PDBsum entry: 1d06

Signaling protein

PDB-id

1d06


	Asymmetric unit

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Description

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Protein chain

Ligands

HEM

Waters ×73

* Residue conservation analysis

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		Biological unit, dimer (as deduced by PQS)

PDB id:

1d06

Name:

Signaling protein

Title:

Structural basis of dimerization and sensory mechanisms of oxygen-sensing domain of rhizobium meliloti fixl determined at 1.4a resolution

Structure:

Nitrogen fixation regulatory protein fixl. Chain: a. Engineered: yes. Mutation: yes

Source:

Sinorhizobium meliloti. Organism_taxid: 382. Expressed in: escherichia coli k12. Expression_system_taxid: 83333.

Biological unit:

Dimer (from PQS)

UniProt:

P10955 (FIXL_RHIME)

Seq:

Struc:

Seq:

505 a.a.

Struc:

130 a.a.*

Key:		PfamA domain			PfamB domain
		Secondary structure			CATH domain

* PDB and UniProt seqs differ at 6 residue positions (black crosses)

Enzyme class:

E.C.2.7.13.3 [IntEnz] [ExPASy] [KEGG] [BRENDA]

Reaction:

ATP + protein L-histidine = ADP + protein N-phospho-L-histidine

Resolution:

1.40Å

R-factor:

0.224

R-free:

0.275

Authors:

H.Miyatake,M.Mukai,S.-Y.Park,S.Adachi,K.Tamura,H.Nakamura, K.Nakamura,T.Tsuchiya,T.Iizuka,Y.Shiro

Key ref:

H.Miyatake et al. (2000). Sensory mechanism of oxygen sensor FixL from Rhizobium meliloti: crystallographic, mutagenesis and resonance Raman spectroscopic studies.. J Mol Biol, 301, 415-431. [PubMed id: 10926518] [DOI: 10.1006/jmbi.2000.3954]

Date:

09-Sep-99

Release date:

15-Mar-00

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Key reference

DOI no: 10.1006/jmbi.2000.3954 J Mol Biol 301:415-431 (2000)

PubMed id: 10926518

Sensory mechanism of oxygen sensor FixL from Rhizobium meliloti: crystallographic, mutagenesis and resonance Raman spectroscopic studies.

H.Miyatake, M.Mukai, S.Y.Park, S.Adachi, K.Tamura, H.Nakamura, K.Nakamura, T.Tsuchiya, T.Iizuka, Y.Shiro.

ABSTRACT

FixL of Rhizobium meliloti (RmFixL) is a sensor histidine kinase of the two-component system, which regulates the expression of the genes related to nitrogen fixation in the root nodule in response to the O(2) levels. The crystal structure of the sensor domain of FixL (RmFixLH), which contains a heme (Fe-porphyrin) as a sensing site, was determined at 1.4 A resolution. Based on the structural and spectroscopic analyses, we propose the O(2) sensing mechanism that differs from the case proposed in BjFixLH as follows; conformational changes in the F/G loop, which are induced by steric repulsion between the bent-bound O(2) and the Ile209 side-chain, would be transmitted to the histidine kinase domain. Interaction between the iron-bound O(2) and Ile209 was also observed in the resonance Raman spectra of RmFixLH as evidenced by the fact that the Fe-O(2) and Fe-CN stretching frequencies were shifted from 575 to 570 cm(-1) (Fe-O(2)), and 504 to 499 cm(-1), respectively, as the result of the replacement of Ile209 with an Ala residue. In the I209A mutant of RmFixL, the O(2) sensing activity was destroyed, thus confirming our proposed mechanism.

Selected figure(s)

Figure 3.
Figure 3. Dimerization interaction at the N-terminal: (a) "Leucine-zipper"-like interaction at helix II with CPK representations. (b) The interaction between helix I and the RmFixLH core region. The pictures (a) and (b) were depicted with MOLSCRIPT and RASTER3D. (c) The amino acid sequences of the leucine zipper-like helices (helix II) of Rhizobium meliloti (RmFixLH), Bradyrhizobium japonicum (BjFixLH) and Azorhizobium caulinodans (AcFixLH) are drawn in a-helical wheels, in order to present the amphipathic nature, in which hydrophobic residues are colored in yellow, while the others are in light blue. Figure 6.
Figure 6. (a) Heme and its surroundings with distances (Å) and electron density map (>1s). Distal side residues (Ile209, Ile210, Leu230, Val232) and proximal residues (His194, Asn181, Asp195) are shown. (b) Top and side views of a van der Waals drawing of the structure at the heme distal region.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2000, 301, 415-431) copyright 2000.

Figures were selected by an automated process.

Literature references that cite this PDB file's key reference

PubMed id Reference

19402751 S.Hennig, H.M.Strauss, K.Vanselow, O.Yildiz, S.Schulze, J.Arens, A.Kramer, and E.Wolf (2009).
Structural and functional analyses of PAS domain interactions of the clock proteins Drosophila PERIOD and mouse PERIOD2.

PLoS Biol, 7, e94.

PDB codes: 3gdi 3gec

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.

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

17693554 A.Busch, J.Lacal, A.Martos, J.L.Ramos, and T.Krell (2007).
Bacterial sensor kinase TodS interacts with agonistic and antagonistic signals.

Proc Natl Acad Sci U S A, 104, 13774-13779.

17200735 V.Buttani, A.Losi, T.Eggert, U.Krauss, K.E.Jaeger, Z.Cao, and W.Gärtner (2007).
Conformational analysis of the blue-light sensing protein YtvA reveals a competitive interface for LOV-LOV dimerization and interdomain interactions.

Photochem Photobiol Sci, 6, 41-49.

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.

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

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.

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

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.

12970182 L.R.Swem, B.J.Kraft, D.L.Swem, A.T.Setterdahl, S.Masuda, D.B.Knaff, J.M.Zaleski, and C.E.Bauer (2003).
Signal transduction by the global regulator RegB is mediated by a redox-active cysteine.

EMBO J, 22, 4699-4708.

14622266 S.Hirata, T.Matsui, Y.Sasakura, S.Sugiyama, T.Yoshimura, I.Sagami, and T.Shimizu (2003).
Characterization of Met95 mutants of a heme-regulated phosphodiesterase from Escherichia coli. Optical absorption, magnetic circular dichroism, circular dichroism, and redox potentials.

Eur J Biochem, 270, 4771-4779.

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.

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.

11297407 A.L.Chang, J.R.Tuckerman, G.Gonzalez, R.Mayer, H.Weinhouse, G.Volman, D.Amikam, M.Benziman, and M.A.Gilles-Gonzalez (2001).
Phosphodiesterase A1, a regulator of cellulose synthesis in Acetobacter xylinum, is a heme-based sensor.

Biochemistry, 40, 3420-3426.

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.

11717509 M.Hefti, J.Hendle, C.Enroth, J.Vervoort, and P.A.Tucker (2001).
Crystallization and preliminary crystallographic data of the PAS domain of the NifL protein from Azotobacter vinelandii.

Acta Crystallogr D Biol Crystallogr, 57, 1895-1896.

11248020 S.Crosson, and K.Moffat (2001).
Structure of a flavin-binding plant photoreceptor domain: insights into light-mediated signal transduction.

Proc Natl Acad Sci U S A, 98, 2995-3000.

PDB code: 1g28

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.