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PDBsum entry 1lsv
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Transferase PDB id
1lsv

 

 

 

 

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Contents
Protein chain
117 a.a. *
Ligands
HEM-CMO
Waters ×38
* Residue conservation analysis
PDB id:
1lsv
Name: Transferase
Title: Crystal structure of the co-bound bjfixl heme domain
Structure: Sensor protein fixl. Chain: a. Fragment: heme domain (residues 141-270). Engineered: yes
Source: Bradyrhizobium japonicum. Organism_taxid: 375. Gene: fixl. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Hexamer (from PQS)
Resolution:
2.40Å     R-factor:   0.215     R-free:   0.251
Authors: B.Hao,C.Isaza,J.Arndt,M.Soltis,M.K.Chan
Key ref:
B.Hao et al. (2002). Structure-based mechanism of O2 sensing and ligand discrimination by the FixL heme domain of Bradyrhizobium japonicum. Biochemistry, 41, 12952-12958. PubMed id: 12390021 DOI: 10.1021/bi020144l
Date:
19-May-02     Release date:   20-Nov-02    
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.
117 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/bi020144l Biochemistry 41:12952-12958 (2002)
PubMed id: 12390021  
 
 
Structure-based mechanism of O2 sensing and ligand discrimination by the FixL heme domain of Bradyrhizobium japonicum.
B.Hao, C.Isaza, J.Arndt, M.Soltis, M.K.Chan.
 
