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PDBsum entry 1dp8
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protein ligands links
Oxygen storage/transport PDB id
1dp8

 

 

 

 

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Contents
Protein chain
118 a.a. *
Ligands
_NO-HEM
Waters ×81
* Residue conservation analysis
PDB id:
1dp8
Name: Oxygen storage/transport
Title: Crystal structure of the nitric oxide bound fixl heme domain
Structure: Fixl protein. Chain: a. Fragment: heme domain. Engineered: yes
Source: Bradyrhizobium japonicum. Organism_taxid: 375. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Hexamer (from PQS)
Resolution:
2.50Å     R-factor:   0.205     R-free:   0.252
Authors: W.Gong,B.Hao,M.K.Chan
Key ref:
W.Gong et al. (2000). New mechanistic insights from structural studies of the oxygen-sensing domain of Bradyrhizobium japonicum FixL. Biochemistry, 39, 3955-3962. PubMed id: 10747783 DOI: 10.1021/bi992346w
Date:
24-Dec-99     Release date:   24-Dec-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P23222  (FIXL_BRADU) -  Sensor protein FixL from Bradyrhizobium diazoefficiens (strain JCM 10833 / BCRC 13528 / IAM 13628 / NBRC 14792 / USDA 110)
Seq:
Struc: 		505 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
 + protein N-phospho-L-histidine
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    reference    
 
 
DOI no: 10.1021/bi992346w Biochemistry 39:3955-3962 (2000)
PubMed id: 10747783  
 
 
New mechanistic insights from structural studies of the oxygen-sensing domain of Bradyrhizobium japonicum FixL.
W.Gong, B.Hao, M.K.Chan.
 
