Primary Citation PubMed: 18387634
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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
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 simultan... ously with this side chain carbonyl group and the α-amino group of Pyl or a Pyl analogue (PDB IDs: 2ZCE , 2ZIN , 2Q7G ).
(b) Structure of the active site of M. mazei PylRS (PDB ID: 2ZCE ).
Consequently, the active site volume decreases from 2883 to 2174 Å 3 when comparing PylRS (PDB ID: 2ZCE ) to MmOmeRS, respectively.
Additionally, the second oxygen atom of the α-carboxyl group of Ome is further solvated by a water molecule that is unusually within hydrogen-bonding distance (2.9 Å) to the thioether sulfur atom of Met344; in contrast, for Pyl-bound PylRS (PDB ID: 2ZCE ), this distance extends to 3.6 Å, which is more consistent with a van der Waals interaction rather than a more stabilizing hydrogen-bonding interaction.
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 ).
(b) Direct coordination of an oxygen atom from the carboxyl group of Pyl to the α-phosphate of AMP-PNP in the crystal structure of PylRS complexed with Pyl and AMP-PNP (PDB ID: 2ZCE ).
Structural alignment of the MmOmeRS structure reported here with the previously reported PylRS structure complexed with AMP-PNP and Pyl (PDB ID: 2ZCE )( 27 ) illustrates conserved AMP-PNP binding with the sterically and chemically divergent amino acid Ome occupying a similar active site location as the wild-type cognate amino acid Pyl.
(b) Interactions between main chain atoms of Pyl and surrounding protein residues in the crystal structure of PylRS complexed with Pyl, Mg 2+ , and AMP-PNP (PDB ID: 2ZCE ).
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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