3
Crystal structure of quinone-dependent alcohol
dehydrogenase from Pseudogluconobacter
saccharoketogenes
4
A versatile dehydrogenase oxidizing alcohols and carbohydrates
1
2
5
6
Henriëtte J. Rozeboom1, Shukun Yu2*, Rene Mikkelsen2; Igor Nikolaev3; Harm J. Mulder3 and
7
Bauke W. Dijkstra*1
8
9
1
Laboratory of Biophysical Chemistry, Groningen Biomolecular Sciences and Biotechnology
10
Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
11
2
12
and 3Archimedesweg 30, 2333 CN Leiden, The Netherlands
13
*
14
e-mail: b.w.dijkstra@rug.nl Phone +31 50 363 4381 / 4378, Fax +31 50 363 4800 or
15
shukun.yu@dupont.com
16
Running title: structure of quinone-dependent alcohol dehydrogenase
DuPont Industrial Biosciences, Edwin Rahrs Vej 38, DK 8220 Brabrand, Aarhus, Denmark
To whom correspondence may be addressed:
17
18
1
1
Figure S1 Multiple sequence alignment. Structure–based alignment of PQQ-ADH from
2
Pseudogluconobacter saccharoketogenes IFO 14464 (4CVB), L-sorbose dehydrogenase SDH
3
from Ketogulonicigenium vulgare
4
ADHIIG (1YIQ)2 and ADHIIB (1KV9)3 from Pseudomonas putida HK5, QH-ADH from
5
Comamonas testosteroni (1KB0)4, QADH from Pseudomonas aeruginosa (1FLG)5 and MDH
6
from Methylacidiphilum fumariolicum SolV (4MAE)6, Methylococcus capsulatus (4TQO)7
7
Methylobacterium extorquens (1W6S) 8, Hyphomicrobium denitrificans (2D0V)9 Paracoccus
8
denitrificans (1LRW)
9
made with Promals3D 12. The secondary structure elements above the sequence alignment are
10
those obtained from the crystal structure of PQQ-ADH. Residues involved in Ca2+ binding
11
have a purple background color, identical residues have a red background color and similar
12
residues have a red color. Residues indicated with blue stars below the sequences are PQQ
13
ligands and with grey stars above the sequence have alternate conformations. The vicinal
14
disulfide bridge has a cyan background. Green boxes indicate the tryptophan docking motifs.
15
Disulfide linkages are indicated in green italics below the sequences. Residues not in the
16
model of SDH are colored orange. The figure was created with ESPript 13.
17
Figure S2 Overlay of the structures of PQQ-ADH with calcium and zinc bound in the
18
active site. In green the structure is shown with calcium and in cyan with zinc bound. The
19
calcium ion is shown as a green sphere and the zinc ion as a brown sphere.
20
Figure S3 Stereo image overlay of the structures of PQQ-ADH (in green) and QH-ADH
21
(in magenta). The PQQ cofactor is shown in grey sticks and the heme cofactor in yellow
22
sticks. Cytochrome c551 from (PDB ID 351C)
23
extorquens (PDB ID 2CS8) 15 superposed on the cytochrome domain of QH-ADH are shown
24
in cyan and blue respectively.
10
(4MH1)1, quinohemoprotein alcohol dehydrogenases
and Methylophilus W3A1 (4AAH)11. The structural alignment was
14
and cytochrome cL from Methylobacterium
25
2
1
References
2
1. Han X, Xiong X, Jiang D, Chen S, Huang E, Zhang W, Liu X (2014) Crystal structure of L-sorbose
3
dehydrogenase, a pyrroloquinoline quinone-dependent enzyme with homodimeric assembly, from
4
Ketogulonicigenium vulgare. Biotechnol Lett 36:1001-1008.
5
2. Toyama H, Chen ZW, Fukumoto M, Adachi O, Matsushita K, Mathews FS (2005) Molecular
6
cloning and structural analysis of quinohemoprotein alcohol dehydrogenase ADH-IIG from
7
Pseudomonas putida HK5. J Mol Biol 352:91-104.
8
3. Chen ZW, Matsushita K, Yamashita T, Fujii TA, Toyama H, Adachi O, Bellamy HD, Mathews FS
9
(2002) Structure at 1.9 A resolution of a quinohemoprotein alcohol dehydrogenase from Pseudomonas
10
putida HK5. Structure 10:837-849.
11
4. Oubrie A, Rozeboom HJ, Kalk KH, Huizinga EG, Dijkstra BW (2002) Crystal structure of
12
quinohemoprotein alcohol dehydrogenase from Comamonas testosteroni - Structural basis for
13
substrate oxidation and electron transfer. J Biol Chem 277:3727-3732.
14
5. Keitel T, Diehl A, Knaute T, Stezowski JJ, Hohne W, Gorisch H (2000) X-ray structure of the
15
quinoprotein ethanol dehydrogenase from Pseudomonas aeruginosa: Basis of substrate specificity. J
16
Mol Biol 297:961-974.
17
6. Pol A, Barends TR, Dietl A, Khadem AF, Eygensteyn J, Jetten MS, Op den Camp HJ (2014) Rare
18
earth metals are essential for methanotrophic life in volcanic mudpots. Environ Microbiol 16:255-264.
19
7. Culpepper MA, Rosenzweig AC (2014) Structure and Protein-Protein Interactions of Methanol
20
Dehydrogenase from Methylococcus capsulatus (Bath). Biochemistry (N Y ) 53:6211-6219.
21
8. Williams PA, Coates L, Mohammed F, Gill R, Erskine PT, Coker A, Wood SP, Anthony C, Cooper
22
JB (2005) The atomic resolution structure of methanol dehydrogenase from Methylobacterium
23
extorquens. Acta Crystallogr D 61:75-79.
24
9. Nojiri M, Hira D, Yamaguchi K, Okajima T, Tanizawa K, Suzuki S (2006) Crystal structures of
25
cytochrome cL and methanol dehydrogenase from Hyphomicrobium denitrificans: structural and
26
mechanistic insights into interactions between the two proteins. Biochemistry 45:3481-3492.
27
10. Xia ZX, He YN, Dai WW, White SA, Boyd GD, Mathews FS (1999) Detailed active site
28
configuration of a new crystal form of methanol dehydrogenase from Methylophilus W3A1 at 1.9 A
3
1
resolution. Biochemistry-Us 38:1214-1220.
2
11. Li J, Gan JH, Mathews FS, Xia ZX (2011) The enzymatic reaction-induced configuration change
3
of the prosthetic group PQQ of methanol dehydrogenase. Biochem Biophys Res Commun 406:621-
4
626.
5
12. Pei J, Tang M, Grishin NV (2008) PROMALS3D web server for accurate multiple protein
6
sequence and structure alignments. Nucleic Acids Res 36:W30-4.
7
13. Gouet P, Courcelle E, Stuart DI, Metoz F (1999) ESPript: analysis of multiple sequence
8
alignments in PostScript. Bioinformatics 15:305-308.
9
14. Matsuura Y, Takano T, Dickerson R (1982) Structure of Cytochrome-C551 from Pseudomonas-
10
Aeruginosa Refined at 1.6 a Resolution and Comparison of the 2 Redox Forms. J Mol Biol 156:389-
11
409.
12
15. Williams P, Coates L, Mohammed F, Gill R, Erskine P, Bourgeois D, Wood S, Anthony C, Cooper
13
J (2006) The 1.6 angstrom X-ray structure of the unusual c-type cytochrome, cytochrome c(L), from
14
the methylotrophic bacterium Methylobacterium extorquens. J Mol Biol 357:151-162.
15
4