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PDBsum entry 2gj3
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protein ligands Protein-protein interface(s) links
Transferase PDB id
2gj3

 

 

 

 

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JSmol PyMol  
Contents
Protein chains
119 a.a. *
Ligands
SO4 ×4
FAD ×2
EOH
Waters ×337
* Residue conservation analysis
PDB id:
2gj3
Name: Transferase
Title: Crystal structure of the fad-containing pas domain of the protein nifl from azotobacter vinelandii.
Structure: Nitrogen fixation regulatory protein. Chain: a, b. Fragment: pas1 of nifl containing fad (residues 21-140). Engineered: yes
Source: Azotobacter vinelandii. Organism_taxid: 354. Gene: nifl. Expressed in: escherichia coli. Expression_system_taxid: 562
Resolution:
1.04Å     R-factor:   0.158     R-free:   0.186
Authors: J.Key,M.Hefti,E.Purcell,K.Moffat
Key ref: J.Key et al. (2007). Structure of the redox sensor domain of Azotobacter vinelandii NifL at atomic resolution: signaling, dimerization, and mechanism. Biochemistry, 46, 3614-3623. PubMed id: 17319691
Date:
30-Mar-06     Release date:   06-Mar-07    
PROCHECK
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 Headers
 References

Protein chains
Pfam   ArchSchema ?
P30663  (NIFL_AZOVI) -  Nitrogen fixation regulatory protein from Azotobacter vinelandii
Seq:
Struc: 		519 a.a.
119 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.2.7.13.3  - histidine kinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + protein L-histidine = ADP + protein N-phospho-L-histidine
ATP
 + protein L-histidine
 =
ADP
Bound ligand (Het Group name = FAD)
matches with 50.94% similarity 		+ protein N-phospho-L-histidine
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    reference    
 
 
Biochemistry 46:3614-3623 (2007)
PubMed id: 17319691  
 
 
Structure of the redox sensor domain of Azotobacter vinelandii NifL at atomic resolution: signaling, dimerization, and mechanism.
J.Key, M.Hefti, E.B.Purcell, K.Moffat.
 
