PDBsum entry 2p5v

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protein ligands metals Protein-protein interface(s) links
Transcription PDB id
Protein chains
(+ 2 more) 156 a.a. *
GOL ×8
_CL ×10
_CA ×8
Waters ×760
* Residue conservation analysis
PDB id:
Name: Transcription
Title: Crystal structure of transcriptional regulator nmb0573 from meningitidis
Structure: Transcriptional regulator, lrp/asnc family. Chain: a, b, c, d, e, f, g, h. Engineered: yes
Source: Neisseria meningitidis. Organism_taxid: 122586. Strain: mc58. Gene: nmb0573. Expressed in: escherichia coli. Expression_system_taxid: 562.
1.99Å     R-factor:   0.179     R-free:   0.238
Authors: J.Ren,S.Sainsbury,R.J.Owens,Oxford Protein Production Facili
Key ref:
J.Ren et al. (2007). The structure and transcriptional analysis of a global regulator from Neisseria meningitidis. J Biol Chem, 282, 14655-14664. PubMed id: 17374605 DOI: 10.1074/jbc.M701082200
16-Mar-07     Release date:   03-Apr-07    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
Q9K0L9  (Q9K0L9_NEIMB) -  Transcriptional regulator, AsnC family
187 a.a.
156 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     intracellular   1 term 
  Biological process     regulation of transcription, DNA-dependent   1 term 
  Biochemical function     sequence-specific DNA binding transcription factor activity     2 terms  


DOI no: 10.1074/jbc.M701082200 J Biol Chem 282:14655-14664 (2007)
PubMed id: 17374605  
The structure and transcriptional analysis of a global regulator from Neisseria meningitidis.
J.Ren, S.Sainsbury, S.E.Combs, R.G.Capper, P.W.Jordan, N.S.Berrow, D.K.Stammers, N.J.Saunders, R.J.Owens.
Neisseria meningitidis, a causative agent of bacterial meningitis, has a relatively small repertoire of transcription factors, including NMB0573 (annotated AsnC), a member of the Lrp-AsnC family of regulators that are widely expressed in both Bacteria and Archaea. In the present study we show that NMB0573 binds to l-leucine and l-methionine and have solved the structure of the protein with and without bound amino acids. This has shown, for the first time that amino acid binding does not induce significant conformational changes in the structure of an AsnC/Lrp regulator although it does appear to stabilize the octameric assembly of the protein. Transcriptional profiling of wild-type and NMB0573 knock-out strains of N. meningitidis has shown that NMB0573 is associated with an adaptive response to nutrient poor conditions reflected in a reduction in major surface protein expression. On the basis of its structure and the transcriptional response, we propose that NMB0573 is a global regulator in Neisseria controlling responses to nutrient availability through indicators of general amino acid abundance: leucine and methionine.
  Selected figure(s)  
Figure 4.
FIGURE 4. The structure of NMB0573. In a, the overall structure, the polypeptide chains are drawn as coils and ribbons, and each monomer is individually colored. The 8 calcium ions in the un-liganded structure are shown as purple spheres. L-Methionines from the NMB0573-L-methionine complex are overlapped onto the un-liganded structure and shown as black spheres to mark the amino acid binding sites. The two amino acid binding sites between adjacent dimers are related by a 2-fold axis of symmetry such that four sites are presented on one face of the octameric array and four on the opposite face. b, is an overlay of the overall structure of NMB0573 with (red trace) or without bound methionine (gray trace). 100% of the two molecules can be overlapped with an r.m.s. deviation of 0.5 Å. Bound methionines are shown as ball and sticks (colored by atom) to mark the amino acid binding sites. In c and d the structure of NMB0573 is compared with E. coli AsnC. c, shows the C backbones of NMB0573 (red) and AsnC (gray) monomers overlaid with every 20 residues of NMB0573 marked by small green spheres and secondary structure features labeled; 75% C s of the two molecules can be overlapped with an r.m.s. deviation of 1.1 Å. Larger differences appear at the N-terminal domain (DNA binding domain) between residues 12 and 32 encompassing the 2 helices and in the C-terminal domain (effector binding domain) in the position of the 4 helices relative to the 2 strands. d, is a ribbon diagram showing the superimposed dimers of NMB0573 (red and green) and AsnC (gray) with the secondary structure features labeled on one pair of dimers. e and f show the amino acid binding site of NMB0573, which comprises residues from three peptide chains, of which the backbones are shown as ribbons and coils and colored individually. The side chains of residues either lining the pocket or having any atom interact with the ligand are drawn as sticks and colored by atoms. Hydrogen bonds are shown as cyan dashed lines. Simulated annealing omit electron density maps contoured at 3.5 for the bound L-methionine (e) and L-leucine (f) are shown as semi-transparent green surfaces.
Figure 5.
