PDBsum entry 1ft9

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Transcription PDB id
Protein chains
210 a.a. *
HEM ×2
Waters ×199
* Residue conservation analysis
PDB id:
Name: Transcription
Title: Structure of the reduced (feii) co-sensing protein from r. Rubrum
Structure: Carbon monoxide oxidation system transcription regulator. Chain: a, b. Synonym: cooa gene product. Engineered: yes
Source: Rhodospirillum rubrum. Organism_taxid: 1085. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Dimer (from PQS)
2.60Å     R-factor:   0.230     R-free:   0.280
Authors: W.N.Lanzilotta,D.J.Schuller,T.L.Poulos,M.V.Thorsteinsson, B.Kirby,G.P.Roberts
Key ref:
W.N.Lanzilotta et al. (2000). Structure of the CO sensing transcription activator CooA. Nat Struct Biol, 7, 876-880. PubMed id: 11017196 DOI: 10.1038/82820
12-Sep-00     Release date:   09-Oct-00    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P72322  (P72322_RHORU) -  CooA protein
222 a.a.
210 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     intracellular   1 term 
  Biological process     transcription, DNA-dependent   2 terms 
  Biochemical function     DNA binding     3 terms  


DOI no: 10.1038/82820 Nat Struct Biol 7:876-880 (2000)
PubMed id: 11017196  
Structure of the CO sensing transcription activator CooA.
W.N.Lanzilotta, D.J.Schuller, M.V.Thorsteinsson, R.L.Kerby, G.P.Roberts, T.L.Poulos.
CooA is a homodimeric transcription factor that belongs to the catabolite activator protein (CAP) family. Binding of CO to the heme groups of CooA leads to the transcription of genes involved in CO oxidation in Rhodospirillum rubrum. The 2.6 A structure of reduced (Fe2+) CooA reveals that His 77 in both subunits provides one heme ligand while the N-terminal nitrogen of Pro 2 from the opposite subunit provides the other ligand. A structural comparison of CooA in the absence of effector and DNA (off state) with that of CAP in the effector and DNA bound state (on state) leads to a plausible model for the mechanism of allosteric control in this class of proteins as well as the CO dependent activation of CooA.
  Selected figure(s)  
Figure 1.
Figure 1. Comparison of the overall fold and conformational differences between CooA and CAP with cAMP and DNA bound. a, Stereo view of CooA and CAP dimers. In both cases, the effector binding domain (residues 2−107 for Cooa, 9−111 for CAP), C helix (residues 108−130 for CooA, 112−135 for CAP), and DNA binding domain (residues 131−213 for CooA, 136−205 for CAP) of monomer A are colored dark blue, dark pink, and purple, respectively. For monomer B, the effector binding domain, C helix, and the DNA binding domain are colored dark green, light green, and cyan, respectively. Both the heme groups of CooA and the cAMP molecules of CAP are represented by red space-filling models. The structure of CAP was adapted from Shultz et al.^4. b, Superposition of the effector domains of monomer B for CooA (shown in blue) and CAP (shown in orange) showing the relative orientations of the C helices. The r.m.s.d. for the alignment of the backbone atoms in the core structural elements of the effector domain was 1.16 Å. Strictly conserved Pro and Leu residues are shown at the N-terminal and C-terminal ends of the C helices, respectively. While an individual effector domain of CooA (green) aligns well with one of CAP (orange), the orientation of the C helix in the second domain is completely different. Of particular interest is the movement of the C helix (yellow arrow) when the structure of CooA (no effector bound) is compared with that of CAP (effector bound). c, View looking down the C helices from the N-terminus toward the C-terminus. The alignment is the same as shown in (b), with the yellow arrow representing movement from the effector free (CooA) to the effector bound (CAP) state. d, Alignment of effector domains in monomer B for CooA and CAP with the DNA binding domains shown. As can be seen, the relative position of the DNA binding domain and subsequently the position of the recognition helix in CooA is rotated 180° away from the position observed in the structure of CAP with effector bound.
Figure 3.
