Primary Citation PubMed: 10216293
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Structures of the first representatives of Pfam family PF06938 (DUF1285) reveal a new fold with repeated structural motifs and possible involvement in signal transduction.
(2010) Acta Crystallogr Sect F Struct Biol Cryst Commun 66
PubMed: 20944214 | PubMedCentral: PMC2954208 | DOI: 10.1107/S1744309109050416
A search against a database of cognate binding sites using IsoCleft (Najmanovich et al. , 2008 ▶ ), a graph-matching algorithm that searches for similarities in both geometry and chemical comp... sition, identified shared features between the inter-domain cleft of SPO0140 and sugar, phosphate and purine-binding proteins [PDB codes 1pwh (Yamada et al. , 2003 ▶ ), 1dqa (Istvan et al. , 2000 ▶ ), 1dm3 (Modis & Wierenga, 2000 ▶ ), 1gpe (Wohlfahrt et al. , 1999 ▶ ), 1v0j (Beis et al. , 2005 ▶ ), 1hwy (Smith et al. , 2001 ▶ ), 2vfs (Forneris et al. , 2008 ▶ ) and 1q6p (Scapin et al. , 2003 ▶ )].
Publication Year: 2010
Construction of mutant glucose oxidases with increased dye-mediated dehydrogenase activity.
(2012) Int J Mol Sci 13
PubMed: 23203056 | PubMedCentral: PMC3509572 | DOI: 10.3390/ijms131114149
Oxygen-Interacting Structural Models for GOxs The currently available GOx crystal structures do not contain oxygen molecule; hence, we constructed oxygen-interacting structural models for GOxs based o... the superimposition of ChOx (1MXT) with 2 representative GOxs—1gpe and 1cf3.
We focused on two representative GOxs, of which crystal structures have already been reported— Penicillium amagasakiense GOx (PDB ID; 1gpe) and Aspergillus niger GOx (PDB ID; 1cf3).
We focused on two representative GOxs, of which crystal structures have been reported— P. amagasakiense -derived GOx (PDB ID; 1gpe) and A. niger -derived GOx (PDB ID; 1cf3).
Figures 1A shows an oxygen molecule in crystal structure of ChOx (PDB ID; 1mxt) [ 11 ] and Figure 1B,C show the oxygen molecule superimposed on 1gpe and 1cf3, respectively.
Publication Year: 2012
The 1.6 Å crystal structure of pyranose dehydrogenase from Agaricus meleagris rationalizes substrate specificity and reveals a flavin intermediate.
(2013) PLoS One 8
PubMed: 23326459 | PubMedCentral: PMC3541233 | DOI: 10.1371/journal.pone.0053567
Automated search model generation in BALBES tested five template models: 2JBV, 1CF3, 1GPE, 1JU2, 1KDG; with sequence identities to PDH of 26.1, 27.0, 25.3, 25.3, and 21.5%, respectively.
Publication Year: 2013
Catalytic mechanism of short ethoxy chain nonylphenol dehydrogenase belonging to a polyethylene glycol dehydrogenase group in the GMC oxidoreductase family.
(2013) Int J Mol Sci 14
PubMed: 23306149 | PubMedCentral: PMC3565318 | DOI: 10.3390/ijms14011218
We chose 1cf3 as the structure template because it yielded fewer gaps than when 1gpe was used as the template.
3D Structure Modeling There are two structurally defined homologues of NPEO-DH, OPEO-DH and PEGDH: GOX (EC 22.214.171.124) from A. niger (Protein Data Base (PDB) code: 1cf3, 25% identity with NPEO-DH) and GOX (EC 126.96.36.199) from P. amagasakiense (PDB code: 1gpe, 26% identity with NPEO-DH) [ 3 ].
IsoCleft Finder - a web-based tool for the detection and analysis of protein binding-site geometric and chemical similarities.
(2013) F1000Res 2
PubMed: 24555058 | PubMedCentral: PMC3892921 | DOI: 10.12688/f1000research.2-117.v2
The IsoCleft Finder analysis of 2re3 ( Table 2 ) identified shared features between the inter-domain cleft of 2re3 and sugar, phosphate and purine-binding proteins (PDB codes 1pwh, 1dqa, 1dm3, 1gpe, 1... 0j, 1hwy, 2vfs and 1q6p) 30 .
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