PDBsum entry 1jvb

Oxidoreductase

PDB id: 1jvb

Contents

Protein chain

347 a.a. *

Metals

_ZN ×2

Waters ×193

* Residue conservation analysis

References listed in PDB file

Key reference

Title

Crystal structure of the alcohol dehydrogenase from the hyperthermophilic archaeon sulfolobus solfataricus at 1.85 a resolution.

Authors

L.Esposito, F.Sica, C.A.Raia, A.Giordano, M.Rossi, L.Mazzarella, A.Zagari.

Ref.

J Mol Biol, 2002, 318, 463-477. [DOI no: 10.1016/S0022-2836(02)00088-8]

PubMed id

12051852

Abstract

The crystal structure of a medium-chain NAD(H)-dependent alcohol dehydrogenase (ADH) from an archaeon has been solved by multiwavelength anomalous diffraction, using a selenomethionine-substituted enzyme. The protein (SsADH), extracted from the hyperthermophilic organism Sulfolobus solfataricus, is a homo-tetramer with a crystallographic 222 symmetry. Despite the low level of sequence identity, the overall fold of the monomer is similar to that of the other homologous ADHs of known structure. However, a significant difference is the orientation of the catalytic domain relative to the coenzyme-binding domain that results in a larger interdomain cleft. At the bottom of this cleft, the catalytic zinc ion is coordinated tetrahedrally and lacks the zinc-bound water molecule that is usually found in ADH apoform structures. The fourth coordination position is indeed occupied by a Glu residue, as found in bacterial tetrameric ADHs. Other differences are found in the architecture of the substrate pocket whose entrance is more restricted than in other ADHs. SsADH is the first tetrameric ADH X-ray structure containing a second zinc ion playing a structural role. This latter metal ion shows a peculiar coordination, with a glutamic acid residue replacing one of the four cysteine ligands that are highly conserved throughout the structural zinc-containing dimeric ADHs.

Figure 1.
Figure 1. A stereo view of the SsADH subunit. The C^a trace is marked with a ball every tenth C^a atom. Figure 1, Figure 3 and Figure 4 were prepared with MOLSCRIPT. [48.]

Figure 5.
Figure 5. Ribbon diagram of the SsADH homo-tetramer generated from crystallographic symmetry. The tetramer is a dimer of dimers (A/B and C/D). The catalytic zinc ions are coloured green. The Figure was prepared with MOLSCRIPT[48.] and Raster3D. [50.]

The above figures are reprinted by permission from Elsevier: J Mol Biol (2002, 318, 463-477) copyright 2002.

Secondary reference #1

Title

Nadp-Dependent bacterial alcohol dehydrogenases: crystal structure, Cofactor-Binding and cofactor specificity of the adhs of clostridium beijerinckii and thermoanaerobacter brockii.

Authors

Y.Korkhin, A.J.Kalb(gilboa), M.Peretz, O.Bogin, Y.Burstein, F.Frolow.

Ref.

J Mol Biol, 1998, 278, 967-981. [DOI no: 10.1006/jmbi.1998.1750]

PubMed id

9836873

Figure 4.
Figure 4. (a) A stereo view of a rib bon diagram of the CBADH tetramer. Monomers are represented in different colors. (b) A side-by-side view of the CBADH tetramer with one monomer removed. A large cavity with a positive (blue) molecular surface potential (left) exists inside the tetramer. This is accessible from outside through narrow channels.

Figure 5.
Figure 5. If dimer CD of CBADH is superimposed on its equivalent from the GDH tetramer, then in order to superimpose dimer AB of CBADH with the second GDH dimer, an additional rotation of approximately 30° is needed around the 2-fold axis which relates monomers in these dimers.

The above figures are reproduced from the cited reference with permission from Elsevier

Secondary reference #2

Title

Three-Dimensional structure of horse liver alcohol dehydrogenase at 2-4 a resolution.

Authors

H.Eklund, B.Nordström, E.Zeppezauer, G.Söderlund, I.Ohlsson, T.Boiwe, B.O.Söderberg, O.Tapia, C.I.Brändén, A.Akeson.

Ref.

J Mol Biol, 1976, 102, 27-59.

PubMed id

178875

Secondary reference #3

Title

Crystal structure of the NADP(h)-Dependent ketose reductase from bemisia argentifolii at 2.3 a resolution.

Authors

M.J.Banfield, M.E.Salvucci, E.N.Baker, C.A.Smith.

Ref.

J Mol Biol, 2001, 306, 239-250. [DOI no: 10.1006/jmbi.2000.4381]

PubMed id

11237597

Figure 2.
Figure 2. Stereoviews showing examples of (a) the experimental MAD/DM electron density map used to build the initial model, and (b) the final weighted 2|F[obs]| -|F[calc]|.f[calc] electron density map. Both maps are contoured at 1.1s, and cover residues 171-188. The Figure was prepared with BOBSCRIPT[45] and Raster3D. [46]

Figure 3.
Figure 3. (a) Stereoview of the C^a trace of the final BaKR model, with the N, C termini, and every tenth amino acid residue labelled. (b) Schematic view of the secondary structure arrangement in BaKR. The two zinc atoms bound in the structure are shown in green. Figure prepared with MOLSCRIPT[47] and Raster3D. [46]

The above figures are reproduced from the cited reference with permission from Elsevier