Figure 3. Stereo views of the heme environment in CooA. a, Back view and b, side view of the F[o] - F[c] omit map (green cage), contoured at 3 by the simulated annealing protocol with Pro 2, Pro 3 and the heme omitted. c, Anomalous difference maps for data collected at 1.91 Å are shown contoured at 14 (purple cage) and 3 (green cage) for the heme iron and sulfur atom of Cys 75, respectively. The peak on the sulfur provides unambiguous confirmation on the correct orientation of the Cys 75 side chain. In going to the on state, one axial heme ligand must be displaced in order to allow CO to coordinate the heme iron. The N-Fe distance is 2.1 Å for both the His and Pro ligands with continuous electron density to the iron, so one bond cannot be judged to be more labile than the other based on the structure alone. Our model of the allosteric switch places the C helix of molecule B very close to the Pro in molecule A that coordinates heme B, suggesting that the allosteric switch involves displacement of the Pro ligand. However, if the entire heme were to move then it is possible that the Pro remains coordinated and that the His ligand is displaced. Our model cannot distinguish between these two possibilities.
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2000, 7, 876-880) copyright 2000.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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20544970 L.J.Smith, A.Kahraman, and J.M.Thornton (2010).
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Spectroscopic and computational investigation of three Cys-to-Ser mutants of nickel superoxide dismutase: insight into the roles played by the Cys2 and Cys6 active-site residues.
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20883501 S.Ukita, T.Fujii, D.Hira, T.Nishiyama, T.Kawase, C.T.Migita, and K.Furukawa (2010).
A heterodimeric cytochrome c complex with a very low redox potential from an anaerobic ammonium-oxidizing enrichment culture.
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20823675 T.Yamashita (2010).
[Recent studies on gas sensors, CooA, FixL, and Dos]
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Guanidine hydrochloride-induced unfolding of the three heme coordination states of the CO-sensing transcription factor, CooA.
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19415759 G.Giardina, S.Rinaldo, N.Castiglione, M.Caruso, and F.Cutruzzolà (2009).
A dramatic conformational rearrangement is necessary for the activation of DNR from Pseudomonas aeruginosa. Crystal structure of wild-type DNR.
  Proteins, 77, 174-180.
PDB code: 3dkw
19805344 H.Sharma, S.Yu, J.Kong, J.Wang, and T.A.Steitz (2009).
Structure of apo-CAP reveals that large conformational changes are necessary for DNA binding.
  Proc Natl Acad Sci U S A, 106, 16604-16609.
PDB codes: 3fwe 3hif
19319934 M.D.Suits, J.Lang, G.P.Pal, M.Couture, and Z.Jia (2009).
Structure and heme binding properties of Escherichia coli O157:H7 ChuX.
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PDB code: 2ovi
19477902 N.Castiglione, S.Rinaldo, G.Giardina, and F.Cutruzzolà (2009).
The transcription factor DNR from Pseudomonas aeruginosa specifically requires nitric oxide and haem for the activation of a target promoter in Escherichia coli.
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19359484 N.Popovych, S.R.Tzeng, M.Tonelli, R.H.Ebright, and C.G.Kalodimos (2009).
Structural basis for cAMP-mediated allosteric control of the catabolite activator protein.
  Proc Natl Acad Sci U S A, 106, 6927-6932.
PDB code: 2wc2
19239487 S.M.Techtmann, A.S.Colman, and F.T.Robb (2009).
'That which does not kill us only makes us stronger': the role of carbon monoxide in thermophilic microbial consortia.
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Posttranslational control of transcription factor FixK2, a key regulator for the Bradyrhizobium japonicum-soybean symbiosis.
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18945896 A.Bettencourt da Cruz, J.Wentzell, and D.Kretzschmar (2008).
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Molecular basis of halorespiration control by CprK, a CRP-FNR type transcriptional regulator.
  Mol Microbiol, 70, 151-167.
PDB codes: 3e5q 3e5u 3e5x 3e6b 3e6c 3e6d
18217776 C.Xu, M.Ibrahim, and T.G.Spiro (2008).
DFT analysis of axial and equatorial effects on heme-CO vibrational modes: applications to CooA and H-NOX heme sensor proteins.
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18575848 E.Oelgeschläger, and M.Rother (2008).
Carbon monoxide-dependent energy metabolism in anaerobic bacteria and archaea.
