4UOX

Crystal structure of YgjG in complex with Pyridoxal-5'-phosphate and putrescine

Summary for 4UOX

• Entry DOI: 10.2210/pdb4uox/pdb
• Related: 4UOY
• Descriptor: PUTRESCINE AMINOTRANSFERASE, PYRIDOXAL-5'-PHOSPHATE, 1,4-DIAMINOBUTANE, ... (7 entities in total)
• Functional Keywords: transferase, polyamine
• Biological source: ESCHERICHIA COLI
• Total number of polymer chains: 4
• Total formula weight: 205052.87

Authors

Jeong, J.H.,Kim, Y.G. (deposition date: 2014-06-11, release date: 2014-12-10, Last modification date: 2024-01-10)

Primary citation

Cha, H.J.,Jeong, J.,Rojviriya, C.,Kim, Y.
Structure of Putrescine Aminotransferase from Escherichia Coli Provides Insights Into the Substrate Specificity Among Class III Aminotransferases.
Plos One, 9:13212-, 2014

PubMed Abstract: YgjG is a putrescine aminotransferase enzyme that transfers amino groups from compounds with terminal primary amines to compounds with an aldehyde group using pyridoxal-5'-phosphate (PLP) as a cofactor. Previous biochemical data show that the enzyme prefers primary diamines, such as putrescine, over ornithine as a substrate. To better understand the enzyme's substrate specificity, crystal structures of YgjG from Escherichia coli were determined at 2.3 and 2.1 Å resolutions for the free and putrescine-bound enzymes, respectively. Sequence and structural analyses revealed that YgjG forms a dimer that adopts a class III PLP-dependent aminotransferase fold. A structural comparison between YgjG and other class III aminotransferases revealed that their structures are similar. However, YgjG has an additional N-terminal helical structure that partially contributes to a dimeric interaction with the other subunit via a helix-helix interaction. Interestingly, the YgjG substrate-binding site entrance size and charge distribution are smaller and more hydrophobic than other class III aminotransferases, which suggest that YgjG has a unique substrate binding site that could accommodate primary aliphatic diamine substrates, including putrescine. The YgjG crystal structures provide structural clues to putrescine aminotransferase substrate specificity and binding.

PubMed: 25423189
DOI: 10.1371/JOURNAL.PONE.0113212

Experimental method

X-RAY DIFFRACTION (2.085 Å)