PDBsum entry 1o51

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protein ligands links
Signaling protein PDB id
Protein chain
89 a.a. *
SO4 ×2
Waters ×39
* Residue conservation analysis
PDB id:
Name: Signaling protein
Title: Crystal structure of a putative pii-like signaling protein ( from thermotoga maritima at 2.50 a resolution
Structure: Hypothetical protein tm0021. Chain: a. Engineered: yes
Source: Thermotoga maritima. Organism_taxid: 2336. Gene: tm0021. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Trimer (from PDB file)
2.50Å     R-factor:   0.190     R-free:   0.229
Authors: Joint Center For Structural Genomics (Jcsg)
Key ref:
R.Schwarzenbacher et al. (2004). Crystal structure of a putative PII-like signaling protein (TM0021) from Thermotoga maritima at 2.5 A resolution. Proteins, 54, 810-813. PubMed id: 14997579 DOI: 10.1002/prot.10647
01-Aug-03     Release date:   19-Aug-03    
Supersedes: 1o2c
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
Q9WXM9  (Y021_THEMA) -  UPF0166 protein TM_0021
102 a.a.
89 a.a.
Key:    PfamA domain  Secondary structure  CATH domain


DOI no: 10.1002/prot.10647 Proteins 54:810-813 (2004)
PubMed id: 14997579  
Crystal structure of a putative PII-like signaling protein (TM0021) from Thermotoga maritima at 2.5 A resolution.
R.Schwarzenbacher, F.von Delft, P.Abdubek, E.Ambing, T.Biorac, L.S.Brinen, J.M.Canaves, J.Cambell, H.J.Chiu, X.Dai, A.M.Deacon, M.DiDonato, M.A.Elsliger, S.Eshagi, R.Floyd, A.Godzik, C.Grittini, S.K.Grzechnik, E.Hampton, L.Jaroszewski, C.Karlak, H.E.Klock, E.Koesema, J.S.Kovarik, A.Kreusch, P.Kuhn, S.A.Lesley, I.Levin, D.McMullan, T.M.McPhillips, M.D.Miller, A.Morse, K.Moy, J.Ouyang, R.Page, K.Quijano, A.Robb, G.Spraggon, R.C.Stevens, H.van den Bedem, J.Velasquez, J.Vincent, X.Wang, B.West, G.Wolf, Q.Xu, K.O.Hodgson, J.Wooley, I.A.Wilson.
No abstract given.

  Selected figure(s)  
Figure 1.
Figure 1. Crystal structure of TM0021. (A) Ribbon diagram of Thermotoga maritima TM0021 color coded from N-terminus (blue) to C-terminus (red) showing the domain organization and the location of the ADP binding site. The ADP molecule is shown in ball and stick. -helices (H1 and H2), -sheet A ( 1, 6, 5, 4) and -sheet B ( 2, 3) are indicated. The disordered T-loop is depicted with a dashed line. (B) Ribbon diagram of the TM0021 trimer with the bound ADP molecules shown in CPK mode. Figures produced with PYMOL (DeLano Scientific LLC).
Figure 2.
Figure 2. (A) Diagram showing the secondary structure elements in TM0021 superimposed on its primary sequence. The residues involved in ADP binding are marked above with a black line. Residues corresponding to the T-loop (46-60) and the B-loop (85-90) are underlined. -hairpins are depicted in red. Produced with PDB sum ( (B) Schematic representation of the interactions between ADP and its coordinating residues. The ADP molecule is depicted in purple and the protein residues are in orange. The atoms are indicated as follows: carbon (black), oxygen (red), nitrogen (blue), and phosphor (purple). Hydrogen bonds are represented as dashed green lines. Residues implicated in hydrophobic interactions are represented as barbed circle sections.
  The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2004, 54, 810-813) copyright 2004.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19884192 A.Bandyopadhyay, A.Arora, S.Jain, A.Laskar, C.Mandal, V.A.Ivanisenko, E.S.Fomin, S.S.Pintus, N.A.Kolchanov, S.Maiti, and S.Ramachandran (2010).
Expression and molecular characterization of the Mycobacterium tuberculosis PII protein.
  J Biochem, 147, 279-289.  
20521335 N.D.Shetty, M.C.Reddy, S.K.Palaninathan, J.L.Owen, and J.C.Sacchettini (2010).
Crystal structures of the apo and ATP bound Mycobacterium tuberculosis nitrogen regulatory PII protein.
  Protein Sci, 19, 1513-1524.
PDB codes: 3bzq 3lf0
18368466 J.Siltberg-Liberles, and A.Martinez (2009).
Searching distant homologs of the regulatory ACT domain in phenylalanine hydroxylase.
  Amino Acids, 36, 235-249.  
19542280 Y.Zhang, E.L.Pohlmann, and G.P.Roberts (2009).
Effect of perturbation of ATP level on the activity and regulation of nitrogenase in Rhodospirillum rubrum.
  J Bacteriol, 191, 5526-5537.  
  18453701 B.Bagautdinov, Y.Matsuura, S.Bagautdinova, N.Kunishima, and K.Yutani (2008).
Structure of putative CutA1 from Homo sapiens determined at 2.05 A resolution.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 351-357.
PDB code: 2zfh
17586767 M.H.Godsey, G.Minasov, L.Shuvalova, J.S.Brunzelle, I.I.Vorontsov, F.R.Collart, and W.F.Anderson (2007).
The 2.2 A 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.
PDB code: 2gx8
17220269 M.J.Conroy, A.Durand, D.Lupo, X.D.Li, P.A.Bullough, F.K.Winkler, and M.Merrick (2007).
The crystal structure of the Escherichia coli AmtB-GlnK complex reveals how GlnK regulates the ammonia channel.
  Proc Natl Acad Sci U S A, 104, 1213-1218.
PDB code: 2nuu
17203075 O.Yildiz, C.Kalthoff, S.Raunser, and W.Kühlbrandt (2007).
Structure of GlnK1 with bound effectors indicates regulatory mechanism for ammonia uptake.
  EMBO J, 26, 589-599.
PDB codes: 2j9c 2j9d 2j9e
16484197 Y.Zhu, M.C.Conrad, Y.Zhang, and G.P.Roberts (2006).
Identification of Rhodospirillum rubrum GlnB variants that are altered in their ability to interact with different targets in response to nitrogen status signals.
  J Bacteriol, 188, 1866-1874.  
16211521 R.Page, A.M.Deacon, S.A.Lesley, and R.C.Stevens (2005).
Shotgun crystallization strategy for structural genomics II: crystallization conditions that produce high resolution structures for T. maritima proteins.
  J Struct Funct Genomics, 6, 209-217.  
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.