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Butamax(TM) Advanced Biofuels LLC v. Gevo, Inc.

United States Court of Appeals, Federal Circuit

February 18, 2014

BUTAMAX(TM) ADVANCED BIOFUELS LLC, Plaintiff-Appellant,
v.
GEVO, INC., Defendant-Appellee

Petition for certiorari filed at, 04/22/2014

Page 1303

Appeal from the United States District Court for the District of Delaware in No. 11-CV-0054, Judge Sue L. Robinson.

LEORA BEN-AMI, Kirkland & Ellis, LLP, of New York, New York, argued for plaintiff-appellant. With her on the brief were THOMAS F. FLEMING, CHRISTOPHER T. JAGOE, and PETER B. SILVERMAN.

MICHELLE S. RHYU, Cooley, LLP, of Palo Alto, California, argued for defendant-appellee. With her on the brief were STEPHEN C. NEAL, BENJAMIN G. DAMSTEDT, DANIEL J. KNAUSS, of Palo Alto, California; and JAMES P. BROGAN, of Broomfield, Colorado.

Before RADER, Chief Judge, LINN, and WALLACH, Circuit Judges.

OPINION

Page 1304

Linn, Circuit Judge .

ButamaxTM Advanced Biofuels LLC (" Butamax" ) owns U.S. Pat. No. 7,851,188 (" '188 patent" ) and No. 7,993,889 (" '889 patent" ) (collectively, the " patents-in-suit" ) and appeals a final judgment entered against it following the district court's 1) claim construction and denial of Butamax's motion for summary judgment of literal infringement of the asserted claims of the '188 and '889 patents by Gevo, Inc. (" Gevo" ), 2) grant of Gevo's motion for summary judgment of noninfringement under the doctrine of equivalents of the asserted claims of the '188 and '889 patents, 3) grant of Gevo's motion for summary judgment of invalidity of claims 12 and 13 of the '889 patent for lack of written description, and 4) judgment of invalidity of claims 12 and 13 of the '889 patent for lack of enablement. Opinion, Butamax[TM] Advanced Biofuels LLC v. Gevo, Inc., 931 F.Supp.2d 589, 2013 WL 3914467 (D. Del. 2013) (" Opinion " ). Because the district court erred in its claim construction, this court vacates the district court's denial of Butamax's motion for summary judgment of infringement and its grant of Gevo's motion of noninfringement under the doctrine of equivalents. Because the district court failed to recognize the existence of genuine issues of material fact on Gevo's motion for summary judgment of invalidity as to claims 12 and 13 of the '889 patent, this court reverses the district court's grant of that motion. Finally, this court reverses the grant of summary judgment of invalidity for lack of enablement because that judgment appears to have been a scrivener's error.

I. Background

A. The '188 Patent

The '188 patent covers a recombinant microbial host cell that uses a particular biosynthetic pathway to produce isobutanol, which is useful as a fuel or fuel additive. Opinion, 931 F.Supp.2d 589, [WL] at *3. The claimed biosynthetic pathway comprises essentially five steps. See '188 Patent fig. 1.

Claim 1 of the '188 patent recites the first four steps:

1. A recombinant microbial host cell comprising heterologous DNA molecules encoding polypeptides that catalyze substrate to product conversions for each step below:

i) pyruvate to acetolactate;

ii) acetolactate to 2,3-dihydroxyisovalerate;

Page 1305

iii) 2,3-dihydroxyisovalerate to a-ketoisovalerate; and
iv) a-ketoisovalerate to isobutyraldehyde;
wherein said microbial host cell produces isobutanol; and wherein
a) the polypeptide that catalyzes a substrate to product conversion of pyruvate to acetolactate is acetolactate synthase having the EC number 2.2.1.6;
b) the polypeptide that catalyzes a substrate to product conversion of acetolactate to 2,3-dihydroxyisovalerate is acetohydroxy acid isomeroreductase having the EC number 1.1.1.86;
c) the polypeptide that catalyzes a substrate to product conversion of 2,3-dihydroxyisovalerate to a-ketoisovalerate is acetohydroxy acid dehydratase having the EC number 4.2.1.9;
d) the polypeptide that catalyzes a substrate to product conversion of a-ketoisovalerate to isobutyraldehyde is branched-chain a-keto acid decarboxylase having the EC number 4.1.1.72.