  ABSTRACT  
 
Structures of the Bradyrhizobium japonicum FixL heme domain have been determined in the absence and presence of specific ligands to elucidate the detailed features of its O2 sensing mechanism. The putative roles of spin-state and steric hindrance were evaluated by the structure determination of ferrous CO-bound BjFixLH and correlating its features with other ligand-bound structures. As found for NO-BjFixLH, no protein conformational change was observed in CO-BjFixLH, suggesting a more complicated mechanism than solely spin state or ligand sterics. To evaluate the role of oxidation state, the structure of the ferrous deoxy-BjFixLH was determined. The structure of deoxy-BjFixLH was found to be virtually identical to the structure of the ferric met-BjFixLH. The role of hydrogen bonding of substrates to a heme-pocket water was evaluated by determining the structure of BjFixLH bound to 1-methyl-imidazole that cannot form a hydrogen bond with this water. In this case, the heme-mediated conformational change was observed, limiting the potential importance of this interaction. Finally, the structure of cyanomet-BjFixLH was revisited to rule out concerns regarding the partial occupancy of the cyanide ligand in a previous structure. In the revised structure, Arg 220 was found to move into the heme pocket to form a hydrogen bond to the bound cyanide ligand. The implications of these results on FixL's sensing mechanism are discussed.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
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.  
19864414 C.Lechauve, L.Bouzhir-Sima, T.Yamashita, M.C.Marden, M.H.Vos, U.Liebl, and L.Kiger (2009).
Heme ligand binding properties and intradimer interactions in the full-length sensor protein dos from Escherichia coli and its isolated heme domain.
  J Biol Chem, 284, 36146-36159.  
19021503 F.W.Outten, and E.C.Theil (2009).
Iron-based redox switches in biology.
  Antioxid Redox Signal, 11, 1029-1046.  
  19342776 H.Zhao, and L.Tang (2009).
Crystallographic characterization of a multidomain histidine protein kinase from an essential two-component regulatory system.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 65, 346-349.  
19246238 J.Green, J.C.Crack, A.J.Thomson, and N.E.LeBrun (2009).
Bacterial sensors of oxygen.
  Curr Opin Microbiol, 12, 145-151.  
19575571 R.Gao, and A.M.Stock (2009).
Biological insights from structures of two-component proteins.
  Annu Rev Microbiol, 63, 133-154.  
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
18222919 E.Geisinger, E.A.George, T.W.Muir, and R.P.Novick (2008).
Identification of ligand specificity determinants in AgrC, the Staphylococcus aureus quorum-sensing receptor.
  J Biol Chem, 283, 8930-8938.  
18708494 J.M.Lee, H.Y.Cho, H.J.Cho, I.J.Ko, S.W.Park, H.S.Baik, J.H.Oh, C.Y.Eom, Y.M.Kim, B.S.Kang, and J.I.Oh (2008).
O2- and NO-sensing mechanism through the DevSR two-component system in Mycobacterium smegmatis.
  J Bacteriol, 190, 6795-6804.
PDB codes: 2vjw 2vks
18672900 K.A.Marvin, R.L.Kerby, H.Youn, G.P.Roberts, and J.N.Burstyn (2008).
The transcription regulator RcoM-2 from Burkholderia xenovorans is a cysteine-ligated hemoprotein that undergoes a redox-mediated ligand switch.
  Biochemistry, 47, 9016-9028.  
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
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
18039668 T.Yamashita, L.Bouzhir-Sima, J.C.Lambry, U.Liebl, and M.H.Vos (2008).
Ligand Dynamics and Early Signaling Events in the Heme Domain of the Sensor Protein Dos from Escherichia coli.
  J Biol Chem, 283, 2344-2352.  
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
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.  
17534535 S.Singh, P.Madzelan, and R.Banerjee (2007).
Properties of an unusual heme cofactor in PLP-dependent cystathionine beta-synthase.
  Nat Prod Rep, 24, 631-639.  
16804678 H.Li, J.Igarashi, J.Jamal, W.Yang, and T.L.Poulos (2006).
Structural studies of constitutive nitric oxide synthases with diatomic ligands bound.
  J Biol Inorg Chem, 11, 753-768.
PDB codes: 2g6h 2g6i 2g6j 2g6k 2g6l 2g6m 2g6n 2g6o
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.  
17023414 M.D.Suits, N.Jaffer, and Z.Jia (2006).
Structure of the Escherichia coli O157:H7 heme oxygenase ChuS in complex with heme and enzymatic inactivation by mutation of the heme coordinating residue His-193.
  J Biol Chem, 281, 36776-36782.
PDB codes: 2hq2 4cdp
16774917 Y.Gao, S.F.El-Mashtoly, B.Pal, T.Hayashi, K.Harada, and T.Kitagawa (2006).
Pathway of information transmission from heme to protein upon ligand binding/dissociation in myoglobin revealed by UV resonance raman spectroscopy.
  J Biol Chem, 281, 24637-24646.  
16640569 Y.Y.Londer, I.S.Dementieva, C.A.D'Ausilio, P.R.Pokkuluri, and M.Schiffer (2006).
Characterization of a c-type heme-containing PAS sensor domain from Geobacter sulfurreducens representing a novel family of periplasmic sensors in Geobacteraceae and other bacteria.
  FEMS Microbiol Lett, 258, 173-181.  
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.  
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.  
15353565 G.P.Roberts, H.Youn, and R.L.Kerby (2004).
CO-sensing mechanisms.
  Microbiol Mol Biol Rev, 68, 453-473.  
14982921 H.Kurokawa, D.S.Lee, M.Watanabe, I.Sagami, B.Mikami, C.S.Raman, and T.Shimizu (2004).
A redox-controlled molecular switch revealed by the crystal structure of a bacterial heme PAS sensor.
  J Biol Chem, 279, 20186-20193.
PDB codes: 1v9y 1v9z
15326187 H.Youn, R.L.Kerby, and G.P.Roberts (2004).
Changing the ligand specificity of CooA, a highly specific heme-based CO sensor.
  J Biol Chem, 279, 45744-45752.  
15373839 M.Watanabe, H.Kurokawa, T.Yoshimura-Suzuki, I.Sagami, and T.Shimizu (2004).
Critical roles of Asp40 at the haem proximal side of haem-regulated phosphodiesterase from Escherichia coli in redox potential, auto-oxidation and catalytic control.
  Eur J Biochem, 271, 3937-3942.  
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.  
14612459 S.Taguchi, T.Matsui, J.Igarashi, Y.Sasakura, Y.Araki, O.Ito, S.Sugiyama, I.Sagami, and T.Shimizu (2004).
Binding of oxygen and carbon monoxide to a heme-regulated phosphodiesterase from Escherichia coli. Kinetics and infrared spectra of the full-length wild-type enzyme, isolated PAS domain, and Met-95 mutants.
  J Biol Chem, 279, 3340-3347.  
12820879 C.M.Dunham, E.M.Dioum, J.R.Tuckerman, G.Gonzalez, W.G.Scott, and M.A.Gilles-Gonzalez (2003).
A distal arginine in oxygen-sensing heme-PAS domains is essential to ligand binding, signal transduction, and structure.
  Biochemistry, 42, 7701-7708.
PDB code: 1y28
14572542 L.Aravind, V.Anantharaman, and L.M.Iyer (2003).
Evolutionary connections between bacterial and eukaryotic signaling systems: a genomic perspective.
  Curr Opin Microbiol, 6, 490-497.  
14551206 T.Yoshimura, I.Sagami, Y.Sasakura, and T.Shimizu (2003).
Relationships between heme incorporation, tetramer formation, and catalysis of a heme-regulated phosphodiesterase from Escherichia coli: a study of deletion and site-directed mutants.
  J Biol Chem, 278, 53105-53111.  
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.  
12962628 W.Zhang, and G.N.Phillips (2003).
Structure of the oxygen sensor in Bacillus subtilis: signal transduction of chemotaxis by control of symmetry.
  Structure, 11, 1097-1110.
PDB codes: 1or4 1or6
12445766 E.D.Getzoff (2002).
PASsing a signal: low carbs, less protein.
  Chem Biol, 9, 1165-1166.  
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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