Crystal structure of liganded rat peroxisomal multifunctional enzyme type 1: a flexible molecule with two interconnected active sites.
The crystal structure of the full-length rat peroxisomal multifunctional enzyme, type 1 (rpMFE1), has been determined at 2.8 A resolution. This enzyme has three catalytic activities and two active sites. The N-terminal part has the crotonase fold, which builds the active site for the Delta(3),Delta(2)-enoyl-CoA isomerase and the Delta(2)-enoyl-CoA hydratase-1 catalytic activities, and the C-terminal part has the (3S)-hydroxyacyl-CoA dehydrogenase fold and makes the (3S)-hydroxyacyl-CoA dehydrogenase active site. rpMFE1 is a multidomain protein having five domains (A-E). The crystal structure of full-length rpMFE1 shows a flexible arrangement of the A-domain with respect to the B-E-domains. Because of a hinge region near the end of the A-domain, two different positions of the A-domain were observed for the two protein molecules (A and B) of the asymmetric unit. In the most closed conformation, the mode of binding of CoA is stabilized by domains A and B (helix-10), as seen in other crotonase fold members. Domain B, although functionally belonging to the N-terminal part, is found tightly associated with the C-terminal part, i.e. fixed to the E-domain. The two active sites of rpMFE1 are approximately 40 A apart, separated by a tunnel, characterized by an excess of positively charged side chains. Comparison of the structures of rpMFE1 with the monofunctional crotonase and (3S)-hydroxyacyl-CoA dehydrogenase superfamily enzymes, as well as with the bacterial alpha(2)beta(2)-fatty acid oxidation multienzyme complex, reveals that this tunnel could be important for substrate channeling, as observed earlier on the basis of the kinetics of rpMFE1 purified from rat liver.
Kasaragod
Prasad
P
Biocenter Oulu and Department of Biochemistry, University of Oulu, FI-90014 Oulu, Finland.
Venkatesan
Rajaram
R
Kiema
Tiila R
TR
Hiltunen
J Kalervo
JK
Wierenga
Rik K
RK
D000595:Amino Acid Sequence; D000818:Animals; D020134:Catalytic Domain; D018360:Crystallography, X-Ray / Q000379:methods*; D004926:Escherichia coli / Q000201:enzymology; D005227:Fatty Acids / Q000737:chemistry; D007700:Kinetics; D008099:Liver / Q000201:enzymology; D008969:Molecular Sequence Data; D009097:Multienzyme Complexes / Q000737:chemistry*; D010100:Oxygen / Q000737:chemistry; D020675:Peroxisomes / Q000378:metabolism*; D011487:Protein Conformation; D017510:Protein Folding; D051381:Rats
C508129:Ehhadh protein, rat; D005227:Fatty Acids; D009097:Multienzyme Complexes; D010100:Oxygen
Bioinformatics. 2007 Nov 1;23(21):2947-8
17846036
Biochemistry. 1999 Mar 9;38(10):2991-9
10074351
J Biol Chem. 1998 Nov 20;273(47):31366-74
9813046
J Biol Chem. 2003 Aug 1;278(31):28901-11
12754260
Curr Opin Struct Biol. 2005 Dec;15(6):621-8
16263264
J Biol Chem. 1999 Apr 30;274(18):12193-6
10212181
J Mol Biol. 1996 Sep 27;262(3):370-4
8845002
J Mol Biol. 2006 Jan 27;355(4):734-46
16330050
Acta Crystallogr D Biol Crystallogr. 2005 Apr;61(Pt 4):458-64
15805601
Acc Chem Res. 2001 Feb;34(2):145-57
11263873
J Biol Chem. 1998 Jan 2;273(1):349-55
9417087
Acta Crystallogr D Biol Crystallogr. 2004 Dec;60(Pt 12 Pt 1):2256-68
15572779
J Biol Chem. 1986 Nov 25;261(33):15390-5
3536901
J Biol Chem. 1990 Feb 15;265(5):2446-9
2303409
Acta Crystallogr D Biol Crystallogr. 2006 Jan;62(Pt 1):72-82
16369096
J Mol Biol. 1998 Feb 6;275(5):847-59
9480773
Curr Opin Struct Biol. 1998 Dec;8(6):679-85
9914247
Acta Crystallogr D Biol Crystallogr. 1997 May 1;53(Pt 3):240-55
15299926
Nucleic Acids Res. 2007 Jul;35(Web Server issue):W375-83
17452350
Biochem J. 2002 Oct 15;367(Pt 2):433-41
12106015
EMBO J. 1996 Oct 1;15(19):5135-45
8895557
EMBO J. 2004 Jul 21;23(14):2745-54
15229654
Biochem Biophys Res Commun. 1996 Apr 16;221(2):271-8
8619845
Structure. 1998 Aug 15;6(8):957-70
9739087
FEBS Lett. 2004 Jan 16;557(1-3):81-7
14741345
J Biol Chem. 1991 Jun 15;266(17):10750-3
2040594
J Lipid Res. 2004 Jun;45(6):1104-11
15060085
J Mol Biol. 2004 Sep 24;342(4):1197-208
15351645
J Biol Chem. 2002 Mar 15;277(11):9127-32
11781327
Biochemistry. 1999 Jul 20;38(29):9508-16
10413528
J Biol Chem. 2000 Sep 1;275(35):27186-96
10840044
J Biol Chem. 1988 Nov 25;263(33):17857-71
3053720
Biochim Biophys Acta. 2008 Aug;1781(8):400-5
18619556
Biochemistry. 2002 Feb 26;41(8):2621-9
11851409
Acta Crystallogr D Biol Crystallogr. 2004 Dec;60(Pt 12 Pt 1):2126-32
15572765
Acc Chem Res. 2003 Jul;36(7):539-48
12859215
Hum Mol Genet. 2004 May 1;13(9):955-65
15016763
Proc Natl Acad Sci U S A. 2003 Jun 10;100(12):6992-7
12764229
Biochim Biophys Acta. 2000 Apr 12;1484(2-3):117-28
10760462
Structure. 2006 Feb;14(2):237-46
16472743
Protein Sci. 1999 Oct;8(10):2010-8
10548046
Cell Mol Life Sci. 2008 Aug;65(16):2507-27
18470480
Acta Crystallogr D Biol Crystallogr. 2002 Apr;58(Pt 4):690-3
11914498
Steroids. 2001 Feb;66(2):107-14
11146090