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PDBsum entry 1s67

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protein ligands Protein-protein interface(s) links
Oxygen storage/transport PDB id
1s67
Jmol
Contents
Protein chains
119 a.a. *
Ligands
HEM-OXY
HEM
Waters ×206
* Residue conservation analysis
PDB id:
1s67
Name: Oxygen storage/transport
Title: Crystal structure of heme domain of direct oxygen sensor from e. Coli
Structure: Hypothetical protein yddu. Chain: l, u. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Gene: yddu, b1489. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Dimer (from PQS)
Resolution:
1.50Å     R-factor:   0.197     R-free:   0.214
Authors: H.J.Park,C.Suquet,J.D.Satterlee,C.H.Kang
Key ref:
H.Park et al. (2004). Insights into signal transduction involving PAS domain oxygen-sensing heme proteins from the X-ray crystal structure of Escherichia coli Dos heme domain (Ec DosH). Biochemistry, 43, 2738-2746. PubMed id: 15005609 DOI: 10.1021/bi035980p
Date:
22-Jan-04     Release date:   22-Jun-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P76129  (DOSP_ECOLI) -  Oxygen sensor protein DosP
Seq:
Struc:
 
Seq:
Struc:
799 a.a.
119 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.1.4.52  - Cyclic-guanylate-specific phosphodiesterase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Cyclic di-3',5'-guanylate + H2O = 5'-phosphoguanylyl(3'->5')guanosine
Cyclic di-3',5'-guanylate
+ H(2)O
= 5'-phosphoguanylyl(3'->5')guanosine
      Cofactor: Heme; Mg(2+); Mn(2+)
Heme
Bound ligand (Het Group name = HEM) matches with 95.00% similarity
Mg(2+)
Mn(2+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     signal transduction   2 terms 
  Biochemical function     signal transducer activity     1 term  

 

 
    reference    
 
 
DOI no: 10.1021/bi035980p Biochemistry 43:2738-2746 (2004)
PubMed id: 15005609  
 
 
Insights into signal transduction involving PAS domain oxygen-sensing heme proteins from the X-ray crystal structure of Escherichia coli Dos heme domain (Ec DosH).
H.Park, C.Suquet, J.D.Satterlee, C.Kang.
 
  ABSTRACT  
 
The X-ray crystal structure of the Escherichia coli (Ec) direct oxygen sensor heme domain (Ec DosH) has been solved to 1.8 A using Fe multiple-wavelength anomalous dispersion (MAD), and the positions of Met95 have been confirmed by selenomethionine ((Se)Met) MAD. Ec DosH is the sensing part of a larger two-domain sensing/signaling protein, in which the signaling domain has phosphodiesterase activity. The asymmetric unit of the crystal lattice contains a dimer comprised of two differently ligated heme domain monomers. Except for the heme ligands, the monomer heme domains are identical. In one monomer, the heme is ligated by molecular oxygen (O(2)), while in the other monomer, an endogenous Met95 with S --> Fe ligation replaces the exogenous O(2) ligand. In both heme domains, the proximal ligand is His77. Analysis of these structures reveals sizable ligand-dependent conformational changes in the protein chain localized in the FG turn, the G(beta)-strand, and the HI turn. These changes provide insight to the mechanism of signal propagation within the heme domain following initiation due to O(2) dissociation.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
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.  
21255112 K.J.Watts, B.L.Taylor, and M.S.Johnson (2011).
PAS/poly-HAMP signalling in Aer-2, a soluble haem-based sensor.
  Mol Microbiol, 79, 686-699.  
20861024 K.Kobayashi, A.Tanaka, H.Takahashi, J.Igarashi, Y.Ishitsuka, N.Yokota, and T.Shimizu (2010).
Catalysis and oxygen binding of Ec DOS: a haem-based oxygen-sensor enzyme from Escherichia coli.
  J Biochem, 148, 693-703.  
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.  
20823675 T.Yamashita (2010).
[Recent studies on gas sensors, CooA, FixL, and Dos].
  Yakugaku Zasshi, 130, 1181-1187.  
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.  
18922794 K.Emami, E.Topakas, T.Nagy, J.Henshaw, K.A.Jackson, K.E.Nelson, E.F.Mongodin, J.W.Murray, R.J.Lewis, and H.J.Gilbert (2009).
Regulation of the Xylan-degrading Apparatus of Cellvibrio japonicus by a Novel Two-component System.
  J Biol Chem, 284, 1086-1096.
PDB code: 2va0
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
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
18771281 A.K.Bidwai, E.Y.Ok, and J.E.Erman (2008).
pH dependence of cyanide binding to the ferric heme domain of the direct oxygen sensor from Escherichia coli and the effect of alkaline denaturation.
  Biochemistry, 47, 10458-10470.  
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
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.  
18450754 S.F.El-Mashtoly, S.Nakashima, A.Tanaka, T.Shimizu, and T.Kitagawa (2008).
Roles of Arg-97 and Phe-113 in regulation of distal ligand binding to heme in the sensor domain of Ec DOS protein. Resonance Raman and mutation study.
  J Biol Chem, 283, 19000-19010.  
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
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.  
17550789 D.A.Landfried, D.A.Vuletich, M.P.Pond, and J.T.Lecomte (2007).
Structural and thermodynamic consequences of b heme binding for monomeric apoglobins and other apoproteins.
  Gene, 398, 12-28.  
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.  
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.  
16724227 J.C.Pinkert, R.W.Clark, and J.N.Burstyn (2006).
Modeling proline ligation in the heme-dependent CO sensor, CooA, using small-molecule analogs.
  J Biol Inorg Chem, 11, 642-650.  
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
16519686 N.Yokota, Y.Araki, H.Kurokawa, O.Ito, J.Igarashi, and T.Shimizu (2006).
Critical roles of Leu99 and Leu115 at the heme distal side in auto-oxidation and the redox potential of a heme-regulated phosphodiesterase from Escherichia coli.
  FEBS J, 273, 1210-1223.  
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.  
16098197 R.Koudo, H.Kurokawa, E.Sato, J.Igarashi, T.Uchida, I.Sagami, T.Kitagawa, and T.Shimizu (2005).
Spectroscopic characterization of the isolated heme-bound PAS-B domain of neuronal PAS domain protein 2 associated with circadian rhythms.
  FEBS J, 272, 4153-4162.  
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.  
15550941 J.Green, and M.S.Paget (2004).
Bacterial redox sensors.
  Nat Rev Microbiol, 2, 954-966.  
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.  
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.