PDBsum entry 1npy

Structural genomics, unknown function

PDB id: 1npy

Contents

Protein chains

269 a.a. *

Ligands

ACE ×3

Waters ×1149

* Residue conservation analysis

PDB id:

1npy

Name:

Structural genomics, unknown function

Title:

Structure of shikimate 5-dehydrogenase-like protein hi0607

Structure:

Hypothetical shikimate 5-dehydrogenase-like protein hi0607. Chain: a, b, c, d. Engineered: yes

Source:

Haemophilus influenzae. Organism_taxid: 727. Gene: hi0607. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.75Å R-factor: 0.181 R-free: 0.219

Authors:

S.Korolev,O.Koroleva,T.Zarembinski,F.Collart,A.Joachimiak,Midwest Center For Structural Genomics (Mcsg)

Key ref:

S.Singh et al. (2005). Crystal structure of a novel shikimate dehydrogenase from Haemophilus influenzae. J Biol Chem, 280, 17101-17108. PubMed id: 15735308 DOI: 10.1074/jbc.M412753200

Date:

20-Jan-03 Release date: 29-Jul-03

Protein chains

P44774  (SHDHL_HAEIN) -  Shikimate dehydrogenase-like protein HI_0607 from Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)

Seq: 271 a.a.

Struc: 269 a.a.

Enzyme reactions

• Enzyme class: E.C.1.1.1.25 - shikimate dehydrogenase (NADP(+)).
• Pathway: Shikimate and Chorismate Biosynthesis
• Reaction: shikimate + NADP⁺ = 3-dehydroshikimate + NADPH + H⁺

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

reference

DOI no: 10.1074/jbc.M412753200

J Biol Chem 280:17101-17108 (2005)

PubMed id: 15735308

Crystal structure of a novel shikimate dehydrogenase from Haemophilus influenzae.

S.Singh, S.Korolev, O.Koroleva, T.Zarembinski, F.Collart, A.Joachimiak, D.Christendat.

ABSTRACT

To date two classes of shikimate dehydrogenases have been identified and characterized, YdiB and AroE. YdiB is a bifunctional enzyme that catalyzes the reversible reductions of dehydroquinate to quinate and dehydroshikimate to shikimate in the presence of either NADH or NADPH. In contrast, AroE catalyzes the reversible reduction of dehydroshikimate to shikimate in the presence of NADPH. Here we report the crystal structure and biochemical characterization of HI0607, a novel class of shikimate dehydrogenase annotated as shikimate dehydrogenase-like. The kinetic properties of HI0607 are remarkably different from those of AroE and YdiB. In comparison with YdiB, HI0607 catalyzes the oxidation of shikimate but not quinate. The turnover rate for the oxidation of shikimate is approximately 1000-fold lower compared with that of AroE. Phylogenetic analysis reveals three independent clusters representing three classes of shikimate dehydrogenases, namely AroE, YdiB, and this newly characterized shikimate dehydrogenase-like protein. In addition, mutagenesis studies of two invariant residues, Asp-103 and Lys-67, indicate that they are important catalytic groups that may function as a catalytic pair in the shikimate dehydrogenase reaction. This is the first study that describes the crystal structure as well as mutagenesis and mechanistic analysis of this new class of shikimate dehydrogenase.

Selected figure(s)

Figure 1.
FIG. 1. Bayesian-inferred, unrooted phylogeny of the shikimate dehydrogenase family of enzymes. The radial tree, produced by MRBAYES version 3.04b, clearly indicates three distinct subgroups, which are AroE, YdiB, and SDH-L. Genetic distances (calculated with MEGA2) between the classes are calculated to be 1.89 (AroE-YdiB), 1.79 (SDH-L-YdiB), and 2.22 (SDH-L-AroE); genetic distances within each group are 0.468 (AroE), 0.601 (SDH-L), and 0.842 (YdiB). NCBI protein data base accession numbers for the proteins of the SDH-L subgroup are as follows: H. influenzae, ZP_00154645; Mannheimia succiniciproducens, YP_089507; Pasteurella multocida, AAK03513 [GenBank] Yersinia pestis, NP_405191 [GenBank] ; Salmonella typhimurium, NP_462758 [GenBank] ; Deinococcus radiodurans, NP_293803 [GenBank] ; Pseudomonas fluorescens, ZP_00263633; Pseudomonas putida, AAN69362 [GenBank] Corynebacterium efficiens, NP_737804 [GenBank] ; and Pseudomonas syringae, ZP_00123871. NCBI protein data base accession numbers for the proteins of the YdiB subgroup are as follows: E. coli, NP_310426 [GenBank] ; Shigella flexneri, NP_837377 [GenBank] ; S. typhimurium, NP_460325 [GenBank] ; Lactobacillus plantarum, NP_786702 [GenBank] ; Streptococcus pyognes, YP_060639; Enterococcus faecalis, NP_815278 [GenBank] ; Enterococcus faecium, ZP_00285321; and Listeria monocytogenes, ZP_00232331. NCBI protein data base accession numbers for the proteins of the AroE subgroup are as follows: E. coli, NP_417740 [GenBank] ; S. flexneri, NP_709069 [GenBank] ; S. typhimurium, NP_462305 [GenBank] ; Y. pestis, NP_403898 [GenBank] ; Ewinia carotovora, YP_052082; and Photorhabdus luminescens, CAE17063 [GenBank] The branch confidence values are given as posterior probabilities. The distance scale is shown at the bottom left.

Figure 2.
FIG. 2. A, ribbon diagram of HI0607 monomer. The protein is essentially composed of two distinct domains, a nucleotide domain and a substrate-binding domain, which are linked by two long helices, helices 4 and 9. B, the biological dimer of HI0607. Dimerization is mediated via hydrophobic interactions between the N-terminal 2 and 1 structures of each monomer. C, HI0607 active site. In addition to the two ionizable groups, Lys-67 and Asp-103, there are a number of polar groups in the active site (Gln-242, Asn-88, and Asn-101). Toward the back of the pocket one encounters a cluster of serines (Ser-11, Ser-13, Ser-17, and Ser-63), Thr-89, and other polar groups including tyrosines (Tyr-37, for example).

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2005, 280, 17101-17108) copyright 2005.

Figures were selected by the author.