PDBsum entry 2vfs

Oxidoreductase

PDB id

2vfs

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Contents

			Protein chain

					414 a.a. *

			Ligands

					FAD


					XYL

			Metals

					_CL

			Waters ×356

* Residue conservation analysis

PDB id:

2vfs

Links

Name:

Oxidoreductase

Title:

Alditol oxidase from streptomyces coelicolor a3(2): complex with xylitol

Structure:

Xylitol oxidase. Chain: a. Synonym: alditol oxidase. Engineered: yes

Source:

Streptomyces coelicolor. Organism_taxid: 100226. Strain: a3(2). Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.60Å

R-factor:

0.175

R-free:

0.211

Authors:

F.Forneris,A.Mattevi

Key ref:

F.Forneris et al. (2008). Structural analysis of the catalytic mechanism and stereoselectivity in Streptomyces coelicolor alditol oxidase. Biochemistry, 47, 978-985. PubMed id: 18154360

Date:

05-Nov-07

Release date:

08-Jan-08

PROCHECK

	Headers

	References

Protein chain

Q9ZBU1 (XYOA_STRCO) - Alditol oxidase from Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145)

Seq: Struc:					418 a.a. 414 a.a.

Key:

PfamA domain

Secondary structure

CATH domain



		Enzyme reactions

Enzyme class:

E.C.1.1.3.41 - alditol oxidase.

[IntEnz] [ExPASy] [KEGG] [BRENDA]

Reaction:

an alditol + O2 = an aldose + H2O2

alditol	+	O2	=	aldose	+	H2O2

Cofactor:

FAD

FAD
Bound ligand (Het Group name = FAD) corresponds exactly

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

	Biochemistry 47:978-985 (2008)
PubMed id: 18154360

Structural analysis of the catalytic mechanism and stereoselectivity in Streptomyces coelicolor alditol oxidase.
F.Forneris, D.P.Heuts, M.Delvecchio, S.Rovida, M.W.Fraaije, A.Mattevi.

ABSTRACT

Alditol oxidase (AldO) from Streptomyces coelicolor A3(2) is a soluble monomeric flavin-dependent oxidase that performs selective oxidation of the terminal primary hydroxyl group of several alditols. Here, we report the crystal structure of the recombinant enzyme in its native state and in complex with both six-carbon (mannitol and sorbitol) and five-carbon substrates (xylitol). AldO shares the same folding topology of the members of the vanillyl-alcohol oxidase family of flavoenzymes and exhibits a covalently linked FAD which is located at the bottom of a funnel-shaped pocket that forms the active site. The high resolution of the three-dimensional structures highlights a well-defined hydrogen-bonding network that tightly constrains the substrate in the productive conformation for catalysis. Substrate binding occurs through a lock-and-key mechanism and does not induce conformational changes with respect to the ligand-free protein. A network of charged residues is proposed to favor catalysis through stabilization of the deprotonated form of the substrate. A His side chain acts as back door that "pushes" the substrate-reactive carbon atom toward the N5-C4a locus of the flavin. Analysis of the three-dimensional structure reveals possible pathways for diffusion of molecular oxygen and a small cavity on the re side of the flavin that may host oxygen during FAD reoxidation. These features combined with the tight shape of the catalytic site provide insights into the mechanism of AldO-mediated regioselective oxidation reactions and its substrate specificity.

Literature references that cite this PDB file's key reference

PubMed id

Reference

21182588

E.Rosini, G.Molla, S.Ghisla, and L.Pollegioni (2011).
On the reaction of D-amino acid oxidase with dioxygen: O2 diffusion pathways and enhancement of reactivity.

FEBS J, 278, 482-492.

21383134

G.Kachalova, K.Decker, A.Holt, and H.D.Bartunik (2011).
Crystallographic snapshots of the complete reaction cycle of nicotine degradation by an amine oxidase of the monoamine oxidase (MAO) family.

Proc Natl Acad Sci U S A, 108, 4800-4805.

PDB code:

3ng7

20944214

G.W.Han, C.Bakolitsa, M.D.Miller, A.Kumar, D.Carlton, R.J.Najmanovich, P.Abdubek, T.Astakhova, H.L.Axelrod, C.Chen, H.J.Chiu, T.Clayton, D.Das, M.C.Deller, L.Duan, D.Ernst, J.Feuerhelm, J.C.Grant, A.Grzechnik, L.Jaroszewski, K.K.Jin, H.A.Johnson, H.E.Klock, M.W.Knuth, P.Kozbial, S.S.Krishna, D.Marciano, D.McMullan, A.T.Morse, E.Nigoghossian, L.Okach, R.Reyes, C.L.Rife, N.Sefcovic, H.J.Tien, C.B.Trame, H.van den Bedem, D.Weekes, Q.Xu, K.O.Hodgson, J.Wooley, M.A.Elsliger, A.M.Deacon, A.Godzik, S.A.Lesley, and I.A.Wilson (2010).
Structures of the first representatives of Pfam family PF06938 (DUF1285) reveal a new fold with repeated structural motifs and possible involvement in signal transduction.

Acta Crystallogr Sect F Struct Biol Cryst Commun, 66, 1218-1225.

PDB codes:

2ra9 2re3

19438712

D.P.Heuts, N.S.Scrutton, W.S.McIntire, and M.W.Fraaije (2009).
What's in a covalent bond? On the role and formation of covalently bound flavin cofactors.

FEBS J, 276, 3405-3427.

19224207

E.van Bloois, R.T.Winter, D.B.Janssen, and M.W.Fraaije (2009).
Export of functional Streptomyces coelicolor alditol oxidase to the periplasm or cell surface of Escherichia coli and its application in whole-cell biocatalysis.

Appl Microbiol Biotechnol, 83, 679-687.

19088070

N.G.Leferink, M.W.Fraaije, H.J.Joosten, P.J.Schaap, A.Mattevi, and W.J.van Berkel (2009).
Identification of a gatekeeper residue that prevents dehydrogenases from acting as oxidases.

J Biol Chem, 284, 4392-4397.

19541622

R.Baron, C.Riley, P.Chenprakhon, K.Thotsaporn, R.T.Winter, A.Alfieri, F.Forneris, W.J.van Berkel, P.Chaiyen, M.W.Fraaije, A.Mattevi, and J.A.McCammon (2009).
Multiple pathways guide oxygen diffusion into flavoenzyme active sites.

Proc Natl Acad Sci U S A, 106, 10603-10608.

18693755

G.Zhao, R.C.Bruckner, and M.S.Jorns (2008).
Identification of the oxygen activation site in monomeric sarcosine oxidase: role of Lys265 in catalysis.

Biochemistry, 47, 9124-9135.

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.