  ABSTRACT  
 
The FixL heme domain serves as the dioxygen switch in the FixL/FixJ two-component system of Rhizobia. Recent structural studies of the Bradyrhizobium japonicum FixL heme domain (BjFixLH) have suggested an allosteric mechanism that is distinct from the classical hemoglobin model. To gain further insight into the FixL sensing mechanism, structures of BjFixLH bound to dioxygen, imidazole, and nitric oxide have been determined. These structures, particularly the structure of BjFixLH bound to its physiological ligand, dioxygen, have helped to address a number of important issues relevant to the BjFixLH sensing mechanism. On the basis of the oxy-BjFixLH structure, a conserved arginine is found to stabilize the dioxygen ligand in a mode reminiscent of the distal histidine in classical myoglobins and hemoglobins. The structure of BjFixLH bound to imidazole elucidates the structural requirements for accommodating sterically bulky ligands. Finally, the structure of BjFixLH bound to nitric oxide provides evidence for a structural intermediate in the heme-driven conformational change.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21325055 C.Song, G.Psakis, C.Lang, J.Mailliet, W.Gärtner, J.Hughes, and J.Matysik (2011).
Two ground state isoforms and a chromophore D-ring photoflip triggering extensive intramolecular changes in a canonical phytochrome.
  Proc Natl Acad Sci U S A, 108, 3842-3847.  
21443850 J.D.Satterlee (2011).
Origins of aging mass loss in recombinant N-terminus and C-terminus deletion mutants of the heme-PAS biosensor domain BjFixLH(140-270).
  J Inorg Biochem, 105, 609-615.  
20223701 J.Cheung, and W.A.Hendrickson (2010).
Sensor domains of two-component regulatory systems.
  Curr Opin Microbiol, 13, 116-123.  
20587053 T.E.Meyer, J.A.Kyndt, and M.A.Cusanovich (2010).
Occurrence and sequence of Sphaeroides Heme Protein and diheme cytochrome C in purple photosynthetic bacteria in the family Rhodobacteraceae.
  BMC Biochem, 11, 24.  
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.  
19594171 A.J.Lee, R.W.Clark, H.Youn, S.Ponter, and J.N.Burstyn (2009).
Guanidine hydrochloride-induced unfolding of the three heme coordination states of the CO-sensing transcription factor, CooA.
  Biochemistry, 48, 6585-6597.  
19021503 F.W.Outten, and E.C.Theil (2009).
Iron-based redox switches in biology.
  Antioxid Redox Signal, 11, 1029-1046.  
19246238 J.Green, J.C.Crack, A.J.Thomson, and N.E.LeBrun (2009).
Bacterial sensors of oxygen.
  Curr Opin Microbiol, 12, 145-151.  
19950993 J.Key, T.H.Scheuermann, P.C.Anderson, V.Daggett, and K.H.Gardner (2009).
Principles of ligand binding within a completely buried cavity in HIF2alpha PAS-B.
  J Am Chem Soc, 131, 17647-17654.
PDB codes: 3h7w 3h82
19653642 R.Tran, E.M.Boon, M.A.Marletta, and R.A.Mathies (2009).
Resonance Raman spectra of an O2-binding H-NOX domain reveal heme relaxation upon mutation.
  Biochemistry, 48, 8568-8577.  
19836334 S.Yamada, H.Sugimoto, M.Kobayashi, A.Ohno, H.Nakamura, and Y.Shiro (2009).
Structure of PAS-linked histidine kinase and the response regulator complex.
  Structure, 17, 1333-1344.
PDB codes: 3a0r 3a0s 3a0t 3a0u 3a0v 3a0w 3a0x 3a0y 3a0z 3a10
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.  
18980385 L.M.Podust, A.Ioanoviciu, and P.R.Ortiz de Montellano (2008).
2.3 A X-ray structure of the heme-bound GAF domain of sensory histidine kinase DosT of Mycobacterium tuberculosis.
  Biochemistry, 47, 12523-12531.
PDB code: 2vzw
18799745 L.O.Essen, J.Mailliet, and J.Hughes (2008).
The structure of a complete phytochrome sensory module in the Pr ground state.
  Proc Natl Acad Sci U S A, 105, 14709-14714.
PDB code: 2vea
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
18326575 R.L.Kerby, H.Youn, and G.P.Roberts (2008).
RcoM: a new single-component transcriptional regulator of CO metabolism in bacteria.
  J Bacteriol, 190, 3336-3343.  
17371046 A.Ioanoviciu, E.T.Yukl, P.Moënne-Loccoz, and P.R.de Montellano (2007).
DevS, a heme-containing two-component oxygen sensor of Mycobacterium tuberculosis.
  Biochemistry, 46, 4250-4260.  
17535805 A.Tanaka, H.Takahashi, and T.Shimizu (2007).
Critical role of the heme axial ligand, Met95, in locking catalysis of the phosphodiesterase from Escherichia coli (Ec DOS) toward Cyclic diGMP.
  J Biol Chem, 282, 21301-21307.  
17318598 M.A.Carrondo, I.Bento, P.M.Matias, and P.F.Lindley (2007).
Crystallographic evidence for dioxygen interactions with iron proteins.
  J Biol Inorg Chem, 12, 429-442.  
17446273 S.G.Kruglik, A.Jasaitis, K.Hola, T.Yamashita, U.Liebl, J.L.Martin, and M.H.Vos (2007).
Subpicosecond oxygen trapping in the heme pocket of the oxygen sensor FixL observed by time-resolved resonance Raman spectroscopy.
  Proc Natl Acad Sci U S A, 104, 7408-7413.  
17893032 T.P.Cash, Y.Pan, and M.C.Simon (2007).
Reactive oxygen species and cellular oxygen sensing.
  Free Radic Biol Med, 43, 1219-1225.  
16513745 K.J.Watts, K.Sommer, S.L.Fry, M.S.Johnson, and B.L.Taylor (2006).
Function of the N-terminal cap of the PAS domain in signaling by the aerotaxis receptor Aer.
  J Bacteriol, 188, 2154-2162.  
17158704 T.Mascher, J.D.Helmann, and G.Unden (2006).
Stimulus perception in bacterial signal-transducing histidine kinases.
  Microbiol Mol Biol Rev, 70, 910-938.  