  Arch Microbiol, 190, 257-269.  
18672900 K.A.Marvin, R.L.Kerby, H.Youn, G.P.Roberts, and J.N.Burstyn (2008).
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  Biochemistry, 47, 9016-9028.  
18326575 R.L.Kerby, H.Youn, and G.P.Roberts (2008).
RcoM: a new single-component transcriptional regulator of CO metabolism in bacteria.
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18688409 S.Aono (2008).
Metal-containing sensor proteins sensing diatomic gas molecules.
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17350996 B.M.Leu, N.J.Silvernail, M.Z.Zgierski, G.R.Wyllie, M.K.Ellison, W.R.Scheidt, J.Zhao, W.Sturhahn, E.E.Alp, and J.T.Sage (2007).
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Crystal structure and function of the zinc uptake regulator FurB from Mycobacterium tuberculosis.
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PDB code: 2o03
17158453 H.Youn, R.L.Kerby, J.Koh, and G.P.Roberts (2007).
A C-helix residue, Arg-123, has important roles in both the active and inactive forms of the cAMP receptor protein.
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17267605 J.C.Crack, J.Green, M.R.Cheesman, N.E.Le Brun, and A.J.Thomson (2007).
Superoxide-mediated amplification of the oxygen-induced switch from [4Fe-4S] to [2Fe-2S] clusters in the transcriptional regulator FNR.
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17327664 M.Borjigin, H.Li, N.D.Lanz, R.L.Kerby, G.P.Roberts, and T.L.Poulos (2007).
Structure-based hypothesis on the activation of the CO-sensing transcription factor CooA.
  Acta Crystallogr D Biol Crystallogr, 63, 282-287.
PDB code: 2hkx
17720248 M.Ibrahim, M.Kuchinskas, H.Youn, R.L.Kerby, G.P.Roberts, T.L.Poulos, and T.G.Spiro (2007).
Mechanism of the CO-sensing heme protein CooA: new insights from the truncated heme domain and UVRR spectroscopy.
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Evolution of allostery in the cyclic nucleotide binding module.
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17082920 R.W.Clark, H.Youn, A.J.Lee, G.P.Roberts, and J.N.Burstyn (2007).
DNA binding by an imidazole-sensing CooA variant is dependent on the heme redox state.
  J Biol Inorg Chem, 12, 139-146.  
17534534 S.Schneider, J.Marles-Wright, K.H.Sharp, and M.Paoli (2007).
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Properties of an unusual heme cofactor in PLP-dependent cystathionine beta-synthase.
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17534526 T.L.Poulos (2007).
The Janus nature of heme.
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17602662 Y.Kamensky, W.Liu, A.L.Tsai, R.J.Kulmacz, and G.Palmer (2007).
Axial ligation and stoichiometry of heme centers in adrenal cytochrome b561.
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17387526 Y.Tong, and M.Guo (2007).
Cloning and characterization of a novel periplasmic heme-transport protein from the human pathogen Pseudomonas aeruginosa.
  J Biol Inorg Chem, 12, 735-750.  
  16682779 H.Komori, K.Satomoto, Y.Ueda, N.Shibata, S.Inagaki, S.Yoshioka, S.Aono, and Y.Higuchi (2006).
Crystallization and preliminary X-ray analysis of CooA from Carboxydothermus hydrogenoformans.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 471-473.  
16260780 H.Youn, R.L.Kerby, M.Conrad, and G.P.Roberts (2006).
Study of highly constitutively active mutants suggests how cAMP activates cAMP receptor protein.
  J Biol Chem, 281, 1119-1127.  
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.  
16959764 L.J.Moore, E.L.Mettert, and P.J.Kiley (2006).
Regulation of FNR dimerization by subunit charge repulsion.
  J Biol Chem, 281, 33268-33275.  
  16946467 M.Akif, Y.Akhter, S.E.Hasnain, and S.C.Mande (2006).
Crystallization and preliminary X-ray crystallographic studies of Mycobacterium tuberculosis CRP/FNR family transcription regulator.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 873-875.  
