2X6T | pdb_00002x6t

AGME bound to ADP-B-mannose

PDB DOI: https://doi.org/10.2210/pdb2X6T/pdb

Classification: ISOMERASE
Organism(s): Escherichia coli
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2010-02-21 Released: 2010-03-02
Deposition Author(s): Kowatz, T., Morrison, J.P., Tanner, M.E., Naismith, J.H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.36 Å
R-Value Free:
0.209 (Depositor), 0.210 (DCC)
R-Value Work:
0.189 (Depositor), 0.192 (DCC)
R-Value Observed:
0.190 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

The Crystal Structure of the Y140F Mutant of Adp-L-Glycero-D-Manno-Heptose 6-Epimerase Bound to Adp-Beta-D-Mannose Suggests a One Base Mechanism.

Kowatz, T., Morrison, J.P., Tanner, M.E., Naismith, J.H.

(2010) Protein Sci 19: 1337

PubMed: 20506248 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1002/pro.410
Primary Citation Related Structures:
2X6T, 2X86

PubMed Abstract:
Bacteria synthesize a wide array of unusual carbohydrate molecules, which they use in a variety of ways. The carbohydrate L-glycero-D-manno-heptose is an important component of lipopolysaccharide and is synthesized in a complex series of enzymatic steps. One step involves the epimerization at the C6'' position converting ADP-D-glycero-D-manno-heptose into ADP-L-glycero-D-manno-heptose. The enzyme responsible is a member of the short chain dehydrogenase superfamily, known as ADP-L-glycero-D-manno-heptose 6-epimerase (AGME). The structure of the enzyme was known but the arrangement of the catalytic site with respect to the substrate is unclear. We now report the structure of AGME bound to a substrate mimic, ADP-beta-D-mannose, which has the same stereochemical configuration as the substrate. The complex identifies the key residues and allows mechanistic insight into this novel enzyme.

Organizational Affiliation

Biomolecular Sciences Research Complex, The University of St Andrews, Fife KY16 9RH, United Kingdom.