FIGURE 5. Comparison of amino acid binding sites. a, shows a stereo pair of an overlay of the apo and methionine-bound sites of NMB0573; the C backbones and side chains of NMB0573/L-methionine are shown in red and orange and those of apo-NMB0573 in cyan and blue, respectively, with the bound amino acid drawn in thicker bonds. Residue Arg-83 is labeled. b, shows a stereo pair of an overlay of the binding sites of NMB0573/L-methionine and E. coli AsnC/asparagine. The C backbones and side chains of NMB0573/L-methionine are shown in red and orange and those of AsnC/asparagine in cyan and blue, respectively, with the bound amino acid drawn in thicker bonds. For clarity only the Ala-101 and Leu-129 in NMB0573 and the corresponding residues Tyr-100 and Gln-128 in E. coli AsnC are labeled. The orientation of both figures is the same as in Fig. 4, e and f.
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2007, 282, 14655-14664) copyright 2007.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21251255 V.M.Isabella, and V.L.Clark (2011).
Deep sequencing-based analysis of the anaerobic stimulon in Neisseria gonorrhoeae.
  BMC Genomics, 12, 51.  
20379743 S.Schielke, M.Frosch, and O.Kurzai (2010).
Virulence determinants involved in differential host niche adaptation of Neisseria meningitidis and Neisseria gonorrhoeae.
  Med Microbiol Immunol, 199, 185-196.  
21136603 T.van Alen, H.Claus, R.P.Zahedi, J.Groh, H.Blazyca, M.Lappann, A.Sickmann, and U.Vogel (2010).
Comparative proteomic analysis of biofilm and planktonic cells of Neisseria meningitidis.
  Proteomics, 10, 4512-4521.  
19076237 C.L.Santos, F.Tavares, J.Thioulouse, and P.Normand (2009).
A phylogenomic analysis of bacterial helix-turn-helix transcription factors.
  FEMS Microbiol Rev, 33, 411-429.  
19170871 E.Peeters, S.V.Albers, A.Vassart, A.J.Driessen, and D.Charlier (2009).
Ss-LrpB, a transcriptional regulator from Sulfolobus solfataricus, regulates a gene cluster with a pyruvate ferredoxin oxidoreductase-encoding operon and permease genes.
  Mol Microbiol, 71, 972-988.  
19385941 G.Bernardini, D.Braconi, P.Lusini, and A.Santucci (2009).
Postgenomics of Neisseria meningitidis: an update.
  Expert Rev Proteomics, 6, 135-143.  
19775246 M.A.Pritchett, S.P.Wilkinson, E.P.Geiduschek, and M.Ouhammouch (2009).
Hybrid Ptr2-like activators of archaeal transcription.
  Mol Microbiol, 74, 582-593.  
19004003 M.Yamada, S.A.Ishijima, and M.Suzuki (2009).
Interactions between the archaeal transcription repressor FL11 and its coregulators lysine and arginine.
  Proteins, 74, 520-525.
PDB codes: 2zny 2znz
18239270 T.Kawashima, H.Aramaki, T.Oyamada, K.Makino, M.Yamada, H.Okamura, K.Yokoyama, S.A.Ishijima, and M.Suzuki (2008).
Transcription Regulation by Feast/Famine Regulatory Proteins, FFRPs, in Archaea and Eubacteria.
  Biol Pharm Bull, 31, 173-186.  
18653535 T.Kumarevel, N.Nakano, K.Ponnuraj, S.C.Gopinath, K.Sakamoto, A.Shinkai, P.K.Kumar, and S.Yokoyama (2008).
Crystal structure of glutamine receptor protein from Sulfolobus tokodaii strain 7 in complex with its effector L-glutamine: implications of effector binding in molecular association and DNA binding.
  Nucleic Acids Res, 36, 4808-4820.
PDB codes: 2e7w 2e7x 2efn 2efo 2efp 2efq 2pmh 2pn6 2yx4 2yx7
17937921 H.Okamura, K.Yokoyama, H.Koike, M.Yamada, A.Shimowasa, M.Kabasawa, T.Kawashima, and M.Suzuki (2007).
A structural code for discriminating between transcription signals revealed by the feast/famine regulatory protein DM1 in complex with ligands.
  Structure, 15, 1325-1338.
PDB codes: 2e1a 2z4p
17906152 J.Xiong, C.E.Bauer, and A.Pancholy (2007).
Insight into the haem d1 biosynthesis pathway in heliobacteria through bioinformatics analysis.
  Microbiology, 153, 3548-3562.  
17962306 T.Shrivastava, and R.Ramachandran (2007).
Mechanistic insights from the crystal structures of a feast/famine regulatory protein from Mycobacterium tuberculosis H37Rv.
  Nucleic Acids Res, 35, 7324-7335.
PDB codes: 2ivm 2vbw 2vbx 2vby 2vbz 2vc0 2vc1
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.