2X86 | pdb_00002x86

AGME bound to ADP-B-mannose

PDB DOI: https://doi.org/10.2210/pdb2X86/pdb

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

Deposited: 2010-03-06 Released: 2010-03-16
Deposition Author(s): Kowatz, T., Morrison, J.P., Tanner, M.E., Naismith, J.H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.272 (Depositor), 0.273 (DCC)
R-Value Work:
0.252 (Depositor), 0.253 (DCC)
R-Value Observed:
0.253 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 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: 824.67 kDa
Atom Count: 51,434
Modeled Residue Count: 6,140
Deposited Residue Count: 7,140
Unique protein chains: 1

Macromolecules

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| 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, K, L, M, N, O, P, Q, R, S, T	357	Escherichia coli	Mutation(s): 1 EC: 5.1.3.20
UniProt
Find proteins for P67911 (Escherichia coli O157:H7) Explore P67911 Go to UniProtKB: P67911
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P67911
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAP Query on NAP Download:Ideal Coordinates CCD File SDF format, chain DB [auth M] SDF format, chain FA [auth E] SDF format, chain GB [auth N] SDF format, chain IA [auth F] SDF format, chain LA [auth G] SDF format, chain MB [auth P] SDF format, chain OA [auth H] SDF format, chain PB [auth Q] SDF format, chain RA [auth I] SDF format, chain VB [auth S] SDF format, chain X [auth B] SDF format, chain XA [auth K] SDF format, chain Z [auth C] SDF format, chain YB [auth T] SDF format, chain UA [auth J] SDF format, chain U [auth A] SDF format, chain SB [auth R] SDF format, chain JB [auth O] SDF format, chain CA [auth D] SDF format, chain AB [auth L] MOL2 format, chain DB [auth M] MOL2 format, chain FA [auth E] MOL2 format, chain GB [auth N] MOL2 format, chain IA [auth F] MOL2 format, chain LA [auth G] MOL2 format, chain MB [auth P] MOL2 format, chain OA [auth H] MOL2 format, chain PB [auth Q] MOL2 format, chain RA [auth I] MOL2 format, chain VB [auth S] MOL2 format, chain X [auth B] MOL2 format, chain XA [auth K] MOL2 format, chain Z [auth C] MOL2 format, chain YB [auth T] MOL2 format, chain UA [auth J] MOL2 format, chain U [auth A] MOL2 format, chain SB [auth R] MOL2 format, chain JB [auth O] MOL2 format, chain CA [auth D] MOL2 format, chain AB [auth L] mmCIF format, chain DB [auth M] mmCIF format, chain FA [auth E] mmCIF format, chain GB [auth N] mmCIF format, chain IA [auth F] mmCIF format, chain LA [auth G] mmCIF format, chain MB [auth P] mmCIF format, chain OA [auth H] mmCIF format, chain PB [auth Q] mmCIF format, chain RA [auth I] mmCIF format, chain VB [auth S] mmCIF format, chain X [auth B] mmCIF format, chain XA [auth K] mmCIF format, chain Z [auth C] mmCIF format, chain YB [auth T] mmCIF format, chain UA [auth J] mmCIF format, chain U [auth A] mmCIF format, chain SB [auth R] mmCIF format, chain JB [auth O] mmCIF format, chain CA [auth D] mmCIF format, chain AB [auth L]	AB [auth L] CA [auth D] DB [auth M] FA [auth E] GB [auth N] AB [auth L], CA [auth D], DB [auth M], FA [auth E], GB [auth N], IA [auth F], JB [auth O], LA [auth G], MB [auth P], OA [auth H], PB [auth Q], RA [auth I], SB [auth R], U [auth A], UA [auth J], VB [auth S], X [auth B], XA [auth K], YB [auth T], Z [auth C]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain AB [auth L] Focus chain CA [auth D] Focus chain DB [auth M] Focus chain FA [auth E] Focus chain GB [auth N] Focus chain IA [auth F] Focus chain JB [auth O] Focus chain LA [auth G] Focus chain MB [auth P] Focus chain OA [auth H] Focus chain PB [auth Q] Focus chain RA [auth I] Focus chain SB [auth R] Focus chain U [auth A] Focus chain UA [auth J] Focus chain VB [auth S] Focus chain X [auth B] Focus chain XA [auth K] Focus chain YB [auth T] Focus chain Z [auth C] Interactions & Density Focus chain AB [auth L] Focus chain CA [auth D] Focus chain DB [auth M] Focus chain FA [auth E] Focus chain GB [auth N] Focus chain IA [auth F] Focus chain JB [auth O] Focus chain LA [auth G] Focus chain MB [auth P] Focus chain OA [auth H] Focus chain PB [auth Q] Focus chain RA [auth I] Focus chain SB [auth R] Focus chain U [auth A] Focus chain UA [auth J] Focus chain VB [auth S] Focus chain X [auth B] Focus chain XA [auth K] Focus chain YB [auth T] Focus chain Z [auth C]
