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[1] J A Morrissey, A Cockayne, P J Hill, P. Williams, Molecular cloning and analysis of a
13
putative siderophore ABC transporter from Staphylococcus aureus, Infect. Immun. 68
22
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(2000) 6281-6288.
[2] M L Cartron, S Maddocks, P Gillingham, C J Craven, S C Andrews, Feo-transport of
ferrous iron into bacteria, Biometals 19 (2006), 143-157.
[3] J Cao, M R Woodhall, J Alvarez, M L Cartron, S C Andrews, EfeUOB (YcdNOB) is a
tripartite, acid-induced and CpxAR-regulated, low-pH Fe2+ transporter that is cryptic in
Escherichia coli K-12 but functional in E. coli O157:H7, Mol. Microbiol. 65 (2007) 857-
875.
[4] X H Liu, Q Du, Z Wang, D Y Zhu, Y Huang, N Li, T D Wei, S J Xu, L C Gu, Crystal
structure and biochemical features of EfeB/YcdB from Escherichia coli O157: ASP235
10
plays divergent roles in different enzyme-catalyzed processes, J. Biol. Chem. 286 (2011)
11
14922-14931.
12
[5] M B Rajasekaran, S Nilapwar, S C Andrews, K A Watson, EfeO-cupredoxins: major
13
new members of the cupredoxin superfamily with roles in bacterial iron transport,
23
A Self-archived copy in
Kyoto University Research Information Repository
https://repository.kulib.kyoto-u.ac.jp
Biometals 23 (2010) 1-17.
[6] C Dennison, Investigating the structure and function of cupredoxins, Coordin. Chem.
Rev. 249 (2005) 3025-3054.
[7] B Fricke, O Parchmann, K Kruse, P Rucknagel A Schierhorn, S Menge,
Characterization and purification of an outer membrane metalloproteinase from
Pseudomonas aeruginosa with fibrinogenolytic activity, Biochim. Biophys. Acta 1454
(1999) 236-250.
[8] J He, A Ochiai, Y Fukuda, W Hashimoto, K Murata, A putative lipoprotein of
Sphingomonas sp. strain A1 binds alginate rather than a lipid moiety, FEMS Microbiol.
10
Lett. 288 (2008) 221-226.
11
[9] K Temtrirath, K Murata, W Hashimoto, Structural insights into alginate binding by
12
bacterial cell-surface protein, Carbohydr. Res. 404 (2015) 39-45.
13
[10] Y A Morch, I Donati, B L Strand, G Skjak-Braek, Effect of Ca2+, Ba2+, and Sr2+ on
24
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https://repository.kulib.kyoto-u.ac.jp
alginate microbeads, Biomacromolecules 7 (2006) 1471-1480.
[11] Z Otwinowski, W Minor, Processing of X-ray diffraction data collected in oscillation
mode, Methods Enzymol. 276 (1997) 307-326.
[12] W Kabsch, Xds, Acta Crystallogr. D Biol. Crystallogr. 66 (2010) 125-132.
[13] A Vagin, A Teplyakov, MOLREP: an automated program for molecular replacement,
J. App. Crystallogr. 30 (1997) 1022-1025.
[14] P D Adams, P V Afonine, G Bunkoczi, V B Chen, I W Davis, N Echols, J Headd, L W
Hung, G J Kapral, R W Grosse-Kunstleve, A J McCoy, N W Moriarty, R Oeffner, R J Read,
D C Richardson, J S Richardson, T C Terwilliger, P H Zwart, PHENIX: a comprehensive
10
Python-based system for macromolecular structure solution, Acta Crystallogr. D Biol.
11
Crystallogr. 66 (2010) 213-221.
12
[15] G N Murshudov, A Vagin, E J Dodson, Refinement of macromolecular structures by
13
the maximum-likelihood method, Acta Crystallogr. D Biol. Crystallogr. 53 (1997) 240-255.
25
A Self-archived copy in
Kyoto University Research Information Repository
https://repository.kulib.kyoto-u.ac.jp
[16] P Emsley, K Cowtan, Coot: model-building tools for molecular graphics, Acta
Crystallogr. D Biol. Crystallogr. 60 (2004) 2126-2132.
[17] L C Schrodinger, The PyMOL molecular graphics system, version 1.3. (2010).
[18] K Temtrirath, K Okumura, Y Maruyama, B Mikami, K Murata, K, W Hashimoto,
Binding mode of metal ions to the bacterial iron import protein EfeO. Biochem. Biophys.
Res. Commun. 493 (2017) 1095-1101.
[19] M Saito, D Horiguchi, K Kina, Spectrophotometric determination of traces of iron(II)
with novel water-soluble nitrosophenol derivatives. BUNSEKI KAGAKU 30 (1981) 525-
1931.
10
[20] Y Fu, H T Tsui, K E Bruce, L Sham, K A Higgins, J P Lisher, K M Kazmierczak, M J
11
Maroney, C E Dann, M E Winkler, D P Giedroc, A new structural paradigm in copper
12
resistance in Streptococcus pneumoniae. Nat. Chem. Biol. 9 (2013) 177-183.
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Figure legends
Fig. 1. EfeUOB cluster and structure/function of EfeB. (A) EfeUOB gene cluster in
Sphingomonas sp. strain A1. Cup and M75 represent cupredoxin and M75 peptidase domains,
respectively. (B) Crystal structure of strain A1 EfeB (cyan) was determined through molecular
replacement using the structure of E. coli EfeB (magenta) (PDB ID: 3O72). Green, blue, and
red in the stick model represent carbon, nitrogen, and oxygen atoms in a heme molecule. (C)
Heme-binding site in strain A1 EfeB. Green, cyan, blue, and red represent carbon in heme,
carbon in EfeB, nitrogen, and oxygen atoms, respectively. Gray and cyan spheres show O2 and
water molecules, respectively. Dotted lines show hydrogen bonds. (D) Peroxidase activity of
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strain A1 EfeB in the presence or absence of reducing agents.