  ABSTRACT  
 
NifL is a multidomain sensor protein responsible for the transcriptional regulation of genes involved in response to changes in cellular redox state and ADP concentration. Cellular redox is monitored by the N-terminal PAS domain of NifL which contains an FAD cofactor. Flavin-based PAS domains of this type have also been referred to as LOV domains. To explore the mechanism of signal recognition and transduction in NifL, we determined the crystal structure of the FAD-bound PAS domain of NifL from Azotobacter vinelandii to 1.04 A resolution. The structure reveals a novel cavity within the PAS domain which contains two water molecules directly coordinated to the FAD. This cavity is connected to solvent by multiple access channels which may facilitate the oxidation of the FAD by molecular oxygen and the release of hydrogen peroxide. The structure contains a dimer of the NifL PAS domain that is structurally very similar to those described in other crystal structures of PAS domains and identifies a conserved dimerization motif. An N-terminal amphipathic helix constitutes part of the dimerization interface, and similar N-terminal helices are identified in other PAS domain proteins. The structure suggests a model for redox-mediated signaling in which a conformational change is initiated by redox-dependent changes in protonation at the N5 atom of FAD that lead to reorganization of hydrogen bonds within the flavin binding pocket. A structural signal is subsequently transmitted to the beta-sheet interface between the monomers of the PAS domain.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21028987 D.F.Becker, W.Zhu, and M.A.Moxley (2011).
Flavin redox switching of protein functions.
  Antioxid Redox Signal, 14, 1079-1091.  
21220116 J.King-Scott, P.V.Konarev, S.Panjikar, R.Jordanova, D.I.Svergun, and P.A.Tucker (2011).
Structural characterization of the multidomain regulatory protein Rv1364c from Mycobacterium tuberculosis.
  Structure, 19, 56-69.  
20545849 A.J.Campbell, K.J.Watts, M.S.Johnson, and B.L.Taylor (2010).
Gain-of-function mutations cluster in distinct regions associated with the signalling pathway in the PAS domain of the aerotaxis receptor, Aer.
  Mol Microbiol, 77, 575-586.  
20067522 H.Nakajima, N.Takatani, K.Yoshimitsu, M.Itoh, S.Aono, Y.Takahashi, and Y.Watanabe (2010).
The role of the Fe-S cluster in the sensory domain of nitrogenase transcriptional activator VnfA from Azotobacter vinelandii.
  FEBS J, 277, 817-832.  
20860483 P.D.Scheu, O.B.Kim, C.Griesinger, and G.Unden (2010).
Sensing by the membrane-bound sensor kinase DcuS: exogenous versus endogenous sensing of C(4)-dicarboxylates in bacteria.
  Future Microbiol, 5, 1383-1402.  
19906177 P.Slavny, R.Little, P.Salinas, T.A.Clarke, and R.Dixon (2010).
Quaternary structure changes in a second Per-Arnt-Sim domain mediate intramolecular redox signal relay in the NifL regulatory protein.
  Mol Microbiol, 75, 61-75.  
20825354 T.Krell, J.Lacal, A.Busch, H.Silva-Jiménez, M.E.Guazzaroni, and J.L.Ramos (2010).
Bacterial sensor kinases: diversity in the recognition of environmental signals.
  Annu Rev Microbiol, 64, 539-559.  
20133866 Z.Xie, L.E.Ulrich, I.B.Zhulin, and G.Alexandre (2010).
PAS domain containing chemoreceptor couples dynamic changes in metabolism with chemotaxis.
  Proc Natl Acad Sci U S A, 107, 2235-2240.  
19836329 A.Möglich, R.A.Ayers, and K.Moffat (2009).
Structure and signaling mechanism of Per-ARNT-Sim domains.
  Structure, 17, 1282-1294.  
19712683 J.S.Lamb, B.D.Zoltowski, S.A.Pabit, L.Li, B.R.Crane, and L.Pollack (2009).
Illuminating solution responses of a LOV domain protein with photocoupled small-angle X-ray scattering.
  J Mol Biol, 393, 909-919.
PDB code: 3is2
19424679 K.P.Michel, A.K.Schröder, M.Zimmermann, S.Brandt, E.K.Pistorius, N.Frankenberg-Dinkel, and D.Staiger (2009).
The hybrid histidine kinase Slr1759 of the cyanobacterium Synechocystis sp. PCC 6803 contains FAD at its PAS domain.
  Arch Microbiol, 191, 553-559.  
19432806 M.S.Brody, V.Stewart, and C.W.Price (2009).
Bypass suppression analysis maps the signalling pathway within a multidomain protein: the RsbP energy stress phosphatase 2C from Bacillus subtilis.
  Mol Microbiol, 72, 1221-1234.  
19129502 T.H.Scheuermann, D.R.Tomchick, M.Machius, Y.Guo, R.K.Bruick, and K.H.Gardner (2009).
Artificial ligand binding within the HIF2alpha PAS-B domain of the HIF2 transcription factor.
  Proc Natl Acad Sci U S A, 106, 450-455.
PDB codes: 3f1n 3f1o 3f1p
19243237 T.Senda, M.Senda, S.Kimura, and T.Ishida (2009).
Redox control of protein conformation in flavoproteins.
  Antioxid Redox Signal, 11, 1741-1766.  
19271777 U.E.Ukaegbu, and A.C.Rosenzweig (2009).
Structure of the redox sensor domain of Methylococcus capsulatus (Bath) MmoS.
  Biochemistry, 48, 2207-2215.
PDB code: 3ewk
18553928 B.D.Zoltowski, and B.R.Crane (2008).
Light activation of the LOV protein vivid generates a rapidly exchanging dimer.
  Biochemistry, 47, 7012-7019.
PDB code: 3d72
18281403 D.M.Doughty, E.G.Kurth, L.A.Sayavedra-Soto, D.J.Arp, and P.J.Bottomley (2008).
Evidence for involvement of copper ions and redox state in regulation of butane monooxygenase in Pseudomonas butanovora.
  J Bacteriol, 190, 2933-2938.  
18667691 D.Strickland, K.Moffat, and T.R.Sosnick (2008).
Light-activated DNA binding in a designed allosteric protein.
  Proc Natl Acad Sci U S A, 105, 10709-10714.  
18441062 K.Geszvain, and K.L.Visick (2008).
The hybrid sensor kinase RscS integrates positive and negative signals to modulate biofilm formation in Vibrio fischeri.
  J Bacteriol, 190, 4437-4446.  
18203838 K.J.Watts, M.S.Johnson, and B.L.Taylor (2008).
Structure-function relationships in the HAMP and proximal signaling domains of the aerotaxis receptor Aer.
  J Bacteriol, 190, 2118-2127.  
18820688 M.Etzkorn, H.Kneuper, P.Dünnwald, V.Vijayan, J.Krämer, C.Griesinger, S.Becker, G.Unden, and M.Baldus (2008).
Plasticity of the PAS domain and a potential role for signal transduction in the histidine kinase DcuS.
  Nat Struct Mol Biol, 15, 1031-1039.
PDB code: 2w0n
18942854 R.A.Ayers, and K.Moffat (2008).
Changes in quaternary structure in the signaling mechanisms of PAS domains.
  Biochemistry, 47, 12078-12086.
PDB codes: 2vv6 2vv7 2vv8
18468622 S.D.Goldberg, C.S.Soto, C.D.Waldburger, and W.F.Degrado (2008).
Determination of the physiological dimer interface of the PhoQ sensor domain.
  J Mol Biol, 379, 656-665.  
18006497 X.Ma, N.Sayed, P.Baskaran, A.Beuve, and F.van den Akker (2008).
PAS-mediated dimerization of soluble guanylyl cyclase revealed by signal transduction histidine kinase domain crystal structure.
  J Biol Chem, 283, 1167-1178.
PDB codes: 2p04 2p08
17764689 A.Möglich, and K.Moffat (2007).
Structural basis for light-dependent signaling in the dimeric LOV domain of the photosensor YtvA.
  J Mol Biol, 373, 112-126.
PDB codes: 2pr5 2pr6
17824925 B.L.Taylor (2007).
Aer on the inside looking out: paradigm for a PAS-HAMP role in sensing oxygen, redox and energy.
  Mol Microbiol, 65, 1415-1424.  
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.

 

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