Model: PDBEurope/BiomedNLP-PubMedBERT-ProteinStructure-NER-v1.4
Author: PDBEurope
Pipeline: token-classification
Library: transformers
Tags: transformers, pytorch, safetensors, bert, token-classification, biology, protein structure, token classification, en, license:mit, model-index, endpoints_compatible, region:us
Card metadata: license: mit
language: en
tags: biology, protein structure, token classification
widget: N-terminal acetylation (Nt-acetylation), carried out by N-terminal acetyltransferases (NATs), is a conserved and primary modification of nascent peptide chains. Naa60 (also named NatF) is a recently identified NAT found only in multicellular eukaryotes. This protein was shown to locate on the Golgi apparatus and mainly catalyze the Nt-acetylation of transmembrane proteins, and it also harbors lysine Nε-acetyltransferase (KAT) activity to catalyze the acetylation of lysine ε-amine. Here, we report the crystal structures of human Naa60 (hNaa60) in complex with Acetyl-Coenzyme A (Ac-CoA) or Coenzyme A (CoA). The hNaa60 protein contains an amphipathic helix following its GNAT domain that may contribute to Golgi localization of hNaa60, and the β7-β8 hairpin adopted different conformations in the hNaa60(1-242) and hNaa60(1-199) crystal structures. Remarkably, we found that the side-chain of Phe 34 can influence the position of the coenzyme, indicating a new regulatory mechanism involving enzyme, co-factor and substrates interactions. Moreover, structural comparison and biochemical studies indicated that Tyr 97 and His 138 are key residues for catalytic reaction and that a non-conserved β3-β4 long loop participates in the regulation of hNaa60 activity.
model-index: name: BiomedNLP-PubMedBERT-ProteinStructure-NER-v1.4
results: task: name: NER
type: token-classification
metrics: name: NER Precision
type: precision
value: 0.9
verified: no, name: NER Recall
type: recall
value: 0.92
verified: no, name: NER F Score
type: f_score
value: 0.91
verified: no
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Created: 2023-10-24 13:17:07