2YHW | pdb_00002yhw

High-resolution crystal structures of N-Acetylmannosamine kinase: Insights about substrate specificity, activity and inhibitor modelling.

PDB DOI: https://doi.org/10.2210/pdb2YHW/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2011-05-08 Released: 2012-02-29
Deposition Author(s): Martinez, J., Nguyen, L.D., Tauberger, E., Hinderlich, S., Zimmer, R., Tauberger, E., Reutter, W., Saenger, W., Fan, H., Moniot, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.64 Å
R-Value Free:
0.170 (Depositor), 0.181 (DCC)
R-Value Work:
0.148 (Depositor), 0.164 (DCC)
R-Value Observed:
0.149 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

Crystal Structures of N-Acetylmannosamine Kinase Provide Insights Into Enzyme Specificity and Inhibition

Martinez, J., Nguyen, L.D., Tauberger, E., Hinderlich, S., Reutter, W., Fan, H., Saenger, W., Moniot, S.

(2012) J Biological Chem 287: 13656

PubMed: 22343627 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1074/jbc.M111.318170
Primary Citation Related Structures:
2YHW, 2YHY, 2YI1

PubMed Abstract:
Sialic acids are essential components of membrane glycoconjugates. They are responsible for the interaction, structure, and functionality of all deuterostome cells and have major functions in cellular processes in health and diseases. The key enzyme of the biosynthesis of sialic acid is the bifunctional UDP-N-acetylglucosamine-2-epimerase/N-acetylmannosamine kinase that transforms UDP-N-acetylglucosamine to N-acetylmannosamine (ManNAc) followed by its phosphorylation to ManNAc 6-phosphate and has a direct impact on the sialylation of cell surface components. Here, we present the crystal structures of the human N-acetylmannosamine kinase (MNK) domain of UDP-N-acetylglucosamine-2-epimerase/N-acetylmannosamine kinase in complexes with ManNAc at 1.64 Å resolution, MNK·ManNAc·ADP (1.82 Å) and MNK·ManNAc 6-phosphate · ADP (2.10 Å). Our findings offer detailed insights in the active center of MNK and serve as a structural basis to design inhibitors. We synthesized a novel inhibitor, 6-O-acetyl-ManNAc, which is more potent than those previously tested. Specific inhibitors of sialic acid biosynthesis may serve to further study biological functions of sialic acid.

Organizational Affiliation

From the Institut für Chemie und Biochemie-Kristallographie, Freie Universität Berlin, Takustrasse 6, 14195 Berlin.

Macromolecule Content

Total Structure Weight: 38 kDa
Atom Count: 2,802
Modeled Residue Count: 309
Deposited Residue Count: 343
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BIFUNCTIONAL UDP-N-ACETYLGLUCOSAMINE 2-EPIMERASE/N-ACETYLMANNOSAMINE KINASE	A	343	Homo sapiens	Mutation(s): 0 EC: 2.7.1.60 (PDB Primary Data), 3.2.1.183 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y223 (Homo sapiens) Explore Q9Y223 Go to UniProtKB: Q9Y223
PHAROS: Q9Y223 GTEx: ENSG00000159921
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9Y223
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
2PE Query on 2PE Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	NONAETHYLENE GLYCOL C₁₈ H₃₈ O₁₀ YZUUTMGDONTGTN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
BM3 Query on BM3 Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	2-acetamido-2-deoxy-alpha-D-mannopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-UOLFYFMNSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain K [auth A] MOL2 format, chain I [auth A] MOL2 format, chain K [auth A] mmCIF format, chain I [auth A] mmCIF format, chain K [auth A]	I [auth A], K [auth A]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain K [auth A] Interactions & Density Focus chain I [auth A] Focus chain K [auth A]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain G [auth A] MOL2 format, chain J [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain G [auth A] mmCIF format, chain J [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A], F [auth A], G [auth A], J [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth A]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain L [auth A] MOL2 format, chain L [auth A] mmCIF format, chain L [auth A]	L [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain L [auth A] Interactions & Density Focus chain L [auth A]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain M [auth A] MOL2 format, chain M [auth A] mmCIF format, chain M [auth A]	M [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain M [auth A] Interactions & Density Focus chain M [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SNN Query on SNN	A	L-PEPTIDE LINKING	C₄ H₆ N₂ O₂		ASN

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.64 Å
R-Value Free: 0.170 (Depositor), 0.181 (DCC)
R-Value Work: 0.148 (Depositor), 0.164 (DCC)
R-Value Observed: 0.149 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.73	α = 90
b = 90.73	β = 90
c = 100.78	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2012-02-29

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-02-29
Type: Initial release
Version 1.1: 2012-05-02
Changes: Other
Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Other, Structure summary
Version 2.0: 2023-11-15
Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
Version 2.1: 2024-11-13
Changes: Structure summary