15755957 A.Brencic, and S.C.Winans (2005).
Detection of and response to signals involved in host-microbe interactions by plant-associated bacteria.
  Microbiol Mol Biol Rev, 69, 155-194.  
15942729 A.Karlsson, J.V.Parales, R.E.Parales, D.T.Gibson, H.Eklund, and S.Ramaswamy (2005).
NO binding to naphthalene dioxygenase.
  J Biol Inorg Chem, 10, 483-489.
PDB codes: 1uuv 1uuw
16407994 E.M.Boon, S.H.Huang, and M.A.Marletta (2005).
A molecular basis for NO selectivity in soluble guanylate cyclase.
  Nat Chem Biol, 1, 53-59.  
15797872 T.Uchida, E.Sato, A.Sato, I.Sagami, T.Shimizu, and T.Kitagawa (2005).
CO-dependent activity-controlling mechanism of heme-containing CO-sensor protein, neuronal PAS domain protein 2.
  J Biol Chem, 280, 21358-21368.  
15711013 V.Balland, L.Bouzhir-Sima, L.Kiger, M.C.Marden, M.H.Vos, U.Liebl, and T.A.Mattioli (2005).
Role of arginine 220 in the oxygen sensor FixL from Bradyrhizobium japonicum.
  J Biol Chem, 280, 15279-15288.  
15653746 W.Zhang, J.S.Olson, and G.N.Phillips (2005).
Biophysical and kinetic characterization of HemAT, an aerotaxis receptor from Bacillus subtilis.
  Biophys J, 88, 2801-2814.  
15353565 G.P.Roberts, H.Youn, and R.L.Kerby (2004).
CO-sensing mechanisms.
  Microbiol Mol Biol Rev, 68, 453-473.  
15009198 M.H.Hefti, K.J.Françoijs, S.C.de Vries, R.Dixon, and J.Vervoort (2004).
The PAS fold. A redefinition of the PAS domain based upon structural prediction.
  Eur J Biochem, 271, 1198-1208.  
14570894 P.M.Schmidt, M.Schramm, H.Schröder, F.Wunder, and J.P.Stasch (2004).
Identification of residues crucially involved in the binding of the heme moiety of soluble guanylate cyclase.
  J Biol Chem, 279, 3025-3032.  
15326296 P.Pellicena, D.S.Karow, E.M.Boon, M.A.Marletta, and J.Kuriyan (2004).
Crystal structure of an oxygen-binding heme domain related to soluble guanylate cyclases.
  Proc Natl Acad Sci U S A, 101, 12854-12859.
PDB codes: 1u4h 1u55 1u56
15263897 R.Dixon, and D.Kahn (2004).
Genetic regulation of biological nitrogen fixation.
  Nat Rev Microbiol, 2, 621-631.  
14517970 D.M.Copeland, A.H.West, and G.B.Richter-Addo (2003).
Crystal structures of ferrous horse heart myoglobin complexed with nitric oxide and nitrosoethane.
  Proteins, 53, 182-192.
PDB codes: 1npf 1npg
12718516 M.A.Cusanovich, and T.E.Meyer (2003).
Photoactive yellow protein: a prototypic PAS domain sensory protein and development of a common signaling mechanism.
  Biochemistry, 42, 4759-4770.  
12486718 S.Kundu, and M.S.Hargrove (2003).
Distal heme pocket regulation of ligand binding and stability in soybean leghemoglobin.
  Proteins, 50, 239-248.  
12767236 U.Liebl, L.Bouzhir-Sima, L.Kiger, M.C.Marden, J.C.Lambry, M.Négrerie, and M.H.Vos (2003).
Ligand binding dynamics to the heme domain of the oxygen sensor Dos from Escherichia coli.
  Biochemistry, 42, 6527-6535.  
12080073 A.Sato, Y.Sasakura, S.Sugiyama, I.Sagami, T.Shimizu, Y.Mizutani, and T.Kitagawa (2002).
Stationary and time-resolved resonance Raman spectra of His77 and Met95 mutants of the isolated heme domain of a direct oxygen sensor from Escherichia coli.
  J Biol Chem, 277, 32650-32658.  
12390021 B.Hao, C.Isaza, J.Arndt, M.Soltis, and M.K.Chan (2002).
Structure-based mechanism of O2 sensing and ligand discrimination by the FixL heme domain of Bradyrhizobium japonicum.
  Biochemistry, 41, 12952-12958.
PDB codes: 1lsv 1lsw 1lsx 1lt0
12198316 H.Park, C.Suquet, M.I.Savenkova, J.D.Satterlee, and C.Kang (2002).
Cloning, purification, crystallization and preliminary X-ray analysis of DOS heme domain, a new heme oxygen sensor in Escherichia coli.
  Acta Crystallogr D Biol Crystallogr, 58, 1504-1506.  
11994013 J.R.Tuckerman, G.Gonzalez, E.M.Dioum, and M.A.Gilles-Gonzalez (2002).
Ligand and oxidation-state specific regulation of the heme-based oxygen sensor FixL from Sinorhizobium meliloti.
  Biochemistry, 41, 6170-6177.  
11821422 S.Aono, T.Kato, M.Matsuki, H.Nakajima, T.Ohta, T.Uchida, and T.Kitagawa (2002).
Resonance Raman and ligand binding studies of the oxygen-sensing signal transducer protein HemAT from Bacillus subtilis.
  J Biol Chem, 277, 13528-13538.  
11939776 T.Tomita, G.Gonzalez, A.L.Chang, M.Ikeda-Saito, and M.A.Gilles-Gonzalez (2002).
A comparative resonance Raman analysis of heme-binding PAS domains: heme iron coordination structures of the BjFixL, AxPDEA1, EcDos, and MtDos proteins.
  Biochemistry, 41, 4819-4826.  
12271121 U.Liebl, L.Bouzhir-Sima, M.Negrerie, J.L.Martin, and M.H.Vos (2002).
Ultrafast ligand rebinding in the heme domain of the oxygen sensors FixL and Dos: general regulatory implications for heme-based sensors.
  Proc Natl Acad Sci U S A, 99, 12771-12776.  
11669630 K.R.Rodgers, L.Tang, G.S.Lukat-Rodgers, and N.L.Wengenack (2001).
Insights into the signal transduction mechanism of RmFixL provided by carbon monoxide recombination kinetics.
  Biochemistry, 40, 12932-12942.  
11282350 M.K.Chan (2001).
Recent advances in heme-protein sensors.
  Curr Opin Chem Biol, 5, 216-222.  
11060017 D.M.Lawson, C.E.Stevenson, C.R.Andrew, and R.R.Eady (2000).
Unprecedented proximal binding of nitric oxide to heme: implications for guanylate cyclase.
  EMBO J, 19, 5661-5671.
PDB codes: 1e83 1e84 1e85 1e86
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.

 

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