F Struct Biol Cryst Commun (2007) 1.13

Functional assignment based on structural analysis: crystal structure of the yggJ protein (HI0303) of Haemophilus influenzae reveals an RNA methyltransferase with a deep trefoil knot. Proteins (2003) 1.12

Crystal structure of the protein kinase domain of yeast AMP-activated protein kinase Snf1. Biochem Biophys Res Commun (2005) 1.12

Structure and function of the phenazine biosynthetic protein PhzF from Pseudomonas fluorescens. Proc Natl Acad Sci U S A (2004) 1.11

Structure and function of carnitine acyltransferases. Ann N Y Acad Sci (2004) 1.11

Is dimerization required for the catalytic activity of bacterial biotin carboxylase? Mol Cell (2006) 1.11

Aspartate dehydrogenase, a novel enzyme identified from structural and functional studies of TM1643. J Biol Chem (2002) 1.09

Dxo1 is a new type of eukaryotic enzyme with both decapping and 5'-3' exoribonuclease activity. Nat Struct Mol Biol (2012) 1.08

Computational design of catalytic dyads and oxyanion holes for ester hydrolysis. J Am Chem Soc (2012) 1.08

The New York Consortium on Membrane Protein Structure (NYCOMPS): a high-throughput platform for structural genomics of integral membrane proteins. J Struct Funct Genomics (2010) 1.07

Structure of histone mRNA stem-loop, human stem-loop binding protein, and 3'hExo ternary complex. Science (2013) 1.07

Mitochondrial poly(A) polymerase and polyadenylation. Biochim Biophys Acta (2011) 1.03

Structural studies of the pigeon cytosolic NADP(+)-dependent malic enzyme. Protein Sci (2002) 1.02

Functional insights from structural genomics. J Struct Funct Genomics (2007) 1.02

Molecular mechanism for the regulation of human mitochondrial NAD(P)+-dependent malic enzyme by ATP and fumarate. Structure (2002) 1.01

Enzymatic basis for N-glycan sialylation: structure of rat α2,6-sialyltransferase (ST6GAL1) reveals conserved and unique features for glycan sialylation. J Biol Chem (2013) 1.01

Structural evidence for direct interactions between the BRCT domains of human BRCA1 and a phospho-peptide from human ACC1. Biochemistry (2008) 0.99

Molecular mechanism of the assembly of an acid-sensing receptor ion channel complex. Nat Commun (2012) 0.98

Crystal structures of substrate complexes of malic enzyme and insights into the catalytic mechanism. Structure (2003) 0.98

Structural basis for dimerization and activity of human PAPD1, a noncanonical poly(A) polymerase. Mol Cell (2011) 0.98

Computational design of a protein-based enzyme inhibitor. J Mol Biol (2013) 0.98

Ionic states of substrates and transition state analogues at the catalytic sites of N-ribosyltransferases. Biochemistry (2003) 0.97

A different mechanism for the inhibition of the carboxyltransferase domain of acetyl-coenzyme A carboxylase by tepraloxydim. Proc Natl Acad Sci U S A (2009) 0.96

The yeast regulator of transcription protein Rtr1 lacks an active site and phosphatase activity. Nat Commun (2012) 0.96

Crystal structure of urea carboxylase provides insights into the carboxyltransfer reaction. J Biol Chem (2012) 0.96

Delineating the structural blueprint of the pre-mRNA 3'-end processing machinery. Mol Cell Biol (2014) 0.96

Structural conservation of the myoviridae phage tail sheath protein fold. Structure (2011) 0.94

Structure of the Bateman2 domain of yeast Snf4: dimeric association and relevance for AMP binding. Structure (2007) 0.94

Age at onset in Huntington's disease is modified by the autophagy pathway: implication of the V471A polymorphism in Atg7. Hum Genet (2010) 0.94

Structural and functional evidence for Bacillus subtilis PaiA as a novel N1-spermidine/spermine acetyltransferase. J Biol Chem (2005) 0.94

An unanticipated architecture of the 750-kDa α6β6 holoenzyme of 3-methylcrotonyl-CoA carboxylase. Nature (2011) 0.94

Cryo-EM analysis reveals new insights into the mechanism of action of pyruvate carboxylase. Structure (2010) 0.94

Use of a synthetic salicylic acid analog to investigate the roles of methyl salicylate and its esterases in plant disease resistance. J Biol Chem (2009) 0.93

Computational design of an unnatural amino acid dependent metalloprotein with atomic level accuracy. J Am Chem Soc (2013) 0.93

Histidine 55 of tryptophan 2,3-dioxygenase is not an active site base but regulates catalysis by controlling substrate binding. Biochemistry (2008) 0.93

Crystal structures of respiratory pathogen neuraminidases. Biochem Biophys Res Commun (2009) 0.92

Distinct domains in ORF52 tegument protein mediate essential functions in murine gammaherpesvirus 68 virion tegumentation and secondary envelopment. J Virol (2011) 0.92

Crystal structure of the PH-BEACH domains of human LRBA/BGL. Biochemistry (2004) 0.92

Structural genomics reveals EVE as a new ASCH/PUA-related domain. Proteins (2009) 0.92

Molecular insights into the biosynthesis of the F420 coenzyme. J Biol Chem (2008) 0.91

Dual functional roles of ATP in the human mitochondrial malic enzyme. Biochemistry (2004) 0.90

An unexpected binding mode for a Pol II CTD peptide phosphorylated at Ser7 in the active site of the CTD phosphatase Ssu72. Genes Dev (2012) 0.90

Mechanism for the inhibition of the carboxyltransferase domain of acetyl-coenzyme A carboxylase by pinoxaden. Proc Natl Acad Sci U S A (2010) 0.90

Target highlights in CASP9: Experimental target structures for the critical assessment of techniques for protein structure prediction. Proteins (2011) 0.89

Real-time fluorescence detection of exoribonucleases. RNA (2009) 0.89

Spherical assemblies from π-conjugated alternating copolymers: toward optoelectronic colloidal crystals. J Am Chem Soc (2013) 0.88

Methyl esterase 1 (StMES1) is required for systemic acquired resistance in potato. Mol Plant Microbe Interact (2010) 0.88

A large conformational change in the putative ATP pyrophosphatase PF0828 induced by ATP binding. Acta Crystallogr Sect F Struct Biol Cryst Commun (2011) 0.87

Structural and functional studies of the abundant tegument protein ORF52 from murine gammaherpesvirus 68. J Biol Chem (2007) 0.87

Structural and biochemical studies of the substrate selectivity of carnitine acetyltransferase. J Biol Chem (2004) 0.86