16803881 M.G.Joyce, C.Levy, K.Gábor, S.M.Pop, B.D.Biehl, T.I.Doukov, J.M.Ryter, H.Mazon, H.Smidt, R.H.van den Heuvel, S.W.Ragsdale, J.van der Oost, and D.Leys (2006).
CprK crystal structures reveal mechanism for transcriptional control of halorespiration.
  J Biol Chem, 281, 28318-28325.
PDB codes: 2h6b 2h6c
16873369 M.Ibrahim, R.L.Kerby, M.Puranik, I.H.Wasbotten, H.Youn, G.P.Roberts, and T.G.Spiro (2006).
Heme displacement mechanism of CooA activation: mutational and Raman spectroscopic evidence.
  J Biol Chem, 281, 29165-29173.  
16439368 M.Kubo, S.Inagaki, S.Yoshioka, T.Uchida, Y.Mizutani, S.Aono, and T.Kitagawa (2006).
Evidence for displacements of the C-helix by CO ligation and DNA binding to CooA revealed by UV resonance Raman spectroscopy.
  J Biol Chem, 281, 11271-11278.  
16410360 R.W.Clark, N.D.Lanz, A.J.Lee, R.L.Kerby, G.P.Roberts, and J.N.Burstyn (2006).
Unexpected NO-dependent DNA binding by the CooA homolog from Carboxydothermus hydrogenoformans.
  Proc Natl Acad Sci U S A, 103, 891-896.  
16234920 H.E.Seward, H.M.Girvan, and A.W.Munro (2005).
Cytochrome P450s: creating novel ligand sets.
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15805503 H.Youn, M.V.Thorsteinsson, M.Conrad, R.L.Kerby, and G.P.Roberts (2005).
Dual roles of an E-helix residue, Glu167, in the transcriptional activator function of CooA.
  J Bacteriol, 187, 2573-2581.  
15613477 J.Yang, K.Ishimori, and M.R.O'Brian (2005).
Two heme binding sites are involved in the regulated degradation of the bacterial iron response regulator (Irr) protein.
  J Biol Chem, 280, 7671-7676.  
15882420 L.Rickman, C.Scott, D.M.Hunt, T.Hutchinson, M.C.Menéndez, R.Whalan, J.Hinds, M.J.Colston, J.Green, and R.S.Buxton (2005).
A member of the cAMP receptor protein family of transcription regulators in Mycobacterium tuberculosis is required for virulence in mice and controls transcription of the rpfA gene coding for a resuscitation promoting factor.
  Mol Microbiol, 56, 1274-1286.  
15813735 M.Eiting, G.Hagelüken, W.D.Schubert, and D.W.Heinz (2005).
The mutation G145S in PrfA, a key virulence regulator of Listeria monocytogenes, increases DNA-binding affinity by stabilizing the HTH motif.
  Mol Microbiol, 56, 433-446.
PDB codes: 2beo 2bgc
15537640 S.Inagaki, C.Masuda, T.Akaishi, H.Nakajima, S.Yoshioka, T.Ohta, B.Pal, T.Kitagawa, and S.Aono (2005).
Spectroscopic and redox properties of a CooA homologue from Carboxydothermus hydrogenoformans.
  J Biol Chem, 280, 3269-3274.  
15866917 S.Mesa, Z.Ucurum, H.Hennecke, and H.M.Fischer (2005).
Transcription activation in vitro by the Bradyrhizobium japonicum regulatory protein FixK2.
  J Bacteriol, 187, 3329-3338.  
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.  
15102444 C.L.Lawson, D.Swigon, K.S.Murakami, S.A.Darst, H.M.Berman, and R.H.Ebright (2004).
Catabolite activator protein: DNA binding and transcription activation.
  Curr Opin Struct Biol, 14, 10-20.  
15239054 D.D.Jones, and P.D.Barker (2004).
Design and characterisation of an artificial DNA-binding cytochrome.
  Chembiochem, 5, 964-971.  
  15548894 E.Nagababu, and J.M.Rifkind (2004).
Heme degradation by reactive oxygen species.
  Antioxid Redox Signal, 6, 967-978.  
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.  
14973040 H.Youn, R.L.Kerby, M.Conrad, and G.P.Roberts (2004).
Functionally critical elements of CooA-related CO sensors.
