6GPL | pdb_00006gpl

Crystal structure of human GDP-D-mannose 4,6-dehydratase in complex with GDP-4k6d-Man

PDB DOI: https://doi.org/10.2210/pdb6GPL/pdb

Classification: LYASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2018-06-06 Released: 2018-07-18
Deposition Author(s): Pfeiffer, M., Krojer, T., Johansson, C., von Delft, F., Bountra, C., Arrowsmith, C.H., Edwards, A., Nidetzky, B., Oppermann, U., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.76 Å
R-Value Free:
0.190 (Depositor), 0.198 (DCC)
R-Value Work:
0.169 (Depositor), 0.178 (DCC)
R-Value Observed:
0.170 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

A Parsimonious Mechanism of Sugar Dehydration by Human GDP-Mannose-4,6-dehydratase.

Pfeiffer, M., Johansson, C., Krojer, T., Kavanagh, K.L., Oppermann, U., Nidetzky, B.

(2019) ACS Catal 9: 2962-2968

PubMed: 30984471 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/acscatal.9b00064
Primary Citation Related Structures:
6GPJ, 6GPK, 6GPL, 6Q94

PubMed Abstract:
Biosynthesis of 6-deoxy sugars, including l-fucose, involves a mechanistically complex, enzymatic 4,6-dehydration of hexose nucleotide precursors as the first committed step. Here, we determined pre- and postcatalytic complex structures of the human GDP-mannose 4,6-dehydratase at atomic resolution. These structures together with results of molecular dynamics simulation and biochemical characterization of wildtype and mutant enzymes reveal elusive mechanistic details of water elimination from GDP-mannose C5″ and C6″, coupled to NADP-mediated hydride transfer from C4″ to C6″. We show that concerted acid-base catalysis from only two active-site groups, Tyr ₁₇₉ and Glu ₁₅₇, promotes a syn 1,4-elimination from an enol (not an enolate) intermediate. We also show that the overall multistep catalytic reaction involves the fewest position changes of enzyme and substrate groups and that it proceeds under conserved exploitation of the basic (minimal) catalytic machinery of short-chain dehydrogenase/reductases.

Organizational Affiliation

Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, 8010 Graz, Austria.

Macromolecule Content

Total Structure Weight: 166.27 kDa
Atom Count: 12,088
Modeled Residue Count: 1,361
Deposited Residue Count: 1,408
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GDP-mannose 4,6 dehydratase	A [auth B], B [auth C], C [auth D], D [auth E]	352	Homo sapiens	Mutation(s): 0 Gene Names: GMDS EC: 4.2.1.47
UniProt & NIH Common Fund Data Resources
Find proteins for O60547 (Homo sapiens) Explore O60547 Go to UniProtKB: O60547
PHAROS: O60547 GTEx: ENSG00000112699
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O60547
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAP Query on NAP Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain M [auth C] SDF format, chain Q [auth D] SDF format, chain V [auth E] MOL2 format, chain G [auth B] MOL2 format, chain M [auth C] MOL2 format, chain Q [auth D] MOL2 format, chain V [auth E] mmCIF format, chain G [auth B] mmCIF format, chain M [auth C] mmCIF format, chain Q [auth D] mmCIF format, chain V [auth E]	G [auth B], M [auth C], Q [auth D], V [auth E]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain G [auth B] Focus chain M [auth C] Focus chain Q [auth D] Focus chain V [auth E] Interactions & Density Focus chain G [auth B] Focus chain M [auth C] Focus chain Q [auth D] Focus chain V [auth E]
F7E Query on F7E Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain L [auth C] SDF format, chain P [auth D] SDF format, chain U [auth E] MOL2 format, chain F [auth B] MOL2 format, chain L [auth C] MOL2 format, chain P [auth D] MOL2 format, chain U [auth E] mmCIF format, chain F [auth B] mmCIF format, chain L [auth C] mmCIF format, chain P [auth D] mmCIF format, chain U [auth E]	F [auth B], L [auth C], P [auth D], U [auth E]	[[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},6~{R})-6-methyl-3,4-bis(oxidanyl)-5-oxidanylidene-oxan-2-yl] hydrogen phosphate C₁₆ H₂₃ N₅ O₁₅ P₂ PNHLMHWWFOPQLK-BKUUWRAGSA-N		Interactions Focus chain F [auth B] Focus chain L [auth C] Focus chain P [auth D] Focus chain U [auth E] Interactions & Density Focus chain F [auth B] Focus chain L [auth C] Focus chain P [auth D] Focus chain U [auth E]
BCN Query on BCN Download:Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B] mmCIF format, chain E [auth B]	E [auth B]	BICINE C₆ H₁₃ N O₄ FSVCELGFZIQNCK-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain N [auth C] SDF format, chain O [auth C] SDF format, chain R [auth D] SDF format, chain S [auth D] SDF format, chain T [auth D] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain N [auth C] MOL2 format, chain O [auth C] MOL2 format, chain R [auth D] MOL2 format, chain S [auth D] MOL2 format, chain T [auth D] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain N [auth C] mmCIF format, chain O [auth C] mmCIF format, chain R [auth D] mmCIF format, chain S [auth D] mmCIF format, chain T [auth D]	H [auth B] I [auth B] J [auth B] K [auth B] N [auth C] H [auth B], I [auth B], J [auth B], K [auth B], N [auth C], O [auth C], R [auth D], S [auth D], T [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain R [auth D] Focus chain S [auth D] Focus chain T [auth D] Interactions & Density Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain R [auth D] Focus chain S [auth D] Focus chain T [auth D]