PDBsum entry 2jvd

Structural genomics, unknown function

PDB id: 2jvd

Contents

Protein chain

48 a.a. *

* Residue conservation analysis

PDB id:

2jvd

Name:

Structural genomics, unknown function

Title:

Solution nmr structure of the folded n-terminal fragment of upf0291 protein ynzc from bacillus subtilis. Northeast structural genomics target sr384-1-46

Structure:

Upf0291 protein ynzc. Chain: a. Fragment: residues 1-46. Engineered: yes

Source:

Bacillus subtilis. Organism_taxid: 1423. Strain: 168. Gene: ynzc, bsu17880. Expressed in: escherichia coli. Expression_system_taxid: 562.

NMR struc:

20 models

Authors:

J.M.Aramini,S.Sharma,Y.J.Huang,L.Zhao,L.A.Owens,K.Stokes,M.Jiang, R.Xiao,M.C.Baran,G.V.T.Swapna,T.B.Acton,G.T.Montelione,Northeast Structural Genomics Consortium (Nesg)

Key ref:

J.M.Aramini et al. (2008). Solution NMR structure of the SOS response protein YnzC from Bacillus subtilis. Proteins, 72, 526-530. PubMed id: 18431750 DOI: 10.1002/prot.22064

Date:

18-Sep-07 Release date: 02-Oct-07

Protein chain

O31818  (YNZC_BACSU) -  UPF0291 protein YnzC from Bacillus subtilis (strain 168)

Seq: 77 a.a.

Struc: 48 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1002/prot.22064

Proteins 72:526-530 (2008)

PubMed id: 18431750

Solution NMR structure of the SOS response protein YnzC from Bacillus subtilis.

J.M.Aramini, S.Sharma, Y.J.Huang, G.V.Swapna, C.K.Ho, K.Shetty, K.Cunningham, L.C.Ma, L.Zhao, L.A.Owens, M.Jiang, R.Xiao, J.Liu, M.C.Baran, T.B.Acton, B.Rost, G.T.Montelione.

ABSTRACT

No abstract given.

Selected figure(s)

Figure 1.
Figure 1. (A) A subset from the multiple sequence alignment of the entire DUF896 (PF05979) protein domain family (Pfam release 22.0) generated using Clustal X. The alignment includes YnzC from Bacillus subtilis plus representatives from the major genera of firmicutes that possess this protein (Streptococcus, Listeria, Staphylococcus, Lactobacillus, Clostridium). Amino acid residues identical or similar in 80% of the entire family are shown in red and blue, respectively. Complete protein sequences were used in the alignment and the conserved residues were colored using the BOXSHADE server. The sequence numbering for YnzC from B. subtilis and the secondary structural elements found in its solution NMR structure (PDB ID, 2HEP) are shown above the alignment. (B) Stereoview of the ribbon representation of the lowest energy conformers (lowest CNS energy) from the final solution NMR structures of full length YnzC (green) and the truncated YnzC-1-46 construct (red). The secondary structural elements are labeled. (C) A view into the core of the YnzC-1-46 structure showing key hydrophobic (gold), aromatic (green) and polar (cyan) side chains that form the interface between the two helices. (D) Electrostatic potential surface diagrams of the interhelical surfaces made by helix 1 and 2 in YnzC. For clarity, the unstructured C-terminal region of the protein has been omitted and only the structured residues (1-42) are shown. (E) ConSurf images of the same interhelical faces of YnzC based on the multiple sequence alignment of the entire DUF896 (PF05979) protein domain family. Residue coloring, reflecting the degree of residue conservation over the entire family, ranges from magenta (highly conserved) to cyan (variable).

The above figure is reprinted by permission from John Wiley & Sons, Inc.: Proteins (2008, 72, 526-530) copyright 2008.

Author's comment

In order to combat the mutagenic effects of exposure to DNA-damaging agents such as UV radiation and genotoxic chemicals, bacteria have evolved elaborate DNA repair mechanisms, collectively termed the SOS response. The SOS response is triggered by the ssDNA-induced binding of RecA to the SOS regulon repressor LexA, and the subsequent activation of a plethora of SOS or damage-inducible (din) genes under its control. In both Escherichia coli and Bacillus subtilis, over 30 genes have been shown to be under the control of the LexA protein (formerly known as DinR in B. subtilis). In B. subtilis, one small SOS response operon under the control of LexA, the yneA operon, is comprised of three genes: yneA, yneB, and ynzC. Of the three gene products, YneA has been shown to suppress cell division during the SOS response, whereas the exact roles of YneB and YnzC are unknown to date.
The ynzC gene of B. subtilis encodes for a 77-residue basic protein [SWISS-PROT ID: YNZC_BACSU; NESG target ID: SR384] that is a member of the DUF896 protein domain family (Pfam identifier: PF05979). This family of small (< 90 aa) proteins with unknown function is found in over 100 bacterial species (Pfam 22.0), almost exclusively from the predominantly Gram-positive firmicutes. The N-terminal half of YnzC folds into an antiparallel helix-loop-helix motif, which remains intact in the truncated construct, whereas the remainder of the protein is disordered in solution. The structure of B. subtilis YnzC constitutes the first structural representative of the DUF896 protein domain family. It is reasonable to suggest that the unfolded C-terminal region of full length YnzC, which features several conserved residues across the DUF896 protein domain family, becomes structured upon binding to its biological target(s). The confirmation of the exact role of YnzC in the B. subtilis SOS response awaits further structural and functional studies.
Contributed by: James M. Aramini