ADP Query on ADP Download:Ideal Coordinates CCD File SDF format, chain EB [auth M] SDF format, chain GA [auth E] SDF format, chain HB [auth N] SDF format, chain JA [auth F] SDF format, chain MA [auth G] SDF format, chain NB [auth P] SDF format, chain PA [auth H] SDF format, chain QB [auth Q] SDF format, chain TB [auth R] SDF format, chain V [auth A] SDF format, chain Y [auth B] SDF format, chain ZB [auth T] SDF format, chain YA [auth K] SDF format, chain WB [auth S] SDF format, chain VA [auth J] SDF format, chain SA [auth I] SDF format, chain KB [auth O] SDF format, chain DA [auth D] SDF format, chain BB [auth L] SDF format, chain AA [auth C] MOL2 format, chain EB [auth M] MOL2 format, chain GA [auth E] MOL2 format, chain HB [auth N] MOL2 format, chain JA [auth F] MOL2 format, chain MA [auth G] MOL2 format, chain NB [auth P] MOL2 format, chain PA [auth H] MOL2 format, chain QB [auth Q] MOL2 format, chain TB [auth R] MOL2 format, chain V [auth A] MOL2 format, chain Y [auth B] MOL2 format, chain ZB [auth T] MOL2 format, chain YA [auth K] MOL2 format, chain WB [auth S] MOL2 format, chain VA [auth J] MOL2 format, chain SA [auth I] MOL2 format, chain KB [auth O] MOL2 format, chain DA [auth D] MOL2 format, chain BB [auth L] MOL2 format, chain AA [auth C] mmCIF format, chain EB [auth M] mmCIF format, chain GA [auth E] mmCIF format, chain HB [auth N] mmCIF format, chain JA [auth F] mmCIF format, chain MA [auth G] mmCIF format, chain NB [auth P] mmCIF format, chain PA [auth H] mmCIF format, chain QB [auth Q] mmCIF format, chain TB [auth R] mmCIF format, chain V [auth A] mmCIF format, chain Y [auth B] mmCIF format, chain ZB [auth T] mmCIF format, chain YA [auth K] mmCIF format, chain WB [auth S] mmCIF format, chain VA [auth J] mmCIF format, chain SA [auth I] mmCIF format, chain KB [auth O] mmCIF format, chain DA [auth D] mmCIF format, chain BB [auth L] mmCIF format, chain AA [auth C]	AA [auth C] BB [auth L] DA [auth D] EB [auth M] GA [auth E] AA [auth C], BB [auth L], DA [auth D], EB [auth M], GA [auth E], HB [auth N], JA [auth F], KB [auth O], MA [auth G], NB [auth P], PA [auth H], QB [auth Q], SA [auth I], TB [auth R], V [auth A], VA [auth J], WB [auth S], Y [auth B], YA [auth K], ZB [auth T]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain AA [auth C] Focus chain BB [auth L] Focus chain DA [auth D] Focus chain EB [auth M] Focus chain GA [auth E] Focus chain HB [auth N] Focus chain JA [auth F] Focus chain KB [auth O] Focus chain MA [auth G] Focus chain NB [auth P] Focus chain PA [auth H] Focus chain QB [auth Q] Focus chain SA [auth I] Focus chain TB [auth R] Focus chain V [auth A] Focus chain VA [auth J] Focus chain WB [auth S] Focus chain Y [auth B] Focus chain YA [auth K] Focus chain ZB [auth T] Interactions & Density Focus chain AA [auth C] Focus chain BB [auth L] Focus chain DA [auth D] Focus chain EB [auth M] Focus chain GA [auth E] Focus chain HB [auth N] Focus chain JA [auth F] Focus chain KB [auth O] Focus chain MA [auth G] Focus chain NB [auth P] Focus chain PA [auth H] Focus chain QB [auth Q] Focus chain SA [auth I] Focus chain TB [auth R] Focus chain V [auth A] Focus chain VA [auth J] Focus chain WB [auth S] Focus chain Y [auth B] Focus chain YA [auth K] Focus chain ZB [auth T]
