Structural Information on IDH

This page was created for an undergraduate Molecular Biology course at Davidson College.

This page utilizes Chime and/or RasMol. Get RasMol here.

All images were obtained at NCBI Structure Group

The images below are of IDH and IDP proteins. Many of the abstracts associated with these images do not specify which subunit of the IDH protein complex is being shown (IDH1 vs IDH2, etc). For this reason I'll provide a link to all IDH nucleotide and amino acid sequences. It can be inferred whether or not we are looking at an IDH or IDP based on the NAD+ vs NADP+ coenzyme binding. Refresh your memory here. Many of these images are a series of mutants used in experiments pertaining to substrate binding. For those shown in sequence it is particularly effective to zoom in on the binding sites, note the subtle structural changes made by the scientists, then note the differential substrate binding. This provides an elegant example of the form equals function relationship.

Chime 1

Figure 1: Crystal Structure Of Isocitrate Dehydrogenase Mutant K230m Bound To Isocitrate And Mn2+

Figure 2: Crystal Structure Of K230m Isocitrate Dehydrogenase In Complex With Alpha- Ketoglutarate

Read the abstract:

Lee ME, Dyer DH, Klein OD, Bolduc JM, Stoddard BL, Koshland DE Jr. Mutational analysis of the catalytic residues lysine 230 and tyrosine 160 in the NADP(+)-dependent isocitrate dehydrogenase from Escherichia coli. Biochemistry 1995 Jan 10;34(1):378-84

Chime 2

Figure 3: Crystal Structure Of Isocitrate Dehydrogenase From Bacillus Subtilis

Read the abstract

Singh SK, Matsuno K, LaPorte DC, Banaszak LJ. Crystal structure of Bacillus subtilis isocitrate dehydrogenase at 1.55 A. Insights into the nature of substrate specificity exhibited by Escherichia coli isocitrate dehydrogenase kinase/phosphatase. Singh SK, Matsuno K, LaPorte DC, Banaszak LJ.J Biol Chem 2001 Jul 13;276(28):26154-63

Chime 3

Figure 4: Isocitrate Dehydrogenase S113e Mutant Complexed With Isopropylmalate, Nadp+ And Magnesium (Flash-Cooled)

Read the abstract:

Doyle SA, Beernink PT, Koshland DE Jr. Structural basis for a change in substrate specificity: crystal structure of S113E isocitrate dehydrogenase in a complex with isopropylmalate, Mg2+, and NADP. Biochemistry 2001 Apr 10;40(14):4234-41

Chime 4

Figure 5: Isocitrate Dehydrogenase From E.Coli (Mutant K230m), Steady-State Intermediate Complex Determined By Laue Crystallography

Read the abstract:

Bolduc JM, Dyer DH, Scott WG, Singer P, Sweet RM, Koshland DE Jr, Stoddard BL. Mutagenesis and Laue structures of enzyme intermediates: isocitrate dehydrogenase. Science 1995 Jun 2;268(5215):1312-8

Chime 5

This is a cool paper about switching the coenzyme specificity an IDH from NADP+ to NAD+. They are using E. coli but do not mention in the abstract which IDH specific IDH gene they are manipulating; however, based on our previous Web Project we know which IDH genes interact with which coenyzme. It therefore seems that they are starting with an IDP ortholog.

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Figures:

6)Isocitrate Dehydrogenase Complexed With Isocitrate, Nadp+, And Calcium (Flash-Cooled)

7) Orbital Steering In The Catalytic Power Of Enzymes: Small Structural Changes With Large Catalytic Consequences

8) Isocitrate Dehydrogenase: Structure Of An Engineered Nadp+ --> Nad+ Specificity-Reversal Mutant

I recomend not rotating the 3 above images, changing the color to Chain, then observing the different coenzyme used by the protiens (it will appear red and the IDH will be blue)

Check out abstract:

Hurley JH, Chen R, Dean AM. Determinants of cofactor specificity in isocitrate dehydrogenase: structure of an engineered NADP+ --> NAD+ specificity-reversal mutant. Biochemistry 1996 May 7;35(18):5670-8

Chime 6

Here is another cool paper that explores in E. coli the structural compents of IDH. In this case a point mutation led to a water molecule replacing an amine of lysine in the active of IDH. This change suggests that this portion of the protein plays a role in catalysis.

Figure 9: Mutant: Crystal Structure Of Isocitrate Dehydrogenase Mutant K230m Bound To Isocitrate And Mn2+

Figure 10: WT: Low Temperature Structure Of Wild-Type Idh Complexed With Mg-Isocitrate

Check out abstract:

Cherbavaz DB, Lee ME, Stroud RM, Koshland DE Jr. Active site water molecules revealed in the 2.1 A resolution structure of a site-directed mutant of isocitrate dehydrogenase. J Mol Biol 2000 Jan 21;295(3):377-85

Chime 7

Figure 11: Isocitrate Dehydrogenase (E.C.1.1.1.42)

Read the abstract:

Hurley JH, Thorsness PE, Ramalingam V, Helmers NH, Koshland DE Jr, Stroud RM. Structure of a bacterial enzyme regulated by phosphorylation, isocitrate dehydrogenase. Proc Natl Acad Sci U S A 1989 Nov;86(22):8635-9

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