PDBsum entry 1s9c

Lyase

PDB id: 1s9c

Contents

Protein chains

248 a.a. *

271 a.a. *

276 a.a. *

250 a.a. *

255 a.a. *

256 a.a. *

Waters ×180

* Residue conservation analysis

PDB id:

1s9c

Name:

Lyase

Title:

Crystal structure analysis of the 2-enoyl-coa hydratase 2 domain of human peroxisomal multifunctional enzyme type 2

Structure:

Peroxisomal multifunctional enzyme type 2. Chain: a, b, c, d, e, f, g, h, i, j, k, l. Fragment: 2-enoyl-coenzyme a hydratase 2 domain. Synonym: mfe-2,d-bifunctional protein, dbp, 17-beta-hydroxysteroid dehydrogenase 4, 17-beta-hsd 4. Engineered: yes. Mutation: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: hsd17b4, edh17b4. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biol. unit:

Dimer (from PQS)

Resolution:

3.00Å R-factor: 0.229 R-free: 0.265

Authors:

M.K.Koski,A.M.Haapalainen,J.K.Hiltunen,T.Glumoff

Key ref:

K.M.Koski et al. (2005). Crystal structure of 2-enoyl-CoA hydratase 2 from human peroxisomal multifunctional enzyme type 2. J Mol Biol, 345, 1157-1169. PubMed id: 15644212 DOI: 10.1016/j.jmb.2004.11.009

Date:

04-Feb-04 Release date: 15-Feb-05

Protein chains

P51659  (DHB4_HUMAN) -  Peroxisomal multifunctional enzyme type 2 from Homo sapiens

Seq: 736 a.a.

Struc: 248 a.a.*

Protein chains

P51659  (DHB4_HUMAN) -  Peroxisomal multifunctional enzyme type 2 from Homo sapiens

Seq: 736 a.a.

Struc: 271 a.a.*

Protein chains

P51659  (DHB4_HUMAN) -  Peroxisomal multifunctional enzyme type 2 from Homo sapiens

Seq: 736 a.a.

Struc: 276 a.a.*

Protein chains

P51659  (DHB4_HUMAN) -  Peroxisomal multifunctional enzyme type 2 from Homo sapiens

Seq: 736 a.a.

Struc: 250 a.a.*

Protein chain

P51659  (DHB4_HUMAN) -  Peroxisomal multifunctional enzyme type 2 from Homo sapiens

Seq: 736 a.a.

Struc: 255 a.a.*

Protein chain

P51659  (DHB4_HUMAN) -  Peroxisomal multifunctional enzyme type 2 from Homo sapiens

Seq: 736 a.a.

Struc: 256 a.a.*

* PDB and UniProt seqs differ at 6 residue positions (black crosses)

Enzyme reactions

• Enzyme class 2: Chains A, B, C, D, E, F, G, H, I, J, K, L: E.C.1.1.1.n12 - ?????
• Enzyme class 3: Chains A, B, C, D, E, F, G, H, I, J, K, L: E.C.4.2.1.107 - 3alpha,7alpha,12alpha-trihydroxy-5beta-cholest-24-enoyl-CoA hydratase.
• Reaction: (24R,25R)-3alpha,7alpha,12alpha,24-tetrahydroxy-5beta-cholestan-26-oyl- CoA = (24E)-3alpha,7alpha,12alpha-trihydroxy-5beta-cholest-24-en-26-oyl- CoA + H2O
• Enzyme class 4: Chains A, B, C, D, E, F, G, H, I, J, K, L: E.C.4.2.1.119 - enoyl-CoA hydratase 2.
• Reaction: a (3R)-3-hydroxyacyl-CoA = a (2E)-enoyl-CoA + H2O

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

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

Key reference

DOI no: 10.1016/j.jmb.2004.11.009

J Mol Biol 345:1157-1169 (2005)

PubMed id: 15644212

Crystal structure of 2-enoyl-CoA hydratase 2 from human peroxisomal multifunctional enzyme type 2.

K.M.Koski, A.M.Haapalainen, J.K.Hiltunen, T.Glumoff.

