3N07

Structure of putative 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase from Vibrio cholerae

DOI: 10.2210/pdb3N07/pdb

Classification: HYDROLASE
Organism(s): Vibrio cholerae
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2010-05-13 Released: 2010-08-04
Deposition Author(s): Liu, W., Ramagopal, U.A., Toro, R., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.76 Å
R-Value Free: 0.201
R-Value Work: 0.170
R-Value Observed: 0.172

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Structural basis for the divergence of substrate specificity and biological function within HAD phosphatases in lipopolysaccharide and sialic acid biosynthesis.

Daughtry, K.D., Huang, H., Malashkevich, V., Patskovsky, Y., Liu, W., Ramagopal, U., Sauder, J.M., Burley, S.K., Almo, S.C., Dunaway-Mariano, D., Allen, K.N.

(2013) Biochemistry 52: 5372-5386

PubMed: 23848398 Search on PubMedSearch on PubMed Central
DOI: 10.1021/bi400659k
Primary Citation of Related Structures:
4HGN, 4HGO, 4HGP, 4HGQ, 4HGR, 3MN1, 3MMZ, 3N07

PubMed Abstract:

The haloacid dehalogenase enzyme superfamily (HADSF) is largely composed of phosphatases that have been particularly successful at adaptating to novel biological functions relative to members of other phosphatase families. Herein, we examine the structural basis for the divergence of function in two bacterial homologues: 2-keto-3-deoxy-d-manno-octulosonate 8-phosphate phosphohydrolase (KDO8P phosphatase, KDO8PP) and 2-keto-3-deoxy-9-O-phosphonononic acid phosphohydrolase (KDN9P phosphatase, KDN9PP). KDO8PP and KDN9PP catalyze the final step in KDO and KDN synthesis, respectively, prior to transfer to CMP to form the activated sugar nucleotide. KDO8PP and KDN9PP orthologs derived from an evolutionarily diverse collection of bacterial species were subjected to steady-state kinetic analysis to determine their specificities toward catalyzed KDO8P and KDN9P hydrolysis. Although each enzyme was more active with its biological substrate, the degree of selectivity (as defined by the ratio of kcat/Km for KDO8P vs KDN9P) varied significantly. High-resolution X-ray structure determination of Haemophilus influenzae KDO8PP bound to KDO/VO3(-) and Bacteriodes thetaiotaomicron KDN9PP bound to KDN/VO3(-) revealed the substrate-binding residues. The structures of the KDO8PP and KDN9PP orthologs were also determined to reveal the differences in their active-site structures that underlie the variation in substrate preference. Bioinformatic analysis was carried out to define the sequence divergence among KDN9PP and KDO8PP orthologs. The KDN9PP orthologs were found to exist as single-domain proteins or fused with the pathway nucleotidyl transferases; the fusion of KDO8PP with the transferase is rare. The KDO8PP and KDN9PP orthologs share a stringently conserved Arg residue that forms a salt bridge with the substrate carboxylate group. The split of the KDN9PP lineage from the KDO8PP orthologs is easily tracked by the acquisition of a Glu/Lys pair that supports KDN9P binding. Moreover, independently evolved lineages of KDO8PP orthologs exist, and are separated by diffuse active-site sequence boundaries. We infer a high tolerance of the KDO8PP catalytic platform to amino acid replacements that in turn influence substrate specificity changes and thereby facilitate the divergence in biological function.

Organizational Affiliation:

Department of Physiology and Biophysics, Boston University School of Medicine, Boston, MA 02118-2394, USA.

Macromolecules

Find similar proteins by:

(by identity cutoff) | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-deoxy-D-manno-octulosonate 8-phosphate phosphatase	A, B, C, D	195	Vibrio cholerae	Mutation(s): 0 Gene Names: VCD_001835, VC_2524 EC: 3.1.3.45
Find proteins for Q9KP52 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KP52 Go to UniProtKB: Q9KP52
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MG Query on MG Download CCD File	A, B, C, D	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Ligand Interaction