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PDBsum entry 2cg4

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protein ligands metals Protein-protein interface(s) links
Transcription PDB id
2cg4
Jmol
Contents
Protein chains
149 a.a. *
Ligands
ASN ×2
Metals
_MG
Waters ×135
* Residue conservation analysis
PDB id:
2cg4
Name: Transcription
Title: Structure of e.Coli asnc
Structure: Regulatory protein asnc. Chain: a, b. Engineered: yes. Mutation: yes
Source: Escherichia coli. Organism_taxid: 562. Strain: b834(de3). Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Octamer (from PDB file)
Resolution:
2.40Å     R-factor:   0.232     R-free:   0.294
Authors: P.Thaw,S.E.Sedelnikova,T.Muranova,S.Wiese,S.Ayora, J.C.Alonso,A.B.Brinkman,J.Akerboom,J.Van Der Oost, J.B.Rafferty
Key ref: P.Thaw et al. (2006). Structural insight into gene transcriptional regulation and effector binding by the Lrp/AsnC family. Nucleic Acids Res, 34, 1439-1449. PubMed id: 16528101
Date:
27-Feb-06     Release date:   04-Apr-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P0ACI6  (ASNC_ECOLI) -  Regulatory protein AsnC
Seq:
Struc:
152 a.a.
149 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     intracellular   1 term 
  Biological process     response to amino acid stimulus   5 terms 
  Biochemical function     protein binding     5 terms  

 

 
Nucleic Acids Res 34:1439-1449 (2006)
PubMed id: 16528101  
 
 
Structural insight into gene transcriptional regulation and effector binding by the Lrp/AsnC family.
P.Thaw, S.E.Sedelnikova, T.Muranova, S.Wiese, S.Ayora, J.C.Alonso, A.B.Brinkman, J.Akerboom, J.van der Oost, J.B.Rafferty.
 
  ABSTRACT  
 
The Lrp/AsnC family of transcriptional regulatory proteins is found in both archaea and bacteria. Members of the family influence cellular metabolism in both a global (Lrp) and specific (AsnC) manner, often in response to exogenous amino acid effectors. In the present study we have determined both the first bacterial and the highest resolution structures for members of the family. Escherichia coli AsnC is a specific gene regulator whose activity is triggered by asparagine binding. Bacillus subtilis LrpC is a global regulator involved in chromosome condensation. Our AsnC-asparagine structure is the first for a regulator-effector complex and is revealed as an octameric disc. Key ligand recognition residues are identified together with a route for ligand access. The LrpC structure reveals a stable octamer supportive of a topological role in dynamic DNA packaging. The structures yield significant clues to the functionality of Lrp/AsnC-type regulators with respect to ligand binding and oligomerization states as well as to their role in specific and global DNA regulation.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20675722 A.Soufi, A.Sawasdichai, A.Shukla, P.Noy, T.Dafforn, C.Smith, P.S.Jayaraman, and K.Gaston (2010).
DNA compaction by the higher-order assembly of PRH/Hex homeodomain protein oligomers.
  Nucleic Acids Res, 38, 7513-7525.  
20140026 S.C.Dillon, and C.J.Dorman (2010).
Bacterial nucleoid-associated proteins, nucleoid structure and gene expression.
  Nat Rev Microbiol, 8, 185-195.  
20351259 S.P.Wilkinson, M.Ouhammouch, and E.P.Geiduschek (2010).
Transcriptional activation in the context of repression mediated by archaeal histones.
  Proc Natl Acad Sci U S A, 107, 6777-6781.  
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.  
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
18300246 K.Miyazono, M.Tsujimura, Y.Kawarabayasi, and M.Tanokura (2008).
Crystal structure of STS042, a stand-alone RAM module protein, from hyperthermophilic archaeon Sulfolobus tokodaii strain 7.
  Proteins, 71, 1557-1562.
PDB code: 2zbc
18042675 M.C.Reddy, K.Gokulan, W.R.Jacobs, T.R.Ioerger, and J.C.Sacchettini (2008).
Crystal structure of Mycobacterium tuberculosis LrpA, a leucine-responsive global regulator associated with starvation response.
  Protein Sci, 17, 159-170.
PDB code: 2qz8
18405378 R.E.Lintner, P.K.Mishra, P.Srivastava, B.M.Martinez-Vaz, A.B.Khodursky, and R.M.Blumenthal (2008).
Limited functional conservation of a global regulator among related bacterial genera: Lrp in Escherichia, Proteus and Vibrio.
  BMC Microbiol, 8, 60.  
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
17178749 E.Peeters, C.Wartel, D.Maes, and D.Charlier (2007).
Analysis of the DNA-binding sequence specificity of the archaeal transcriptional regulator Ss-LrpB from Sulfolobus solfataricus by systematic mutagenesis and high resolution contact probing.
  Nucleic Acids Res, 35, 623-633.  
17675388 G.Fiorentino, R.Ronca, R.Cannio, M.Rossi, and S.Bartolucci (2007).
MarR-like transcriptional regulator involved in detoxification of aromatic compounds in Sulfolobus solfataricus.
  J Bacteriol, 189, 7351-7360.  
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
17640269 H.Yang, L.Wang, Z.Xie, Y.Tian, G.Liu, and H.Tan (2007).
The tyrosine degradation gene hppD is transcriptionally activated by HpdA and repressed by HpdR in Streptomyces coelicolor, while hpdA is negatively autoregulated and repressed by HpdR.
  Mol Microbiol, 65, 1064-1077.  
17337545 J.R.Borden, and E.T.Papoutsakis (2007).
Dynamics of genomic-library enrichment and identification of solvent tolerance genes for Clostridium acetobutylicum.
  Appl Environ Microbiol, 73, 3061-3068.  
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.  
  18007052 N.Nakano, T.Kumarevel, E.Matsunaga, A.Shinkai, S.Kuramitsu, and S.Yokoyama (2007).
Purification, crystallization and preliminary X-ray crystallographic analysis of ST1022, a putative member of the Lrp/AsnC family of transcriptional regulators isolated from Sulfolobus tokodaii strain 7.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 964-966.  
17223133 S.de los Rios, and J.J.Perona (2007).
Structure of the Escherichia coli leucine-responsive regulatory protein Lrp reveals a novel octameric assembly.
  J Mol Biol, 366, 1589-1602.
PDB code: 2gqq
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
  16946463 N.Nakano, N.Okazaki, S.Satoh, K.Takio, S.Kuramitsu, A.Shinkai, and S.Yokoyama (2006).
Structure of the stand-alone RAM-domain protein from Thermus thermophilus HB8.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 855-860.
PDB code: 2djw
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.