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PDB ID Mentions in PubMed Central Article count: 5

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PDB ID Mentions in PubMed Central

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Fold-recognition and comparative modeling of human alpha2,3-sialyltransferases reveal their sequence and structural similarities to CstII from Campylobacter jejuni.

(2006) BMC Struct Biol 6

PubMed: 16620397 | PubMedCentral: PMC1508147 | DOI: 10.1186/1472-6807-6-9

PDB id 1B37 is for polyamine oxidase, 1FC4 is for 2-amino-3-ketobutyrate CoA ligase, 1FIU is for restriction endonuclease NgoMIV from Neisseria gonorrhoeae , 1H7D is for aminolevulinic acid synthase 2... 1JF9 is for Escherichia coli selenocysteine lyase, 1K3R is for the hypothetical protein MT0001 from Methanobacterium thermoautotrophicum , 1KA1 is for PAPase Hal2p, 1R1G is for scorpion toxin BmBKTtx1 and 1RO7 is for sialyltransferase CstII from Campylobacter jejuni , 1W36 is for Recbcd DNA complex, 1W78 is for Escherichia coli FOLC.

Publication Year: 2006

Characterization of the cofactor-binding site in the SPOUT-fold methyltransferases by computational docking of S-adenosylmethionine to three crystal structures.

(2003) BMC Bioinformatics 4

PubMed: 12689347 | PubMedCentral: PMC153507 | DOI: null

Methods Preparation of the ligand and target molecules for docking Structures of Protein Data Bank (PDB) entries 1gz0, 1ipa and 1k3r were used for docking simulations of AdoMet.

The alignment of all sequences was guided by structural superposition of the SPOUT domain of 1gz0, 1ipa, and 1k3r.

structure min docking energy [kcal/mol] max docking energy [kcal/mol] rmsd for top 50 clusters [Å] 1gz0 -14.18 -12.55 1.70 1ipa -14.00 -12.65 1.82 1k3r -15.01 -13.56 0.90 Despite similar conformations, the protein-ligand interactions in the CbiF, SET and SPOUT superfamilies are different.

The 3'-hydroxyl hydrogen-bonds to the backbone carbonyl of a semi-conserved Thr residue in 1ipa and 1k3r (but not in 1gz0) and to the backbone carbonyl of a nearly invariant G196 in 1gz0 (G218 in 1k3r; in 1ipa, the H-bond with G215 is present in many solutions, but not in the top-scoring one).

Sequence and structure analysis Orthologs of the SPOUT MTases 1gz0, 1ipa, and 1k3r were identified and aligned using PSI-BLAST [ 26 ].

Acknowledgements We would like to thank Dr. Miroslaw Cygler for providing the 1gz0 structure and preprint of the manuscript before publication and Dr. Andrzej Joachimiak for releasing the 1k3r structure to the public (in PDB) before publication of its analysis.

The values of the estimated energy of protein-ligand interactions for the best docking solutions are summarized in Table 2 ; the ligand-binding pockets of 1gz0, 1ipa, and 1k3r are shown in Figure 4 .

We consider it significant that the three independent docking simulations identified a homologous region of the protein structure as the most likely cofactor-binding site, even in the absence of significant sequence similarity between the structures of 1ipa and 1gz0 and the structure of 1k3r.

We hypothesize that the unbound structures (1gz0, 1ipa, and 1k3r) represent a "closed", catalytically inactive conformation, and that a structural change is required to open the barrier between the two grooves and thereby allow the substrate to carry out an enzyme-assisted nucleophilic attack on the methyl group of AdoMet.

Results and Discussion Identification of the AdoMet-binding site To aid the experimental analysis of the SPOUT MTases in the absence of appropriate co-crystal structures, we decided to investigate the binding of AdoMet to the three available crystal structures (1ipa, 1gz0, and 1k3r) using the computational docking program AutoDock 3.05 [ 19 ].

Figure 4 Lowest-energy docking solutions obtained for a) 1gz0, b) 1ipa, c) 1k3r.

Publication Year: 2003

Structural and evolutionary bioinformatics of the SPOUT superfamily of methyltransferases.

(2007) BMC Bioinformatics 8

PubMed: 17338813 | PubMedCentral: PMC1829167 | DOI: 10.1186/1471-2105-8-73

It groups together functionally uncharacterized proteins from Archaea and Eukaryota, of which one (functionally uncharacterized putative MTase MT1 from Methanothermobacter thermoautotrophicus ) had a ... tructure determined by the structural genomics factory (1k3r in PDB, [ 37 ]).

Publication Year: 2007

RNomics and Modomics in the halophilic archaea Haloferax volcanii: identification of RNA modification genes.

(2008) BMC Genomics 9

PubMed: 18844986 | PubMedCentral: PMC2584109 | DOI: 10.1186/1471-2164-9-470

HVO_0180 1189 See text 2619 (2584) m 3 U Prediction, this work and [ 93 ] HVO_2565 2016 See text, 1K3R 2621 (2586) Ψ Cbf5+ sRNA See Additional file 8 Guide RNA protein machinery Cbf5 Homology ... . furiosus Cbf5* [ 183 ] HVO_2493 0103 2AUS, 2RFK, 2APO Gar1p Homology P. furiosus Gar1p* [ 183 ] HVO_1108 3277 2HVY, 2EY4 2RFK Nop10 Homology P. furiosus Nop10* [ 183 ] HVO_0698 2260 2AUS L7Ae Homology S. solfataricus L7* [ 184 ] HVO_2737 1358 1PXW, 2FC3, 1RLG, 1SDS, 2QA4 Fibrillarin Homology with S. solfataricus aFib* [ 184 ] HVO_1669 1889 1NT2, 1PRY 1G8S, 1FBN, 1G8A Nop56/58 Homology S. solfataricus Nop56/58* [ 184 ] HVO_1670 1498 1NT2 a RefSeq annotation in; b if the structure of an Archaeal member of the family is available the PDB code is given ; *Experimentally verified; c H. volcanii numbering corresponding E. coli numbering given in brackets; d H. marismortui positions corresponding E. coli position in brackets Remarkably, Halobacteria show more degenerated C, C', D and D' boxes and a longer region between D' and C' boxes (19 to 21 pb) than other orders (4 to 10 pb).

Publication Year: 2008

The protein composition of mitotic chromosomes determined using multiclassifier combinatorial proteomics.

(2010) Cell 142

PubMed: 20813266 | PubMedCentral: PMC2982257 | DOI: 10.1016/j.cell.2010.07.047

Sequence names (and UniProt accession codes in parentheses) for the analysis of CENP-32 are as follows: hCENP32 (Q5T280) Homo sapiens ; Fly (Q8MSZ6) Drosophila melanogaster ; Worm (Q10950) Caenorhabdi... is elegans ; Plant (Q6NLH7) Arabidopsis thaliana ; YGR283C (P53336) Saccharomyces cerevisiae ; YMR310C (Q04867) S. cerevisiae ; S_pombe (O13641) Schizosaccharomyces pombe ; 1K3R (O26109) Methanobacterium thermoautotrophicum protein of known structure.

Publication Year: 2010