PDBsum entry: 1say

Oxidoreductase

PDB-id: 1say

Asymmetric unit

Contents

Description

Header details

Header records

References

PROCHECK

Protein chain

361 a.a. *

Ligands

PYR

Waters ×96

* Residue conservation analysis

Tools

Clefts Calculation

Biological unit, hexamer
- as defined in PDB file (see also PQS)

PDB id:

1say

Name:

Oxidoreductase

Title:

L-alanine dehydrogenase complexed with pyruvate

Structure:

L-alanine dehydrogenase. Chain: a. Engineered: yes

Source:

Phormidium lapideum. Organism_taxid: 32060. Gene: aladh. Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: matsue hot springs

Biological unit:

Homo-hexamer (from PDB file)

UniProt:

O52942 (O52942_PHOLP)

Seq:

Struc:

Seq:

361 a.a.

Struc:

361 a.a.

Key:	PfamA domain
Secondary structure	CATH domain

Enzyme class:

E.C.1.4.1.1   [IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

Reaction:

L-alanine + H₂O + NAD⁺ = pyruvate + NH₃ + NADH (see diagram below)

Resolution:

2.10Å

R-factor:

0.180

R-free:

0.250

Authors:

P.J.Baker,Y.Sawa,H.Shibata,S.E.Sedelnikova,D.W.Rice

Key ref:

P.J.Baker et al. (1998). Analysis of the structure and substrate binding of Phormidium lapideum alanine dehydrogenase.. Nat Struct Biol, 5, 561-567. [PubMed id: 9665169] [DOI: 10.1038/817]

Date:

05-Jun-98

Release date:

08-Jun-99

Quick_links

Procheck

Clefts

Surface

Key reference

DOI no: 10.1038/817

Nat Struct Biol 5:561-567 (1998)

PubMed id: 9665169

Analysis of the structure and substrate binding of Phormidium lapideum alanine dehydrogenase.

P.J.Baker, Y.Sawa, H.Shibata, S.E.Sedelnikova, D.W.Rice.

ABSTRACT

The structure of the hexameric L-alanine dehydrogenase from Phormidium lapideum reveals that the subunit is constructed from two domains, each having the common dinucleotide binding fold. Despite there being no sequence similarity, the fold of alanine dehydrogenase is closely related to that of the family of D-2-hydroxyacid dehydrogenases, with a similar location of the active site, suggesting that these enzymes are related by divergent evolution. L-alanine dehydrogenase and the 2-hydroxyacid dehydrogenases also use equivalent functional groups to promote substrate recognition and catalysis. However, they are arranged differently on the enzyme surface, which has the effect of directing opposite faces of the keto acid to the dinucleotide in each case, forcing a change in absolute configuration of the product.

Selected figure(s)

Figure 1.
Figure 1. Assembly of the hexamer of AlaDH. a, The C stereo backbone of a single subunit, with every 10^th residue drawn as a black dot and every 20^th numbered. b, A schematic diagram of the dimer, with domain 1 furthest from the two-fold axis and the dinucleotide binding domain 2 closest to the two-fold axis. c, A space filling representation of the hexamer viewed down the three-fold axis.

Figure 3.
Figure 3. a, The superposition of the structures of the binary complex of AlaDH with NAD^+ (green) and the free enzyme (blue) showing the movement of the 238−246, the 266−271 and the 296−299 loops, which occurs on dinucleotide binding. The position of the NAD^+ is shown in atom colors. b , A stereo diagram of the pyruvate binding site in the binary complex of AlaDH with pyruvate (atom colours) with the corresponding |3F[O] - 2F[C]| electron density map, contoured at 1 (orange). c, The proposed intermediates of the AlaDH catalytic cycle, after Grimshaw et al.^14. In panel (i) the hydride transfer from the C of the alanine to the C4 of the nicotinamide ring leads to the iminopyruvate shown in panel (ii). The ensuing attack by a water molecule, facilitated by the base, B, results in the formation of the carbinolamine shown in panel (iii). Subsequent collapse of this intermediate yields pyruvate and ammonia (panel iv).

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (1998, 5, 561-567) copyright 1998.

Figures were selected by an automated process.