3CPM
plant peptide deformylase PDF1B crystal structure
Summary for 3CPM
| Entry DOI | 10.2210/pdb3cpm/pdb |
| Descriptor | Peptide deformylase, chloroplast, SULFATE ION, ZINC ION, ... (4 entities in total) |
| Functional Keywords | alpha beta, chloroplast, hydrolase, iron, metal-binding, protein biosynthesis, transit peptide |
| Biological source | Arabidopsis thaliana (Mouse-ear cress) |
| Cellular location | Plastid, chloroplast stroma: Q9FUZ2 |
| Total number of polymer chains | 1 |
| Total formula weight | 22275.71 |
| Authors | Rodgers, D.W.,Houtz, R.L.,Dirk, L.M.A.,Schmidt, J.J.,Cai, Y. (deposition date: 2008-03-31, release date: 2008-07-22, Last modification date: 2024-02-21) |
| Primary citation | Dirk, L.M.,Schmidt, J.J.,Cai, Y.,Barnes, J.C.,Hanger, K.M.,Nayak, N.R.,Williams, M.A.,Grossman, R.B.,Houtz, R.L.,Rodgers, D.W. Insights into the substrate specificity of plant peptide deformylase, an essential enzyme with potential for the development of novel biotechnology applications in agriculture Biochem.J., 413:417-427, 2008 Cited by PubMed Abstract: The crystal structure of AtPDF1B [Arabidopsis thaliana PDF (peptide deformylase) 1B; EC 3.5.1.88], a plant specific deformylase, has been determined at a resolution of 2.4 A (1 A=0.1 nm). The overall fold of AtPDF1B is similar to other peptide deformylases that have been reported. Evidence from the crystal structure and gel filtration chromatography indicates that AtPDF1B exists as a symmetric dimer. PDF1B is essential in plants and has a preferred substrate specificity towards the PS II (photosystem II) D1 polypeptide. Comparative analysis of AtPDF1B, AtPDF1A, and the type 1B deformylase from Escherichia coli, identifies a number of differences in substrate binding subsites that might account for variations in sequence preference. A model of the N-terminal five amino acids from the D1 polypeptide bound in the active site of AtPDF1B suggests an influence of Tyr(178) as a structural determinant for polypeptide substrate specificity through hydrogen bonding with Thr(2) in the D1 sequence. Kinetic analyses using a polypeptide mimic of the D1 N-terminus was performed on AtPDF1B mutated at Tyr(178) to alanine, phenylalanine or arginine (equivalent residue in AtPDF1A). The results suggest that, whereas Tyr(178) can influence catalytic activity, other residues contribute to the overall preference for the D1 polypeptide. PubMed: 18412546DOI: 10.1042/BJ20071641 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.4 Å) |
Structure validation
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