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14990568 M.Puranik, S.B.Nielsen, H.Youn, A.N.Hvitved, J.L.Bourassa, M.A.Case, C.Tengroth, G.Balakrishnan, M.V.Thorsteinsson, J.T.Groves, G.L.McLendon, G.P.Roberts, J.S.Olson, and T.G.Spiro (2004).
Dynamics of carbon monoxide binding to CooA.
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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
15026411 T.Yamashita, Y.Hoashi, K.Watanabe, Y.Tomisugi, Y.Ishikawa, and T.Uno (2004).
Roles of heme axial ligands in the regulation of CO binding to CooA.
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15326178 T.Yamashita, Y.Hoashi, Y.Tomisugi, Y.Ishikawa, and T.Uno (2004).
The C-helix in CooA rolls upon CO binding to ferrous heme.
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12529359 A.M.Gardner, C.R.Gessner, and P.R.Gardner (2003).
Regulation of the nitric oxide reduction operon (norRVW) in Escherichia coli. Role of NorR and sigma54 in the nitric oxide stress response.
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12796503 C.M.Coyle, M.Puranik, H.Youn, S.B.Nielsen, R.D.Williams, R.L.Kerby, G.P.Roberts, and T.G.Spiro (2003).
Activation mechanism of the CO sensor CooA. Mutational and resonance Raman spectroscopic studies.
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A globin in the nucleus!
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14638413 H.Körner, H.J.Sofia, and W.G.Zumft (2003).
Phylogeny of the bacterial superfamily of Crp-Fnr transcription regulators: exploiting the metabolic spectrum by controlling alternative gene programs.
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The role of the hydrophobic distal heme pocket of CooA in ligand sensing and response.
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Ligand binding dynamics to the heme domain of the oxygen sensor Dos from Escherichia coli.
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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.
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12446832 E.M.Dioum, J.Rutter, J.R.Tuckerman, G.Gonzalez, M.A.Gilles-Gonzalez, and S.L.McKnight (2002).
NPAS2: a gas-responsive transcription factor.
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12121986 H.Youn, R.L.Kerby, M.V.Thorsteinsson, R.W.Clark, J.N.Burstyn, and G.P.Roberts (2002).
Analysis of the L116K variant of CooA, the heme-containing CO sensor, suggests the presence of an unusual heme ligand resulting in novel activity.
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11839496 J.L.Huffman, and R.G.Brennan (2002).
Prokaryotic transcription regulators: more than just the helix-turn-helix motif.
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12042067 M.Paoli, J.Marles-Wright, and A.Smith (2002).
Structure-function relationships in heme-proteins.
  DNA Cell Biol, 21, 271-280.  
12411478 V.A.Bamford, S.Bruno, T.Rasmussen, C.Appia-Ayme, M.R.Cheesman, B.C.Berks, and A.M.Hemmings (2002).
Structural basis for the oxidation of thiosulfate by a sulfur cycle enzyme.
  EMBO J, 21, 5599-5610.
PDB codes: 1h31 1h32 1h33
11296236 D.M.van Aalten, C.C.DiRusso, and J.Knudsen (2001).
The structural basis of acyl coenzyme A-dependent regulation of the transcription factor FadR.
  EMBO J, 20, 2041-2050.
PDB codes: 1h9g 1h9t
11551932 H.Youn, R.L.Kerby, M.V.Thorsteinsson, M.Conrad, C.R.Staples, J.Serate, J.Beack, and G.P.Roberts (2001).
The heme pocket afforded by Gly117 is crucial for proper heme ligation and activity of CooA.
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11343786 J.G.Harman (2001).
Allosteric regulation of the cAMP receptor protein.
  Biochim Biophys Acta, 1547, 1.  
11522788 J.Leduc, M.V.Thorsteinsson, T.Gaal, and G.P.Roberts (2001).
Mapping CooA.RNA polymerase interactions. Identification of activating regions 2 and 3 in CooA, the co-sensing transcriptional activator.
  J Biol Chem, 276, 39968-39973.  
11282350 M.K.Chan (2001).
Recent advances in heme-protein sensors.
  Curr Opin Chem Biol, 5, 216-222.  
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.