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PDBsum entry 1s9c

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protein Protein-protein interface(s) links
Lyase PDB id
1s9c
Jmol
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    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P51659  (DHB4_HUMAN) -  Peroxisomal multifunctional enzyme type 2
Seq:
Struc:
 
Seq:
Struc:
736 a.a.
248 a.a.*
Protein chains
Pfam   ArchSchema ?
P51659  (DHB4_HUMAN) -  Peroxisomal multifunctional enzyme type 2
Seq:
Struc:
 
Seq:
Struc:
736 a.a.
271 a.a.*
Protein chains
Pfam   ArchSchema ?
P51659  (DHB4_HUMAN) -  Peroxisomal multifunctional enzyme type 2
Seq:
Struc:
 
Seq:
Struc:
736 a.a.
276 a.a.*
Protein chains
Pfam   ArchSchema ?
P51659  (DHB4_HUMAN) -  Peroxisomal multifunctional enzyme type 2
Seq:
Struc:
 
Seq:
Struc:
736 a.a.
250 a.a.*
Protein chain
Pfam   ArchSchema ?
P51659  (DHB4_HUMAN) -  Peroxisomal multifunctional enzyme type 2
Seq:
Struc:
 
Seq:
Struc:
736 a.a.
255 a.a.*
Protein chain
Pfam   ArchSchema ?
P51659  (DHB4_HUMAN) -  Peroxisomal multifunctional enzyme type 2
Seq:
Struc:
 
Seq:
Struc:
736 a.a.
256 a.a.*
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* 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  - Alcohol dehydrogenase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction:
1. An alcohol + NAD+ = an aldehyde or ketone + NADH
2. A secondary alcohol + NAD+ = a ketone + NADH
alcohol
+ NAD(+)
= aldehyde or ketone
+ NADH
secondary alcohol
+ NAD(+)
= ketone
+ NADH
      Cofactor: Zn(2+) or Fe cation
   Enzyme class 3: Chains A, B, C, D, E, F, G, H, I, J, K, L: E.C.4.2.1.107  - 3-alpha,7-alpha,12-alpha-trihydroxy-5-beta-cholest-24-enoyl-CoA
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: (24R,25R)-3-alpha,7-alpha,12-alpha,24-tetrahydroxy-5-beta-cholestanoyl- CoA = (24E)-3-alpha,7-alpha,12-alpha-trihydroxy-5-beta-cholest-24-enoyl- 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.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: (3R)-3-hydroxyacyl-CoA = (2E)-2-enoyl-CoA + H2O
(3R)-3-hydroxyacyl-CoA
= (2E)-2-enoyl-CoA
+ H(2)O
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
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   1 term 
  Biochemical function     oxidoreductase activity     1 term  

 

 
    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.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21243161 J.Jin, and U.Hanefeld (2011).
The selective addition of water to C=C bonds; enzymes are the best chemists.
  Chem Commun (Camb), 47, 2502-2510.  
21320074 T.J.Haataja, M.K.Koski, J.K.Hiltunen, and T.Glumoff (2011).
Peroxisomal multifunctional enzyme type 2 from the fruitfly: dehydrogenase and hydratase act as separate entities, as revealed by structure and kinetics.
  Biochem J, 435, 771-781.
PDB code: 3oml
20544026 G.Möller, B.Husen, D.Kowalik, L.Hirvelä, D.Plewczynski, L.Rychlewski, J.Messinger, H.Thole, and J.Adamski (2010).
Species used for drug testing reveal different inhibition susceptibility for 17beta-hydroxysteroid dehydrogenase type 1.
  PLoS One, 5, e10969.  
21079635 J.M.Crawford, and C.A.Townsend (2010).
New insights into the formation of fungal aromatic polyketides.
  Nat Rev Microbiol, 8, 879-889.  
20731893 T.Maier, M.Leibundgut, D.Boehringer, and N.Ban (2010).
Structure and function of eukaryotic fatty acid synthases.
  Q Rev Biophys, 43, 373-422.  
19847268 J.M.Crawford, T.P.Korman, J.W.Labonte, A.L.Vagstad, E.A.Hill, O.Kamari-Bidkorpeh, S.C.Tsai, and C.A.Townsend (2009).
Structural basis for biosynthetic programming of fungal aromatic polyketide cyclization.
  Nature, 461, 1139-1143.
PDB codes: 3hrq 3hrr
19473548 L.S.Pidugu, K.Maity, K.Ramaswamy, N.Surolia, and K.Suguna (2009).
Analysis of proteins with the 'hot dog' fold: prediction of function and identification of catalytic residues of hypothetical proteins.
  BMC Struct Biol, 9, 37.  
17431175 S.Jenni, M.Leibundgut, D.Boehringer, C.Frick, B.Mikolásek, and N.Ban (2007).
Structure of fungal fatty acid synthase and implications for iterative substrate shuttling.
  Science, 316, 254-261.
PDB codes: 2uv9 2uva 2uvb 2uvc
16963641 P.Johansson, A.Castell, T.A.Jones, and K.Bäckbro (2006).
Structure and function of Rv0130, a conserved hypothetical protein from Mycobacterium tuberculosis.
  Protein Sci, 15, 2300-2309.
PDB code: 2c2i
16385454 S.Ferdinandusse, M.S.Ylianttila, J.Gloerich, M.K.Koski, W.Oostheim, H.R.Waterham, J.K.Hiltunen, R.J.Wanders, and T.Glumoff (2006).
Mutational spectrum of D-bifunctional protein deficiency and structure-based genotype-phenotype analysis.
  Am J Hum Genet, 78, 112-124.  
16513976 S.Jenni, M.Leibundgut, T.Maier, and N.Ban (2006).
Architecture of a fungal fatty acid synthase at 5 A resolution.
  Science, 311, 1263-1267.
PDB code: 2cdh
16513975 T.Maier, S.Jenni, and N.Ban (2006).
Architecture of mammalian fatty acid synthase at 4.5 A resolution.
  Science, 311, 1258-1262.
PDB code: 2cf2
16482509 V.Brown, R.A.Brown, A.Ozinsky, J.R.Hesselberth, and S.Fields (2006).
Binding specificity of Toll-like receptor cytoplasmic domains.
  Eur J Immunol, 36, 742-753.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.