'188 Patent col. 335 ll. 21-44 (emphasis added). In the fifth step, isobutyraldehyde is converted into isobutanol. See '188 Patent col. 336 ll. 43-48 (dependent claim 18, reciting a method for producing isobutanol from the recombinant microbial host cell of claim 1).

Claim 15 depends from claim 1 and recites " [a] host cell according to claim 1 wherein the acetohydroxy acid isomeroreductase has an amino acid sequence selected from the group consisting of SEQ ID NO:43, SEQ ID NO:181, SEQ ID NO:183, and SEQ ID NO:185." '188 Patent col. 336 ll. 33-36. SEQ ID NO:183 is a sequence of Methanococcus .

This appeal primarily concerns step (ii): the conversion of acetolactate (" AL" ) to 2,3-dihydroxyisovalerate (" DHIV" ), catalyzed by the polypeptide enzyme acetohydroxy acid isomeroreductase (also known as keto-acid reductoisomerase, or " KARI" ) " having the EC number 1.1.1.86." KARI assists reactions by rearranging (i.e., isomerizing) a reagent and also by " reducing" (the process of adding electrons) this rearranged molecule. To accomplish the reduction, KARI needs a source for the added electrons. This electron source is known as the " cofactor" or " coenzyme." Two such cofactors are NADH (nicotinamide adenine dinucleotide hydrogen) and NADPH (nicotinamide adenine dinucleotide phosphate hydrogen).

The '188 patent's specification provides " definitions . . . to be used for the interpretation of the claims," including a definition of KARI:

an enzyme that catalyzes the conversion of acetolactate to 2,3-dihydroxyisovalerate using NADPH (reduced nicotinamide adenine dinucleotide phosphate) as an electron donor. Preferred acetohydroxy acid isomeroreductases are known by the EC number 1.1.1.86 and sequences are available from a vast array of microorganisms, including but not limited to . . . Methanococcus maripaludis . . . .

'188 Patent col. 7 ll. 35-47.

EC number 1.1.1.86, referenced in both this definition and claim 1, is an Enzyme Commission number for an enzyme known by the names KARI, " acetohydroxy acid isomeroreductase," and several other names. The EC enzyme classification system was developed in the 1950s to standardize enzyme nomenclature. Opinion, 931 F.Supp.2d 589, [WL] at *15. Notably, Rule 18 of the EC system states that " [f]or oxidoreductases using NAD or NADP [the oxidized states of NADH and NADPH, respectively], the

Page 1306

coenzyme should always be named as the acceptor" unless a certain exception applies, which is irrelevant here. Id. However, it also appears common to assign different EC numbers to the same enzyme, where the difference between the numbers is the identity of the cofactor named. 931 F.Supp.2d 589, Id. at 15 n.8. EC number 1.1.1.86 names only NADP as an acceptor, and neither party calls attention to another EC number for KARI naming any other cofactor as an acceptor.

Butamax alleges that Gevo infringes claim 1 of the '188 patent and claims 2-4, 13-15, 17, and 36 dependent therefrom, as well as claim 18 and claims 19-25, and 34-35 dependent therefrom.

B. The '889 Patent

The '889 patent issued from a divisional of the application from which the '188 patent issued. The patents' specifications largely are identical, each for example including the KARI definition quoted above. See '889 Patent col. 7 ll. 8-20. The '889 patent focuses on a method of producing isobutanol from a recombinant yeast microorganism that expresses the five-step biosynthetic pathway described above.

Claim 1 of the '889 patent states:

1. A method for producing isobutanol comprising;
a. providing a fermentation media comprising carbon substrate; and

b. contacting said media with a recombinant yeast microorganism expressing an engineered isobutanol biosynthetic pathway wherein said pathway comprises the following substrate to product conversions;

i. pyruvate to acetolactate (pathway step a);
ii. acetolactate to 2,3-dihydroxyisovalerate (pathway step b);
iii. 2,3-dihydroxyisovalerate to a-ketoisovalerate (pathway step c);
iv. a-ketoisovalerate to isobutyraldehyde (pathway step d); and
v. isobutyraldehyde to isobutanol (pathway step e);
and wherein
a) the substrate to product conversion of step (i) is performed by an acetolactate synthase enzyme;
b) the substrate to product conversion of step (ii) is performed by an acetohydroxy acid isomeroreductase enzyme;
c) the substrate to product conversion of step (iii) is performed by an acetohydroxy acid dehydratase enzyme;
d) the substrate to product conversion of step (iv) is performed by a decarboxylase enzyme; and
e) the substrate to product conversion of step (v) is performed by an alcohol ...

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