1R4V

1.9A crystal structure of protein AQ328 from Aquifex aeolicus

Summary for 1R4V

• Entry DOI: 10.2210/pdb1r4v/pdb
• Descriptor: Hypothetical protein AQ_328, ZINC ION, CACODYLATE ION, ... (4 entities in total)
• Functional Keywords: structural genomics, all-alpha, histon fold, psi, protein structure initiative, midwest center for structural genomics, mcsg, unknown function
• Biological source: Aquifex aeolicus
• Total number of polymer chains: 1
• Total formula weight: 20484.22

Authors

Qiu, Y.,Tereshko, V.,Kim, Y.,Zhang, R.,Collart, F.,Joachimiak, A.,Kossiakoff, A.,Midwest Center for Structural Genomics (MCSG) (deposition date: 2003-10-08, release date: 2004-03-30, Last modification date: 2024-10-30)

Primary citation

Qiu, Y.,Tereshko, V.,Kim, Y.,Zhang, R.,Collart, F.,Yousef, M.,Kossiakoff, A.,Joachimiak, A.
The crystal structure of Aq_328 from the hyperthermophilic bacteria Aquifex aeolicus shows an ancestral histone fold.
Proteins, 62:8-16, 2006

PubMed Abstract: The structure of Aq_328, an uncharacterized protein from hyperthermophilic bacteria Aquifex aeolicus, has been determined to 1.9 A by using multi-wavelength anomalous diffraction (MAD) phasing. Although the amino acid sequence analysis shows that Aq_328 has no significant similarity to proteins with a known structure and function, the structure comparison by using the Dali server reveals that it: (1) assumes a histone-like fold, and (2) is similar to an ancestral nuclear histone protein (PDB code 1F1E) with z-score 8.1 and RMSD 3.6 A over 124 residues. A sedimentation equilibrium experiment indicates that Aq_328 is a monomer in solution, with an average sedimentation coefficient of 2.4 and an apparent molecular weight of about 20 kDa. The overall architecture of Aq_328 consists of two noncanonical histone domains in tandem repeat within a single chain, and is similar to eukaryotic heterodimer (H2A/H2B and H3/H4) and an archaeal histone heterodimer (HMfA/HMfB). The sequence comparisons between the two histone domains of Aq_328 and six eukaryotic/archaeal histones demonstrate that most of the conserved residues that underlie the Aq_328 architecture are used to build and stabilize the two cross-shaped antiparallel histone domains. The high percentage of salt bridges in the structure could be a factor in the protein's thermostability. The structural similarities to other histone-like proteins, molecular properties, and potential function of Aq_328 are discussed in this paper.

PubMed: 16287087
DOI: 10.1002/prot.20590

Experimental method

X-RAY DIFFRACTION (1.9 Å)