BMA Query on BMA Download:Ideal Coordinates CCD File SDF format, chain CB [auth L] SDF format, chain FB [auth M] SDF format, chain HA [auth E] SDF format, chain KA [auth F] SDF format, chain LB [auth O] SDF format, chain QA [auth H] SDF format, chain RB [auth Q] SDF format, chain UB [auth R] SDF format, chain XB [auth S] SDF format, chain ZA [auth K] SDF format, chain WA [auth J] SDF format, chain W [auth A] SDF format, chain TA [auth I] SDF format, chain OB [auth P] SDF format, chain NA [auth G] SDF format, chain IB [auth N] SDF format, chain EA [auth D] SDF format, chain BA [auth C] SDF format, chain AC [auth T] MOL2 format, chain CB [auth L] MOL2 format, chain FB [auth M] MOL2 format, chain HA [auth E] MOL2 format, chain KA [auth F] MOL2 format, chain LB [auth O] MOL2 format, chain QA [auth H] MOL2 format, chain RB [auth Q] MOL2 format, chain UB [auth R] MOL2 format, chain XB [auth S] MOL2 format, chain ZA [auth K] MOL2 format, chain WA [auth J] MOL2 format, chain W [auth A] MOL2 format, chain TA [auth I] MOL2 format, chain OB [auth P] MOL2 format, chain NA [auth G] MOL2 format, chain IB [auth N] MOL2 format, chain EA [auth D] MOL2 format, chain BA [auth C] MOL2 format, chain AC [auth T] mmCIF format, chain CB [auth L] mmCIF format, chain FB [auth M] mmCIF format, chain HA [auth E] mmCIF format, chain KA [auth F] mmCIF format, chain LB [auth O] mmCIF format, chain QA [auth H] mmCIF format, chain RB [auth Q] mmCIF format, chain UB [auth R] mmCIF format, chain XB [auth S] mmCIF format, chain ZA [auth K] mmCIF format, chain WA [auth J] mmCIF format, chain W [auth A] mmCIF format, chain TA [auth I] mmCIF format, chain OB [auth P] mmCIF format, chain NA [auth G] mmCIF format, chain IB [auth N] mmCIF format, chain EA [auth D] mmCIF format, chain BA [auth C] mmCIF format, chain AC [auth T]	AC [auth T] BA [auth C] CB [auth L] EA [auth D] FB [auth M] AC [auth T], BA [auth C], CB [auth L], EA [auth D], FB [auth M], HA [auth E], IB [auth N], KA [auth F], LB [auth O], NA [auth G], OB [auth P], QA [auth H], RB [auth Q], TA [auth I], UB [auth R], W [auth A], WA [auth J], XB [auth S], ZA [auth K]	beta-D-mannopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-RWOPYEJCSA-N		Interactions Focus chain AC [auth T] Focus chain BA [auth C] Focus chain CB [auth L] Focus chain EA [auth D] Focus chain FB [auth M] Focus chain HA [auth E] Focus chain IB [auth N] Focus chain KA [auth F] Focus chain LB [auth O] Focus chain NA [auth G] Focus chain OB [auth P] Focus chain QA [auth H] Focus chain RB [auth Q] Focus chain TA [auth I] Focus chain UB [auth R] Focus chain W [auth A] Focus chain WA [auth J] Focus chain XB [auth S] Focus chain ZA [auth K] Interactions & Density Focus chain AC [auth T] Focus chain BA [auth C] Focus chain CB [auth L] Focus chain EA [auth D] Focus chain FB [auth M] Focus chain HA [auth E] Focus chain IB [auth N] Focus chain KA [auth F] Focus chain LB [auth O] Focus chain NA [auth G] Focus chain OB [auth P] Focus chain QA [auth H] Focus chain RB [auth Q] Focus chain TA [auth I] Focus chain UB [auth R] Focus chain W [auth A] Focus chain WA [auth J] Focus chain XB [auth S] Focus chain ZA [auth K]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.272 (Depositor), 0.273 (DCC)
R-Value Work: 0.252 (Depositor), 0.253 (DCC)
R-Value Observed: 0.253 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 138.074	α = 90
b = 162.458	β = 101.45
c = 185.027	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2010-03-16

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-03-16
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2017-06-28
Changes: Data collection
Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Other, Structure summary
Version 1.4: 2023-12-20
Changes: Data collection, Database references, Refinement description, Structure summary