Macromolecule Content

Total Structure Weight: 413.41 kDa
Atom Count: 26,879
Modeled Residue Count: 3,071
Deposited Residue Count: 3,570
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ADP-L-GLYCERO-D-MANNO-HEPTOSE-6-EPIMERASE	A, B, C, D, E A, B, C, D, E, F, G, H, I, J	357	Escherichia coli	Mutation(s): 1 EC: 5.1.3.20
UniProt
Find proteins for P67910 (Escherichia coli (strain K12)) Explore P67910 Go to UniProtKB: P67910
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P67910
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAP Query on NAP Download:Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain EA [auth F] SDF format, chain IA [auth G] SDF format, chain K [auth A] SDF format, chain O [auth B] SDF format, chain OA [auth H] SDF format, chain SA [auth I] SDF format, chain W [auth D] SDF format, chain WA [auth J] SDF format, chain S [auth C] MOL2 format, chain AA [auth E] MOL2 format, chain EA [auth F] MOL2 format, chain IA [auth G] MOL2 format, chain K [auth A] MOL2 format, chain O [auth B] MOL2 format, chain OA [auth H] MOL2 format, chain SA [auth I] MOL2 format, chain W [auth D] MOL2 format, chain WA [auth J] MOL2 format, chain S [auth C] mmCIF format, chain AA [auth E] mmCIF format, chain EA [auth F] mmCIF format, chain IA [auth G] mmCIF format, chain K [auth A] mmCIF format, chain O [auth B] mmCIF format, chain OA [auth H] mmCIF format, chain SA [auth I] mmCIF format, chain W [auth D] mmCIF format, chain WA [auth J] mmCIF format, chain S [auth C]	AA [auth E] EA [auth F] IA [auth G] K [auth A] O [auth B] AA [auth E], EA [auth F], IA [auth G], K [auth A], O [auth B], OA [auth H], S [auth C], SA [auth I], W [auth D], WA [auth J]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain AA [auth E] Focus chain EA [auth F] Focus chain IA [auth G] Focus chain K [auth A] Focus chain O [auth B] Focus chain OA [auth H] Focus chain S [auth C] Focus chain SA [auth I] Focus chain W [auth D] Focus chain WA [auth J] Interactions & Density Focus chain AA [auth E] Focus chain EA [auth F] Focus chain IA [auth G] Focus chain K [auth A] Focus chain O [auth B] Focus chain OA [auth H] Focus chain S [auth C] Focus chain SA [auth I] Focus chain W [auth D] Focus chain WA [auth J]
ADP Query on ADP Download:Ideal Coordinates CCD File SDF format, chain GA [auth F] SDF format, chain M [auth A] SDF format, chain MA [auth G] SDF format, chain QA [auth H] SDF format, chain UA [auth I] SDF format, chain Y [auth D] SDF format, chain YA [auth J] SDF format, chain U [auth C] SDF format, chain Q [auth B] SDF format, chain CA [auth E] MOL2 format, chain GA [auth F] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth G] MOL2 format, chain QA [auth H] MOL2 format, chain UA [auth I] MOL2 format, chain Y [auth D] MOL2 format, chain YA [auth J] MOL2 format, chain U [auth C] MOL2 format, chain Q [auth B] MOL2 format, chain CA [auth E] mmCIF format, chain GA [auth F] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth G] mmCIF format, chain QA [auth H] mmCIF format, chain UA [auth I] mmCIF format, chain Y [auth D] mmCIF format, chain YA [auth J] mmCIF format, chain U [auth C] mmCIF format, chain Q [auth B] mmCIF format, chain CA [auth E]	CA [auth E] GA [auth F] M [auth A] MA [auth G] Q [auth B] CA [auth E], GA [auth F], M [auth A], MA [auth G], Q [auth B], QA [auth H], U [auth C], UA [auth I], Y [auth D], YA [auth J]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain CA [auth E] Focus chain GA [auth F] Focus chain M [auth A] Focus chain MA [auth G] Focus chain Q [auth B] Focus chain QA [auth H] Focus chain U [auth C] Focus chain UA [auth I] Focus chain Y [auth D] Focus chain YA [auth J] Interactions & Density Focus chain CA [auth E] Focus chain GA [auth F] Focus chain M [auth A] Focus chain MA [auth G] Focus chain Q [auth B] Focus chain QA [auth H] Focus chain U [auth C] Focus chain UA [auth I] Focus chain Y [auth D] Focus chain YA [auth J]
BMA Query on BMA Download:Ideal Coordinates CCD File SDF format, chain HA [auth F] SDF format, chain N [auth A] SDF format, chain NA [auth G] SDF format, chain R [auth B] SDF format, chain RA [auth H] SDF format, chain V [auth C] SDF format, chain VA [auth I] SDF format, chain Z [auth D] SDF format, chain ZA [auth J] SDF format, chain DA [auth E] MOL2 format, chain HA [auth F] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth G] MOL2 format, chain R [auth B] MOL2 format, chain RA [auth H] MOL2 format, chain V [auth C] MOL2 format, chain VA [auth I] MOL2 format, chain Z [auth D] MOL2 format, chain ZA [auth J] MOL2 format, chain DA [auth E] mmCIF format, chain HA [auth F] mmCIF format, chain N [auth A] mmCIF format, chain NA [auth G] mmCIF format, chain R [auth B] mmCIF format, chain RA [auth H] mmCIF format, chain V [auth C] mmCIF format, chain VA [auth I] mmCIF format, chain Z [auth D] mmCIF format, chain ZA [auth J] mmCIF format, chain DA [auth E]	DA [auth E] HA [auth F] N [auth A] NA [auth G] R [auth B] DA [auth E], HA [auth F], N [auth A], NA [auth G], R [auth B], RA [auth H], V [auth C], VA [auth I], Z [auth D], ZA [auth J]	beta-D-mannopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-RWOPYEJCSA-N		Interactions Focus chain DA [auth E] Focus chain HA [auth F] Focus chain N [auth A] Focus chain NA [auth G] Focus chain R [auth B] Focus chain RA [auth H] Focus chain V [auth C] Focus chain VA [auth I] Focus chain Z [auth D] Focus chain ZA [auth J] Interactions & Density Focus chain DA [auth E] Focus chain HA [auth F] Focus chain N [auth A] Focus chain NA [auth G] Focus chain R [auth B] Focus chain RA [auth H] Focus chain V [auth C] Focus chain VA [auth I] Focus chain Z [auth D] Focus chain ZA [auth J]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain BA [auth E] SDF format, chain FA [auth F] SDF format, chain JA [auth G] SDF format, chain L [auth A] SDF format, chain P [auth B] SDF format, chain PA [auth H] SDF format, chain T [auth C] SDF format, chain TA [auth I] SDF format, chain X [auth D] SDF format, chain XA [auth J] MOL2 format, chain BA [auth E] MOL2 format, chain FA [auth F] MOL2 format, chain JA [auth G] MOL2 format, chain L [auth A] MOL2 format, chain P [auth B] MOL2 format, chain PA [auth H] MOL2 format, chain T [auth C] MOL2 format, chain TA [auth I] MOL2 format, chain X [auth D] MOL2 format, chain XA [auth J] mmCIF format, chain BA [auth E] mmCIF format, chain FA [auth F] mmCIF format, chain JA [auth G] mmCIF format, chain L [auth A] mmCIF format, chain P [auth B] mmCIF format, chain PA [auth H] mmCIF format, chain T [auth C] mmCIF format, chain TA [auth I] mmCIF format, chain X [auth D] mmCIF format, chain XA [auth J]	BA [auth E] FA [auth F] JA [auth G] L [auth A] P [auth B] BA [auth E], FA [auth F], JA [auth G], L [auth A], P [auth B], PA [auth H], T [auth C], TA [auth I], X [auth D], XA [auth J]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain BA [auth E] Focus chain FA [auth F] Focus chain JA [auth G] Focus chain L [auth A] Focus chain P [auth B] Focus chain PA [auth H] Focus chain T [auth C] Focus chain TA [auth I] Focus chain X [auth D] Focus chain XA [auth J] Interactions & Density Focus chain BA [auth E] Focus chain FA [auth F] Focus chain JA [auth G] Focus chain L [auth A] Focus chain P [auth B] Focus chain PA [auth H] Focus chain T [auth C] Focus chain TA [auth I] Focus chain X [auth D] Focus chain XA [auth J]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain KA [auth G] SDF format, chain LA [auth G] MOL2 format, chain KA [auth G] MOL2 format, chain LA [auth G] mmCIF format, chain KA [auth G] mmCIF format, chain LA [auth G]	KA [auth G], LA [auth G]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain KA [auth G] Focus chain LA [auth G] Interactions & Density Focus chain KA [auth G] Focus chain LA [auth G]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.36 Å
R-Value Free: 0.209 (Depositor), 0.210 (DCC)
R-Value Work: 0.189 (Depositor), 0.192 (DCC)
R-Value Observed: 0.190 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 341.993	α = 90
b = 60.787	β = 91.41
c = 191.789	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2010-03-02

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-03-02
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Other, Structure summary
Version 1.3: 2023-12-20
Changes: Data collection, Database references, Refinement description, Structure summary