3f1z

Protein Summary

Note: This structure has been accepted for publication in ActaF. Detailed structural analysis is presented in that manuscript which is in press, as of April 2010.

Pfam update: This is a family of bacterial, archeael and viral proteins that is related to the tRNA_anti family Pfam:PF01336. The major characteristic of families like tRNA_anti is their OB-fold, and many of them bind DNA. and found, after a couple of rounds of iteration, one overlap to tRNA_anti, so went on and found more; so I have put it into the OB_-fold clan.

This protein appears to be very novel in sequence. PSI-BLAST does not return significant hits with any other sequence. It does not have any PfamA annotation yet but a search against PfamA shows weak similarity (exp=0.71) to the family tRNA_anti PF01336 which contains proteins with the OB-fold/nucleic acid binding domain.

FFAS also does not show any significant hits.

The protein sequence has a predicted signal sequence which was removed during the gene construct design. The cloned construct comprises amino acids 23-145 of the full-length protein from 1-145.

There are 10 protomers in the asymmetric unit of the crystal lattice. They form a dimer of a stacked pentameric ring:

However, crystal packing analysis using the PISA server does not indicate that this decameric structure is stable in solution and the prediction for solution state is a monomer. Size exclusion chromatography coupled with static light scattering (SEC/SLS) also indicate a monomer as the oligomeric form in solution. So it is rather interesting to see this assembly in the crystal structure.

The structure of the monomer resembles that of an OB-fold:

 A search for proteins of similar structure using SSM at EBI shows the top hits (although Q-score is < 0.5) to the Shiga toxin protein and Human RepA (a single-stranded DNA binding protein with OB-fold). The Shiga toxin can also form a pentameric ring, but the diameter of the Shiga toxin ring is much smaller than the diameter of the pentamer that is observed here (~36 Angstroms). A search of similar structures using DALI shows some similarity to the aspartyl-tRNA synthetases anticodon domain which belongs to the PFam listed above.

Further analysis of this structure will be made to understand possible structure-function relationships.

KPN_03535 is predicted lipoprotein with SPaseII-cleaved signal peptide. This part was contributed by Piotr Kozbial.

Prediction of lipoprotein signal peptides by LipoP-1.0 server [Juncker et al 2003, http://www.cbs.dtu.dk/services/LipoP-1.0/] supports twilight zone protein sequence similarity of KPN_03535 (GenBank: YP_001337197) to bacterial lipoproteins. The predicted cleavage site by LipoP-1.0 server (score: 17.664) is located before Cys-20 (SLLSG^CGLAS). The further analysis of this putative lipoprotein will answer the question if KPN_03535 belongs to known bacterial lipoproteins or has a completely new function.

Homologs.

There is only one known homolog of KPN_03535 that is annotated as predicted lipoprotein (KPK_0575, GenBank: ACI09130.1, Klebsiella pneumoniae 342). KPK_0575 is encoded next to its genomic neighbour KPK_0576 (it is also annotated as putative lipoprotein) but on the opposite strand. Detailed analysis should reveal whether KPK_0575 and KPK_0576 are expressed and what regulate their expression (to do: see if the expression of one of them is inhibiting expression of the other one). 

Ligand Summary