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Fig. 2. Binding of rare earth element by and crystal structure of Algp7 (EfeOII). (A) DSF
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analysis of Algp7 (EfeOII) in the absence or presence of rare earth element (Sm3+). The curves
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show the negative derivative plot obtained from the fluorescence profile. Thermal shift to higher
temperature was observed in the presence of the rare earth element (Sm3+). (B) Structure of
Algp7 (EfeOII) was determined through molecular replacement using the previously clarified
structure of Algp7 (EfeOII) (PDB ID: 3AT7). Pink, Algp7 (EfeOII) determined here; blue, Algp7
(EfeOII) complexed with Cu2+ (PDB ID: 5Y4C). The right structure is rotated 90o toward the
reader relative to that of left. (C) Copper-binding site in Algp7 (EfeOII). Pink, carbon atoms of
Algp7 (EfeOII) determined here; blue, carbon atoms of Algp7 (EfeOII) complexed with Cu2+
(PDB ID: 5Y4C).
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Fig. 3. Crystal structure of EfeOI. (A) Left, overall structure of E. coli EfeOI. Red and yellow
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represent cupredoxin and M75 peptidase domains, respectively. Right, zinc bound (magenta) at
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the metal-binding site in the M75 peptidase domain of EfeOI. Water molecules are colored blue.
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Glu159 and Glu255 are disordered. The Phenix Polder omit map for zinc and ligated residues
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is shown with more than 3.5 σ. (B) Superimposition of the cupredoxin domain (red) of EfeOI
and CupA (cyan). (C) Superimposition of the M75 peptidase domain (yellow) of EfeOI and
Algp7 (EfeOII) (blue). Zinc bound to EfeOI and copper bound to Algp7 (EfeOII) are shown as
magenta and green spheres, respectively.
Fig. 4. Structural alignment of metal-binding sites in EfeO. (A) Three-dimensional arrangement
of site I (green) and II (yellow) residues in the cupredoxin domain (red) of EfeOI. (B) Multiple
sequence alignment of the EfeOI cupredoxin domain and other cupredoxin proteins. The residue
numberings for EfeOI are shown at the top. Site I (green), site II (yellow), copper binding site
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(cyan) residues. (C) Left, close-up site III (left, magenta colored) in EfeOI. Right, close-up
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metal-binding site in the M75 peptidase domain of EfeOI (yellow) and Algp7 (EfeOII) (blue).
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Zinc bound to EfeOI and copper bound to Algp7 (EfeOII) are shown as magenta and green
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spheres, respectively. (D) Multiple sequence alignment of M75 peptidase domain proteins
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(orange, EfeOI; cyan, EfeOII). The residue numberings for EfeOI are shown at the top. Site III
(magenta), metal-binding site residues (blue).
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Figure 1
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Figure 2
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Figure 3
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Figure 4
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Table S1. X-ray data collection and structure refinement statistics.
Data collection
Wavelength (Å)
Space group
Unit cell parameters (Å, °)
Resolution limit (Å)
Total reflections
Unique reflections
Completeness (%)
I/σ (I)
Rmerge (%)
CC(1/2)
Wilson B (Å )
Refinement
Resolution limit (Å)
R-factor (%)
Rfree (%)
Final model
r.m.s.d.
Bond (Å)
Angle (°)
Ramachandran plot (%)
Favored regions
Allowed regions
Outliers
Clashscore
Rotamer ouliers (%)
PDB ID
EfeB
Algp7 (EfeOII)
EfeOI
1.0000
P212121
a = 100.0, b = 105.0,
c = 83.8
1.0000
P212121
a = 52.8, b = 97.5,
c = 104.9
1.0000
C2
a = 139.9, b = 51.9,
c = 117.4
α= 90.0, β = 112.4, γ = 90.0
50.0 – 1.85 (1.96 – 1.85)
249,772 (33,933)
65,646 (9,994)
97.7 (92.8)
18.5 (2.48)
3.9 (40.0)
99.9 (91.8)
37.9
50.0 – 1.88 (1.91 – 1.88)
307,493 (14,878)
44,838 (2,188)
99.8 (99.3)
36.5 (5.3)
7.2 (48.3)
99.9 (95.7)
28.0
44.5 – 2.30 (2.36 – 2.30)
23.4 (24.8)
29.8 (36.0)
781 residues, 257 waters,
24 1,2-ethanediol,
1 oxygen molecule,
5 di (hydroxyethyl) ether,
3 triethylene glycol, 2
heme
46.5 – 1.88 (1.92 – 1.88)
18.2 (25.1)
21.8 (33.0)
502 residues, 421 waters,
9 1,2-ethanediol, 1 citrate
48.2 – 1.85 (1.87 – 1.85)
20.1 (34.0)
24.4 (37.3)
697 residues, 322 waters,
30 1,2-ethanediol,
1 acetate, 1 sulfate,
1 triethylene glycol,
1 zinc ion
0.008
0.971
0.01
1.47
0.006
0.806
96.0
3.5
0.5
0.63
6JBN
98.0
1.8
0.2
6JBO
98.1
1.7
0.14
5.85
2.5
7WGU
50.0 – 2.30 (2.44 – 2.30)
307,536 (50,278)
38,892 (6,217)
97.5 (97.9)
19.4 (10.2)
6.1 (14.8)
99.9 (99.7)
31.2
Data on highest shells are given in parenthesis.
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