PDBsum entry: 2gx8

Structural genomics, unknown function

PDB id: 2gx8

Contents

Protein chains

359 a.a. *

Ligands

EPE ×5

TRS

Metals

_ZN ×6

Waters ×616

* Residue conservation analysis

PDB id:

2gx8

Name:

Structural genomics, unknown function

Title:

The crystal stucture of bacillus cereus protein related to n

Structure:

Nif3-related protein. Chain: a, b, c. Engineered: yes

Source:

Bacillus cereus. Organism_taxid: 226900. Strain: atcc 14579. Gene: aap11199. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biol. unit:

Hexamer (from PDB file)

Resolution:

2.20Å R-factor: 0.199 R-free: 0.261

Authors:

G.Minasov,J.S.Brunzelle,L.Shuvalova,I.I.Vorontsov,F.R.Collar A.Joachimiak,W.F.Anderson,Midwest Center For Structural Gen (Mcsg)

Key ref:

M.H.Godsey et al. (2007). The 2.2Å resolution crystal structure of Bacillus cereus Nif3-family protein YqfO reveals a conserved dimetal-binding motif and a regulatory domain. Protein Sci, 16, 1285-1293. PubMed id: 17586767 DOI: 10.1110/ps.062674007

Date:

08-May-06 Release date: 16-May-06

Protein chains

Q818H0  (Q818H0_BACCR) -  NIF3-related protein

Seq: 373 a.a.

Struc: 359 a.a.

 Gene Ontology (GO) functional annotation 

• Biochemical function: metal ion binding (1 term)

DOI no: 10.1110/ps.062674007

Protein Sci 16:1285-1293 (2007)

PubMed id: 17586767

The 2.2Å resolution crystal structure of Bacillus cereus Nif3-family protein YqfO reveals a conserved dimetal-binding motif and a regulatory domain.

M.H.Godsey, G.Minasov, L.Shuvalova, J.S.Brunzelle, I.I.Vorontsov, F.R.Collart, W.F.Anderson.

ABSTRACT

YqfO of Bacillus cereus is a member of the widespread Nif3 family of proteins, which has been highlighted as an important target for structural genomics. The N- and C-terminal domains are conserved across the family and contain a dimetal-binding motif in a putative active site. YqfO contains an insert in the middle of the protein, present in a minority of bacterial family members. The structure of YqfO was determined at a resolution of 2.2 A and reveals conservation of the putative active site. It also reveals the previously unknown structure of the insert, which despite extremely limited sequence conservation, bears great similarity to PII, CutA, and a number of other trimeric regulatory proteins. Our results suggest that this domain acts as a signal sensor to regulate the still-unknown catalytic activity of the more-conserved domains.

Selected figure(s)

Figure 1.
Figure 1. Structural overview. (A) Stereo figure looking down the imperfect noncrystallographic threefold axis at D2. The trimer is colored by chain from yellow to red. Bound Zn2+ ions are shown as magenta spheres and buffer molecules as green sticks. (B) Surface colored by chain and rotated 180-A0 from A. (C) The crystallographically related trimer is shown in cyan. Domains 1 and 3 are found in the center torus, and the trimers formed by domains 2 can be seen off to either side.

Figure 2.
Figure 2. Sequence alignment of Nif3 or Nif3-like proteins. Secondary structures$(B!G(B assignments are based upon YqfO structure. E. coli YbgI and S. pneumoniae TIGR4 proteins were aligned by structural features to YqfO; others were aligned to the resulting profile using CLUSTALX (Thompson et al. 1994). Sequence conservation is shown from weak (light) to strong (dark) as calculated using ALSCRIPT (Barton 1993). Absolutely conserved residues are highlighted as white on black background. The region corresponding to domain 2 of YqfO is shaded. Residues that bind the metal ions in YqfO are indicated with triangles. Shown are: B. cereus Nif3-like protein YqfO (Accession No. AAP11199), S. pneumoniae TIGR4 (Accession No. AAK75693), Staphylococcus aureus (Accession No. NP372083), E. coli YbgI (Accession No. P0AFP6), Saccharomyces cerevisiae Nif3 (Accession No. P53081), Drosophila melanogaster (Accession No. NP609790), and human Nif3L1 (Accession No. AAG44846). (Note: the D. melanogaster sequence continues for 18 aa past the end of the alignment.) The area corresponding to the PII T-loop is located between b6 and b7.)

The above figures are reprinted by permission from the Protein Society: Protein Sci (2007, 16, 1285-1293) copyright 2007.

Figures were selected by the author.