Primary Citation PubMed: 7703247
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Prediction of catalytic residues using Support Vector Machine with selected protein sequence and structural properties.
(2006) BMC Bioinformatics 7
PubMed: 16790052 | PubMedCentral: PMC1534064 | DOI: 10.1186/1471-2105-7-312
The 79 proteins (identified by the PDB code) were: 1a26, 1a4i, 1a4s, 1ab8, 1ae7, 1afw, 1ah7, 1akm, 1aop, 1apx, 1apy, 1aq2, 1aw8, lb3r, lb57, lb93, 1bo1, 1brm, 1bs4, 1btl, 1bzy, 1cd5, 1chd, 1ctt, 1d4a,... 1daa, 1dae, 1db3, 1dbt, 1dco, 1diz, 1dj0, 1dnk, 1dnp, 1dqs, 1dzr, 1e2a, 1ef8, 1eyi, 1fua, 1gim, 1gpm, 1gpr, 1grc, 1hxq, 1iph, 1jdw, 1kas, 1kra, 1lba, 11xa, 1mbb, 1mek, 1mla, 1moq, 1mpy, 1nba, 1nsp, 1pfk, 1pjb, 1pnl, 1pud, 1qfe, 1smn, 1uae, 1ula, 1uok, 1uox, 1wgi, 1xva, 2acy, 2alr, 2bbk, 2cpo, 2hgs, 2jcw, 2pfl, 2plc, 3eca.
Publication Year: 2006
Molecular modeling of peroxidase and polyphenol oxidase: substrate specificity and active site comparison.
(2010) Int J Mol Sci 11
PubMed: 20957092 | PubMedCentral: PMC2956093 | DOI: 10.3390/ijms11093266
In our computational study, the amino acid sequence of grape peroxidase (ABX) was used for the construction of models employing homology modeling method based on the X-ray structure of cytosolic ascor... ate peroxidase from pea (PDB ID:1APX), whereas the model of grape polyphenol oxidase was obtained directly from the available X-ray structure (PDB ID:2P3X).
We used the crystal structure of pea cytosolic ascorbate peroxidase (PDB ID:1APX) [ 22 ] as the template to build the 3D structure of grape ascorbate peroxidase.
As a result, 1APX—with the highest sequence similarity to grape peroxidase (80% sequence identity and an E-value of 2.62E-116)—was chosen as the template.
Three-Dimensional Model of Grape Ascorbate Peroxidase and Polyphenol Oxidase By BLAST searching, five structurally determined peroxidases, including cytosolic ascorbate peroxidase of pea (1APX; 80% identity), cytosolic ascorbate peroxidase of soybean (2GHC; 79% identity), chloroplastic ascorbate peroxidase of tobacco (1IYN; 42% identity), cytochrome c peroxidase of yeast (2EUT; 34% identity) and peroxidase of Arabidopsis (1PA2; 32% identity) were found with substantial sequence similarity to that of grape peroxidase.
Publication Year: 2010
Engineered ascorbate peroxidase as a genetically encoded reporter for electron microscopy.
(2012) Nat Biotechnol 30
PubMed: 23086203 | PubMedCentral: PMC3699407 | DOI: 10.1038/nbt.2375
(B) Mutations were introduced at the dimer interface of wild-type (wt) APX (from PDB ID 1APX 18 ).
Publication Year: 2012
Dual regulation of cytosolic ascorbate peroxidase (APX) by tyrosine nitration and S-nitrosylation.
(2014) J Exp Bot 65
PubMed: 24288182 | PubMedCentral: PMC3904709 | DOI: 10.1093/jxb/ert396
Evolutionary analysis carried out at the Evolutionary Trace server ( Mihalek et al. , 2004 ) using the tertiary structure of pea APX as input (PDB code 1apx) and the entire UniProtKB database (30,342,... 20 sequences) output rho values of 57.68 and 4.95 for Tyr5 and Tyr235, respectively, and 14.17 for Cys32 calculated from 416 sequences.
(A) Structure of homodimeric pea APX (PDB ID: 1apx).
Publication Year: 2014
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