Primary Citation PubMed: 14684898
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Structural analysis of FAD synthetase from Corynebacterium ammoniagenes.
(2008) BMC Microbiol 8
PubMed: 18811972 | PubMedCentral: PMC2573891 | DOI: 10.1186/1471-2180-8-160
PDB SUBSTRATES (%) IDENTITIES (%) CONSERVATIVE SUBSTITUTIONS REFERENCE FAD synthetases T. maritima 1mrz 29.3 40.2 [ 14 ] N-terminal a 30.6 39.2 C-terminal b 27.6 41.5 T. maritima complexed 1s4m RF 29.... 40.2 [ 15 ] 1t6x ADP 1t6y FMN, ADP, AMP Nucleotydyltransferases a GCT B. subtilis 1coz CTP 12.4 23.1 [ 30 ] NMNAT M. jannaschii 1f9a Mg 2+ , ATP 12.9 22.0 [ 32 ] NMNAT H. sapiens 1kku 10.8 18.3 [ 31 ] NMNAT M. thermoautotropicum 1ej2 NAD + , Na + 13.0 22.6 [ 33 ] PPAT E. coli 1b6t dPCoA 13.0 26.3 [ 34 ] 1gn8 ATP, Mn 2+ [ 37 ] PPAT T. thermophilus 1od6 Ppant 11.3 22.0 [ 35 ] Riboflavinkinases b H. sapiens 1p4m ADP, Mg 2+ , FMN 25.7 41.4 [ 21 ] 1q9s ADP, Mg 2+ , FMN [ 22 ] 1nb0 ADP, Mg 2+ [ 21 ] S. pombe 1n06 ADP [ 23 ] 1n07 FMN, ADP 23 38.2 1n08 Zn 2+ , ADP Parameters derived from the structure-based sequence alignment of the produced Ca FADS models over structural databases.
Publication Year: 2008
FLORA: a novel method to predict protein function from structure in diverse superfamilies.
(2009) PLoS Comput Biol 5
PubMed: 19714201 | PubMedCentral: PMC2721411 | DOI: 10.1371/journal.pcbi.1000485
Thermophilus pantetheine phosphate adenylyltransferase PDB: 1od6), is a relatively small protein and consists of a homo-hexamer of single HUP domain subunits.
Publication Year: 2009
Predicted class-I aminoacyl tRNA synthetase-like proteins in non-ribosomal peptide synthesis.
(2010) Biol Direct 5
PubMed: 20678224 | PubMedCentral: PMC2922099 | DOI: 10.1186/1745-6150-5-48
This search recovered catalytic domains of the class-I AAtRSs, namely tyrosyl-tRS (PDB: 2cyc ; p = 7 × 10 -6 ) and tryptophanyl-tRS (PDB: 3foc ; p = 4 × 10 -5 ) and the HIGH-motif nucl... otidyltransferase, phosphopantetheine adenylyltransferase (1od6; p = 3 × 10 -4 ) as the best hits.
Publication Year: 2010
Structures of phosphopantetheine adenylyltransferase from Burkholderia pseudomallei.
(2011) Acta Crystallogr Sect F Struct Biol Cryst Commun 67
PubMed: 21904046 | PubMedCentral: PMC3169398 | DOI: 10.1107/S1744309111004349
The first PPAT crystal structures were solved from Escherichia coli (PDB entries 1qjc , 1gn8 , 1h1t and 1b6t ; Izard, 2002 ▶ , 2003 ▶ ; Izard & Geerlof, 1999 ▶ ; Izard ... t al. , 1999 ▶ ) and were followed by a number of other PPAT crystal structures from Archaeoglobus fulgidus (PDB entry 3do8 ; R. Zhang, R. Wu, R. Jedrzejczak & A. Joachimiak, unpublished work), Bacillus subtilis (PDB entry 1o6b ; Badger et al. , 2005 ▶ ), Mycobacterium tuberculosis (PDB entry 1tfu ; Morris & Izard, 2004 ▶ ), Thermotoga maritima (PDB entry 1vlh ; Joint Center for Structural Genomics, unpublished work), Thermus thermophilus (PDB entry 1od6 ; Takahashi et al. , 2004 ▶ ), Staphylococcus aureus (PDB entry 3f3m ; Lee et al. , 2009 ▶ ) and Yersinia pestis (PDB entries 3l92 and 3l93 ; J. Osipiuk, N. Maltseva, M. Makowska-grzyska, K. Kwon, W. F. Anderson & A. Joachimiak, unpublished work).
On the whole, these structures include apo enzymes (PDB entries 3l93 , 3do8 and 1tfu ), a variety of substrate-bound states ( e.g. 4′-phosphopantetheine in PDB entries 1od6 and 1qjc and ATP in PDB entry 1gn8 ) and product states (dephospho-coenzyme A), as well as non-native states ( e.g. ADP, coenzyme A).
Sequences are shown from B. pseudomallei ( Bp PPAT; PDB entry 3pxu ; present study), E. coli (PDB entry 1b6t ; Izard & Geerlof, 1999 ▶ ), Y. pestis (PDB entry 3l93 ; Osipiuk et al. , unpublished work), T. maritima (PDB entry 1vlh ; Joint Center for Structural Genomics, unpublished work), M. tuberculosis (PDB entry 1tfu ; Morris & Izard, 2004 ▶ ), B. subtilis (PDB entry 1o6b ; Badger et al. , 2005 ▶ ) and T. thermophilus (PDB entry 1od6 ; Takahashi et al. , 2004 ▶ ).
Publication Year: 2011
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