PDBsum entry 2pmu

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protein ligands metals Protein-protein interface(s) links
Transcription regulation PDB id
Protein chains
98 a.a. *
103 a.a. *
92 a.a. *
93 a.a. *
PO4 ×4
UNX ×4
GLY ×3
__K ×3
_CL ×4
Waters ×489
* Residue conservation analysis
PDB id:
Name: Transcription regulation
Title: Crystal structure of the DNA-binding domain of phop
Structure: Response regulator phop. Chain: a, b, c, d, e, f. Fragment: DNA-binding domain, residues 144-247. Synonym: possible two component system response transcripti positive regulator phop. Engineered: yes
Source: Mycobacterium tuberculosis. Organism_taxid: 83332. Strain: h37rv. Gene: phop. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
1.78Å     R-factor:   0.198     R-free:   0.238
Authors: S.Wang
Key ref: S.Wang et al. (2007). Structure of the DNA-binding domain of the response regulator PhoP from Mycobacterium tuberculosis. Biochemistry, 46, 14751-14761. PubMed id: 18052041
23-Apr-07     Release date:   26-Feb-08    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
Q7D9B8  (Q7D9B8_MYCTU) -  DNA-binding response regulator
240 a.a.
98 a.a.
Protein chains
Pfam   ArchSchema ?
Q7D9B8  (Q7D9B8_MYCTU) -  DNA-binding response regulator
240 a.a.
103 a.a.
Protein chain
Pfam   ArchSchema ?
Q7D9B8  (Q7D9B8_MYCTU) -  DNA-binding response regulator
240 a.a.
92 a.a.
Protein chain
Pfam   ArchSchema ?
Q7D9B8  (Q7D9B8_MYCTU) -  DNA-binding response regulator
240 a.a.
93 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     two-component signal transduction system (phosphorelay)   2 terms 
  Biochemical function     DNA binding     1 term  


Biochemistry 46:14751-14761 (2007)
PubMed id: 18052041  
Structure of the DNA-binding domain of the response regulator PhoP from Mycobacterium tuberculosis.
S.Wang, J.Engohang-Ndong, I.Smith.
The PhoP-PhoR two-component signaling system from Mycobacterium tuberculosis is essential for the virulence of the tubercle bacillus. The response regulator, PhoP, regulates expression of over 110 genes. In order to elucidate the regulatory mechanism of PhoP, we determined the crystal structure of its DNA-binding domain (PhoPC). PhoPC exhibits a typical fold of the winged helix-turn-helix subfamily of response regulators. The structure starts with a four-stranded antiparallel beta-sheet, followed by a three-helical bundle of alpha-helices, and then a C-terminal beta-hairpin, which together with a short beta-strand between the first and second helices forms a three-stranded antiparallel beta-sheet. Structural elements are packed through a hydrophobic core, with the first helix providing a scaffold for the rest of the domain to pack. The second and third helices and the long, flexible loop between them form the helix-turn-helix motif, with the third helix being the recognition helix. The C-terminal beta-hairpin turn forms the wing motif. The molecular surfaces around the recognition helix and the wing residues show strong positive electrostatic potential, consistent with their roles in DNA binding and nucleotide sequence recognition. The crystal packing of PhoPC gives a hexamer ring, with neighboring molecules interacting in a head-to-tail fashion. This packing interface suggests that PhoPC could bind DNA in a tandem association. However, this mode of DNA binding is likely to be nonspecific because the recognition helix is partially blocked and would be prevented from inserting into the major groove of DNA. Detailed structural analysis and implications with respect to DNA binding are discussed.

Literature references that cite this PDB file's key reference

  PubMed id Reference
20548782 A.H.Li, S.J.Waddell, J.Hinds, C.A.Malloff, M.Bains, R.E.Hancock, W.L.Lam, P.D.Butcher, and R.W.Stokes (2010).
Contrasting transcriptional responses of a virulent and an attenuated strain of Mycobacterium tuberculosis infecting macrophages.
  PLoS One, 5, e11066.  
  20944208 D.Das, N.V.Grishin, A.Kumar, D.Carlton, C.Bakolitsa, M.D.Miller, P.Abdubek, T.Astakhova, H.L.Axelrod, P.Burra, C.Chen, H.J.Chiu, M.Chiu, T.Clayton, M.C.Deller, L.Duan, K.Ellrott, D.Ernst, C.L.Farr, J.Feuerhelm, A.Grzechnik, S.K.Grzechnik, J.C.Grant, G.W.Han, L.Jaroszewski, K.K.Jin, H.A.Johnson, H.E.Klock, M.W.Knuth, P.Kozbial, S.S.Krishna, D.Marciano, D.McMullan, A.T.Morse, E.Nigoghossian, A.Nopakun, L.Okach, S.Oommachen, J.Paulsen, C.Puckett, R.Reyes, C.L.Rife, N.Sefcovic, H.J.Tien, C.B.Trame, H.van den Bedem, D.Weekes, T.Wooten, Q.Xu, K.O.Hodgson, J.Wooley, M.A.Elsliger, A.M.Deacon, A.Godzik, S.A.Lesley, and I.A.Wilson (2010).
The structure of the first representative of Pfam family PF09836 reveals a two-domain organization and suggests involvement in transcriptional regulation.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 66, 1174-1181.
PDB code: 3dee
19948799 M.B.Ryndak, S.Wang, I.Smith, and G.M.Rodriguez (2010).
The Mycobacterium tuberculosis high-affinity iron importer, IrtA, contains an FAD-binding domain.
  J Bacteriol, 192, 861-869.  
  19652341 J.M.Hickey, P.S.Hefty, and A.L.Lamb (2009).
Expression, purification, crystallization and preliminary X-ray analysis of the DNA-binding domain of a Chlamydia trachomatis OmpR/PhoB-subfamily response regulator homolog, ChxR.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 65, 791-794.  
19820095 S.Gupta, A.Pathak, A.Sinha, and D.Sarkar (2009).
Mycobacterium tuberculosis PhoP recognizes two adjacent direct-repeat sequences to form head-to-head dimers.
  J Bacteriol, 191, 7466-7476.  
18793412 A.S.Leung, V.Tran, Z.Wu, X.Yu, D.C.Alexander, G.F.Gao, B.Zhu, and J.Liu (2008).
Novel genome polymorphisms in BCG vaccine strains and impact on efficacy.
  BMC Genomics, 9, 413.  
18757548 J.Gonzalo-Asensio, C.Y.Soto, A.Arbués, J.Sancho, M.del Carmen Menéndez, M.J.García, B.Gicquel, and C.Martín (2008).
The Mycobacterium tuberculosis phoPR operon is positively autoregulated in the virulent strain H37Rv.
  J Bacteriol, 190, 7068-7078.  
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 code is shown on the right.