Primary Citation PubMed: 19022179
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Stereochemical basis for engineered pyrrolysyl-tRNA synthetase and the efficient in vivo incorporation of structurally divergent non-native amino acids.
(2011) ACS Chem Biol 6
PubMed: 21545173 | PubMedCentral: PMC3137230 | DOI: 10.1021/cb200057a
(c) Interactions between main chain atoms of Boc-Lys and surrounding protein residues in the crystal structure of PylRS complexed with Boc-Lys and AMP-PNP (PDB ID: 2ZIN ).
It was previously thought that the carbonyl group of the Pyl side chain played a critical role during the aminoacylation reaction catalyzed by PylRS;( 26 ) Asn346 in wild type PylRS interacts simultaneously with this side chain carbonyl group and the α-amino group of Pyl or a Pyl analogue (PDB IDs: 2ZCE , 2ZIN , 2Q7G ).
The α-amino-carboxyl group flip was also seen in the previously reported crystal structure of PylRS complexed with AMP-PNP and Boc-Lys (PDB ID: 2ZIN ).
The orientation of the main chain atoms in Ome is not uncommon among structures of PylRS complexed with various analogues; for example, Boc-Lys also has its α-amino group close to the α-phosphate of AMP-PNP (PDB ID: 2ZIN , Figure 6 c).
The overall tertiary structure of MmOmeRS (Figure 4 a) is consistent with all previously reported crystal structures for PylRSs, generating root-mean-square deviation (rmsd) values ranging from 0.16 to 0.23 Å upon superposition of C-α atoms with representative family members (PDB IDs 2ZCE , 2ZIN , and 2Q7G ).
(c) Hydrogen-bonding network of the amino group of Boc-Lys and an oxygen atom of the α-phosphate of AMP-PNP in the crystal structure of PylRS complexed with Boc-Lys and AMP-PNP (PDB ID: 2ZIN ).
Publication Year: 2011
Unleashing the power of meta-threading for evolution/structure-based function inference of proteins.
(2013) Front Genet 4
PubMed: 23802014 | PubMedCentral: PMC3686302 | DOI: 10.3389/fgene.2013.00118
In parentheses are the PDB IDs of weakly homologous (<40% sequence identity) templates identified by e Thread for 2zgm (1c1l, 1d2s, 1g86, 1gzw, 1hdk, 1is3, 1kel, 1kjl, 1kjr, 1lhu, 1lhw, 1ngx, ... qfm, 1qkq, 1slt, 1t2q, 1w6o, 1w6p, 2bkl, 2d03, 2d6m, 2eak, 2eal, 2nmo, 2ny1, 2r0h, 2vno, 2wkk, 2wt0, 2wt1, 2xg3, 2z3z, 2zaa, 2zab, 2zac, 2zhk, 2zhl, 2zhm, 3a71, 3a72, 3ap6, 3ap7, 3gal, 3h3l, 3htl, 3nv3, 3nv4, 3o4h, 4gal); 3mey (1b8a, 1e1t, 1e22, 1e24, 1eqr, 1evk, 1evl, 1fyf, 1kog, 1nyq, 1qf6, 1x54, 1x55, 2cim, 2cja, 2i4o, 2j3m, 2q7e, 2q7g, 2rhq, 2rhs, 2xgt, 2xti, 2zcd, 2zce, 2zin, 3a31, 3a74, 3bju, 3e9h, 3e9i, 3nem, 3qtc); 2fug (1cc1, 1e3d, 1fp4, 1frf, 1frv, 1g20, 1g21, 1h1l, 1h2a, 1h2r, 1l5h, 1l9g, 1m1n, 1m1y, 1m34, 1mio, 1n2c, 1qgu, 1qh1, 1qh8, 1ui0, 1ui1, 1vk2, 1yqw, 1yrq, 2a5h, 2afh, 2afi, 2afk, 2d3y, 2ddg, 2dp6, 2frv, 2min, 2wpn, 2xdq, 3aek, 3aet, 3k1a, 3min, 3myr, 3pdi); 1pue (1if1, 1j59, 1k79, 1lb2, 1o3s, 1run, 1t2k, 1xsd, 1yo5, 2cgp, 3e54, 3jtg); and 2ec2 (1a9n, 1hr6, 1y13, 2a6m, 2a6o, 2ar9, 2vic, 2vih, 2vju, 3a4i, 3a74, 3bju, 3lmb).
Publication Year: 2013
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