PDBsum entry: 1nvm

Lyase/oxidoreductase

PDB id: 1nvm

Contents

Protein chains

340 a.a. *

312 a.a. *

Ligands

OXL ×4

SO4 ×12

MPD ×6

NAD ×3

Metals

_MN ×4

Waters ×2811

* Residue conservation analysis

PDB id:

1nvm

Name:

Lyase/oxidoreductase

Title:

Crystal structure of a bifunctional aldolase-dehydrogenase : sequestering a reactive and volatile intermediate

Structure:

4-hydroxy-2-oxovalerate aldolase. Chain: a, c, e, g. Synonym: hoa. Engineered: yes. Acetaldehyde dehydrogenase (acylating). Chain: b, d, f, h. Engineered: yes

Source:

Pseudomonas sp.. Organism_taxid: 79676. Strain: cf600. Gene: dmpg. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: dmpf.

Biol. unit:

Tetramer (from PQS)

Resolution:

1.70Å R-factor: 0.189 R-free: 0.230

Authors:

A.B.Manjasetty,J.Powlowski,A.Vrielink

Key ref:

B.A.Manjasetty et al. (2003). Crystal structure of a bifunctional aldolase-dehydrogenase: sequestering a reactive and volatile intermediate. Proc Natl Acad Sci U S A, 100, 6992-6997. PubMed id: 12764229 DOI: 10.1073/pnas.1236794100

Date:

04-Feb-03 Release date: 17-Jun-03

Protein chains

P51016  (HOA_PSEUF) -  4-hydroxy-2-oxovalerate aldolase

Seq: 345 a.a.

Struc: 340 a.a.

Protein chains

Q52060  (ACDH_PSEUF) -  Acetaldehyde dehydrogenase

Seq: 312 a.a.

Struc: 312 a.a.

Enzyme reactions

• Enzyme class 1: Chains A, C, E, G: E.C.4.1.3.39 - 4-hydroxy-2-oxovalerate aldolase.
• Reaction: 4-hydroxy-2-oxopentanoate = acetaldehyde + pyruvate

4-hydroxy-2-oxopentanoate (Bound ligand (Het Group name = MPD) matches with 70.00% similarity) = acetaldehyde + pyruvate (Bound ligand (Het Group name = OXL) matches with 71.43% similarity)

• Cofactor: Manganese
• Enzyme class 2: Chains B, D, F, H: E.C.1.2.1.10 - Acetaldehyde dehydrogenase (acetylating).
• Reaction: Acetaldehyde + CoA + NAD⁺ = acetyl-CoA + NADH

Acetaldehyde (Bound ligand (Het Group name = OXL) matches with 50.00% similarity) + CoA + NAD(+) (Bound ligand (Het Group name = NAD) corresponds exactly) = acetyl-CoA + NADH

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 

• Cellular component: cytoplasm (1 term)
• Biological process: metabolic process (4 terms)
• Biochemical function: catalytic activity (13 terms)

reference

DOI no: 10.1073/pnas.1236794100

Proc Natl Acad Sci U S A 100:6992-6997 (2003)

PubMed id: 12764229

Crystal structure of a bifunctional aldolase-dehydrogenase: sequestering a reactive and volatile intermediate.

B.A.Manjasetty, J.Powlowski, A.Vrielink.

ABSTRACT

The crystal structure of the bifunctional enzyme 4-hydroxy-2-ketovalerate aldolase (DmpG)/acylating acetaldehyde dehydrogenase (DmpF), which is involved in the bacterial degradation of toxic aromatic compounds, has been determined by multiwavelength anomalous dispersion (MAD) techniques and refined to 1.7-A resolution. Structures of the two polypeptides represent a previously unrecognized subclass of metal-dependent aldolases, and of a CoA-dependent dehydrogenase. The structure reveals a mixed state of NAD+ binding to the DmpF protomer. Domain movements associated with cofactor binding in the DmpF protomer may be correlated with channeling and activity at the DmpG protomer. In the presence of NAD+ a 29-A-long sequestered tunnel links the two active sites. Two barriers are visible along the tunnel and suggest control points for the movement of the reactive and volatile acetaldehyde intermediate between the two active sites.

Selected figure(s)

Figure 2.
Fig. 2. (a) Active site of DmpG. The Mn2^+ ion is shown as a yellow sphere. Red spheres correspond to bound water molecules. The oxalate ligand is shown with blue bonds. The dotted lines represent coordinating interactions between active site residues and the bound metal ion. (b)2F[o] - F[c] electron density in the active site of DmpG. The density is contoured at a 1.5- level. (c) Model of the substrate-bound complex of DmpG. The modeled substrate, 4-hydroxy-2-ketovalerate, is shown in blue bonds. The secondary structure elements are colored as described for Fig. 1.

Figure 3.
Fig. 3. (a and b) Worm representation of DmpFG showing the apo form with the buried surface of the intermediate channel (a) and the holo form with the buried surface of the intermediate channel extending completely between the two active sites (b). (c and d) Worm representation showing a close-up view of the buried surface of the intermediate channel around the second barrier for the apo form (c) and the holo form (d) of the enzyme. The side chains of the residues that adopt multiple conformations at this barrier point are shown in a single conformation. In the holo form (d) this conformational arrangement results in an opening of the second barrier point from the intermediate tunnel to the active site of the DmpF molecule. (e and f) Worm representation showing the substrate entrance tunnel in the closed conformation blocked by the side chain of His-21 (e) and the open substrate entrance channel with His-21 in an alternative side-chain conformation (f). The DmpG chain is shown in purple and the DmpF chain is in magenta. Specific amino acid residues and the NAD cofactor are represented as ball-and-stick models, and the Mn2^+ cofactor is shown as a yellow sphere. The intermediate channel is blue and the substrate entrance channel is gray. Hydrogen bonding interactions are shown in dotted lines. The solvent-accessible surfaces were computed with the program SPOCK (23), using a probe radius of 1.4 Å.

Figures were selected by the author.