Crystal structure at 2.4 A resolution of Borrelia burgdorferi inosine 5'-monophosphate dehydrogenase: evidence of a substrate-induced hinged-lid motion by loop 6.
The conversion of inosine 5'-monophosphate (IMP) to xanthosine 5'-monophosphate (XMP) is the committed and rate-limiting reaction in de novo guanine nucleotide biosynthesis. Inosine 5'- monophosphate dehydrogenase (IMPDH) is the enzyme that catalyzes the oxidation of IMP to XMP with the concomitant reduction of nicotinamide adenine dinucleotide (from NAD(+) to NADH). Because of its critical role in purine biosynthesis, IMPDH is a drug design target for anticancer, antiinfective, and immunosuppressive chemotherapy. We have determined the crystal structure of IMPDH from Borrelia burgdorferi, the bacterial spirochete that causes Lyme disease, with a sulfate ion bound in the IMP phosphate binding site. This is the first structure of IMPDH in the absence of substrate or cofactor where the active-site loop (loop 6), which contains the essential catalytic residue Cys 229, is clearly defined in the electron density. We report that a seven residue region of loop 6, including Cys229, is tilted more than 6 A away from its position in substrate- or substrate analogue-bound structures of IMPDH, suggestive of a conformational change. The location of this loop between beta6 and alpha6 links IMPDH to a family of beta/alpha barrel enzymes known to utilize this loop as a functional lid during catalysis. Least-squares minimization, root-mean-square deviation analysis, and inspection of the molecular surface of the loop 6 region in the substrate-free B. burgdorferi IMPDH and XMP-bound Chinese hamster IMPDH show that loop 6 follows a similar pattern of hinged rigid-body motion and indicates that IMPDH may be using loop 6 to bind and sequester substrate and to recruit an essential catalytic residue.
McMillan
F M
FM
The Rosenstiel Basic Medical Sciences Research Center and Department of Biochemistry, Brandeis University, Waltham, Massachussetts 02454, USA.
Cahoon
M
M
White
A
A
Hedstrom
L
L
Petsko
G A
GA
Ringe
D
D
D000595:Amino Acid Sequence; D000818:Animals; D001665:Binding Sites; D015748:Borrelia burgdorferi Group / Q000201:enzymology*; D020134:Catalytic Domain; D018360:Crystallography, X-Ray; D003545:Cysteine / Q000737:chemistry / Q000378:metabolism; D015195:Drug Design; D006801:Humans; D007168:IMP Dehydrogenase / Q000737:chemistry* / Q000378:metabolism*; D007291:Inosine Monophosphate / Q000378:metabolism; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009038:Motion; D009243:NAD / Q000378:metabolism; D018583:Pliability; D011487:Protein Conformation; D012265:Ribonucleotides / Q000378:metabolism; D016415:Sequence Alignment; D012997:Solvents; D055672:Static Electricity; D013329:Structure-Activity Relationship; D013431:Sulfates / Q000378:metabolism; D019820:Xanthine
D012265:Ribonucleotides; D012997:Solvents; D013431:Sulfates; D009243:NAD; D007291:Inosine Monophosphate; D019820:Xanthine; C011141:xanthosine monophosphate; D007168:IMP Dehydrogenase; D003545:Cysteine