ABSTRACT

2-Enoyl-CoA hydratase 2 is the middle part of the mammalian peroxisomal multifunctional enzyme type 2 (MFE-2), which is known to be important in the beta-oxidation of very-long-chain and alpha-methyl-branched fatty acids as well as in the synthesis of bile acids. Here, we present the crystal structure of the hydratase 2 from the human MFE-2 to 3A resolution. The three-dimensional structure resembles the recently solved crystal structure of hydratase 2 from the yeast, Candida tropicalis, MFE-2 having a two-domain subunit structure with a C-domain complete hot-dog fold housing the active site, and an N-domain incomplete hot-dog fold housing the cavity for the aliphatic acyl part of the substrate molecule. The ability of human hydratase 2 to utilize such bulky compounds which are not physiological substrates for the fungal ortholog, e.g. CoA esters of C26 fatty acids, pristanic acid and di/trihydroxycholestanoic acids, is explained by a large hydrophobic cavity formed upon the movements of the extremely mobile loops I-III in the N-domain. In the unliganded form of human hydratase 2, however, the loop I blocks the entrance of fatty enoyl-CoAs with chain-length >C8. Therefore, we expect that upon binding of substrates bulkier than C8, the loop I gives way, contemporaneously causing a secondary effect in the CoA-binding pocket and/or active site required for efficient hydration reaction. This structural feature would explain the inactivity of human hydratase 2 towards short-chain substrates. The solved structure is also used as a tool for analyzing the various inactivating mutations, identified among others in MFE-2-deficient patients. Since hydratase 2 is the last functional unit of mammalian MFE-2 whose structure has been solved, the organization of the functional units in the biologically active full-length enzyme is also discussed.

Selected figure(s)

Figure 3.
Figure 3. Ribbon representations of the HsMFE-2(dDhSCP-2LD) dimer. (a) The upper image shows the four-helix bundle dimerization motif of hydratase 2 formed by the a-helices a1, a5, a1' and a5' as well as the two salt bridges formed between Glu366 and Arg506 (side-chains shown as ball-and-stick representations). The arrows point to the active sites with catalytic Asp510 and His515 also shown as magenta. The N and C-domains are colored as in Figure 2(b). Note that the flexible loops I-III are fragmented in the lower subunit (subunit J in the crystal structure of HsMFE-2(dDhSCP-2LD)). The lower image shows a close-up of the salt bridge Glu366-Arg506. (b) The upper image shows the dimer after a 90° rotation around the vertical axis of the upper image of (a). The side-chains of Asn457 and Tyr347 are shown as ball-and-stick representations, and the active sites of the human hydratase 2 dimer are indicated by black arrows. The lower image shows in detail the interactions of a2 with a1 and with the N-domain b-sheet layer. The connections shown are described in detail in Discussion.

Figure 4.
Figure 4. Comparison of the ligand-binding pockets of the human and C. tropicalis hydratase 2 subunits. (a) Electrostatic surface potentials of the HsMFE-2(dDhSCP-2LD) ligand-binding pocket. The positively and negatively charged regions are colored blue and red, respectively. The residues suggested to interact with the CoA moiety of the fatty enoyl-CoA substrate are illustrated. The C-domain overhanging segment is labelled as the H2-motif. (b) Electrostatic surface potentials of CtMfe2p(dh[a+b]D) ligand-binding pocket with the bound (3R)-hydroxydecanoyl-CoA (Protein Data Bank accession code ID 1PN417). The ligand binds to the positively charged CoA-binding pocket in a bent conformation, where the adenine ring of the 3'-phosphate-ADP moiety points toward the protein, while the phosphate groups are solvent-exposed. The stronger positive charge at the surface of the ligand-binding pocket of CtMfe2p(dh[a+b]D) is created by the side-chains of two lysine residues (Lys820 and Lys823 of the C-domain overhanging segment) and an arginine (Arg760 of b-strand b5), which are not found in HsMFE-2(dDhSCP-2LD). Nevertheless, those residues are not directly involved in substrate binding. (c) A close-up view of the CoA-binding pocket after superimposing the apo form of HsMFE-2(dDhSCP-2LD) (magenta) with the holo form of CtMfe2p(dh[a+b]D) (light gray). The salt bridge between the Lys729 of CtMfe2p(dh[a+b]D) and 3'-phosphate of the substrate as well as the stacking interaction between Arg855 of CtMfe2p(dh[a+b]D) and adenine ring of the substrate are shown with black lines. (d) The differences in the region of the flexible loop I of hydratase 2s from human (green), C. tropicalis apoenzyme (gray) and C. tropicalis holoenzyme (red) after superimposition of the three structures. The (3R)-hydroxydecanoyl-CoA molecule of the C. tropicalis holoenzyme is also shown. The b-strands b2 and b5 and the C-domain are only partially shown for clarity. The side-chains of Met386 and Val404 of HsMFE-2(dDhSCP-2LD) (in pink) as well as Leu697 of CtMfe2p(dh[a+b]D) (in yellow) are shown. The black arrow points to the position of the a-methyl group of branched-chain fatty acids.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2005, 345, 1157-1169) copyright 2005.

Figures were selected by an automated process.