1IZ6

Crystal Structure of Translation Initiation Factor 5A from Pyrococcus Horikoshii

Summary for 1IZ6

• Entry DOI: 10.2210/pdb1iz6/pdb
• Descriptor: Initiation Factor 5A (2 entities in total)
• Functional Keywords: sh3-like barrel, ob fold, biosynthetic protein
• Biological source: Pyrococcus horikoshii
• Cellular location: Cytoplasm: O50089
• Total number of polymer chains: 3
• Total formula weight: 45916.91

Authors

Yao, M.,Ohsawa, A.,Kikukawa, S.,Tanaka, I.,Kimura, M. (deposition date: 2002-09-25, release date: 2003-01-28, Last modification date: 2023-10-25)

Primary citation

Yao, M.,Ohsawa, A.,Kikukawa, S.,Tanaka, I.,Kimura, M.
Crystal Structure of Hyperthermophilic Archaeal Initiation Factor 5A: A Homologue of Eukaryotic Initiation Factor 5A (eIF-5A)
J.BIOCHEM.(TOKYO), 133:75-81, 2003

PubMed Abstract: Eukaryotic initiation factor 5A (eIF-5A) is ubiquitous in eukaryotes and archaebacteria and is essential for cell proliferation and survival. The crystal structure of the eIF-5A homologue (PhoIF-5A) from a hyperthermophilic archaebacterium Pyrococcus horikoshii OT3 was determined at 2.0 A resolution by the molecular replacement method. PhoIF-5A is predominantly composed of beta-strands comprising two distinct folding domains, an N-domain (residues 1-69) and a C-domain (residues 72-138), connected by a short linker peptide (residues 70-71). The N-domain has an SH3-like barrel, while the C-domain folds in an (oligonucleotide/oligosaccharide binding) OB fold. Comparison of the structure of PhoIF-5A with those of archaeal homologues from Methanococcus jannaschii and Pyrobaculum aerophilum showed that the N-domains could be superimposed with root mean square deviation (rmsd) values of 0.679 and 0.624 A, while the C-domains gave higher values of 1.824 and 1.329 A, respectively. Several lines of evidence suggest that eIF-5A functions as a biomodular protein capable of interacting with protein and nucleic acid. The surface representation of electrostatic potential shows that PhoIF-5A has a concave surface with positively charged residues between the N- and C-domains. In addition, a flexible long hairpin loop, L1 (residues 33-41), with a hypusine modification site is positively charged, protruding from the N-domain. In contrast, the opposite side of the concave surface at the C-domain is mostly negatively charged. These findings led to the speculation that the concave surface and loop L1 at the N-domain may be involved in RNA binding, while the opposite side of the concave surface in the C-domain may be involved in protein interaction.

PubMed: 12761201
DOI: 10.1093/jb/mvg011

Experimental method

X-RAY DIFFRACTION (2 Å)