3PUX

Crystal Structure of an outward-facing MBP-Maltose transporter complex bound to ADP-BeF3

PDB DOI: https://doi.org/10.2210/pdb3PUX/pdb

Classification: HYDROLASE/TRANSPORT PROTEIN
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli
Mutation(s): No
Membrane Protein: Yes PDBTMMemProtMDmpstruc

Deposited: 2010-12-06 Released: 2011-08-10
Deposition Author(s): Oldham, M.L., Chen, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.265
R-Value Work: 0.228
R-Value Observed: 0.230

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Snapshots of the maltose transporter during ATP hydrolysis.

Oldham, M.L., Chen, J.

(2011) Proc Natl Acad Sci U S A 108: 15152-15156

PubMed: 21825153 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1073/pnas.1108858108
Primary Citation of Related Structures:
3PUV, 3PUW, 3PUX, 3RLF

PubMed Abstract:
ATP-binding cassette transporters are powered by ATP, but the mechanism by which these transporters hydrolyze ATP is unclear. In this study, four crystal structures of the full-length wild-type maltose transporter, stabilized by adenosine 5'-(β,γ-imido)triphosphate or ADP in conjunction with phosphate analogs BeF(3)(-), VO(4)(3-), or AIF(4)(-), were determined to 2.2- to 2.4-Å resolution. These structures led to the assignment of two enzymatic states during ATP hydrolysis and demonstrate specific functional roles of highly conserved residues in the nucleotide-binding domain, suggesting that ATP-binding cassette transporters catalyze ATP hydrolysis via a general base mechanism.

Organizational Affiliation

Department of Biological Sciences, Purdue University, Howard Hughes Medical Institute, 240 Martin Jischke Boulevard, West Lafayette, IN 47907, USA.

Macromolecule Content

Total Structure Weight: 224.65 kDa
Atom Count: 15,273
Modelled Residue Count: 1,886
Deposited Residue Count: 1,950
Unique protein chains: 4

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Maltose-binding periplasmic protein	A [auth E]	378	Escherichia coli K-12	Mutation(s): 0 Gene Names: b4034, ECDH10B_4223, JW3994, malE Membrane Entity: Yes
UniProt
Find proteins for P0AEX9 (Escherichia coli (strain K12)) Explore P0AEX9 Go to UniProtKB: P0AEX9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0AEX9
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Maltose transport system permease protein malF	B [auth F]	514	Escherichia coli K-12	Mutation(s): 0 Gene Names: b4033, ECDH10B_4222, JW3993, malF Membrane Entity: Yes
UniProt
Find proteins for P02916 (Escherichia coli (strain K12)) Explore P02916 Go to UniProtKB: P02916
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P02916
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Maltose transport system permease protein malG	C [auth G]	296	Escherichia coli K-12	Mutation(s): 0 Gene Names: b4032, ECDH10B_4221, JW3992, malG Membrane Entity: Yes
UniProt
Find proteins for P68183 (Escherichia coli (strain K12)) Explore P68183 Go to UniProtKB: P68183
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P68183
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Maltose/maltodextrin import ATP-binding protein MalK	D [auth A], E [auth B]	381	Escherichia coli K-12	Mutation(s): 0 Gene Names: b4035, ECDH10B_4224, JW3995, malK EC: 3.6.3.19 (PDB Primary Data), 7.5.2.1 (UniProt) Membrane Entity: Yes
UniProt
Find proteins for P68187 (Escherichia coli (strain K12)) Explore P68187 Go to UniProtKB: P68187
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P68187
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	F [auth C]	2		N/A	Interactions Focus chain F [auth C] Interactions & Density Focus chain F [auth C]
Glycosylation Resources
GlyTouCan: G07411ON GlyCosmos: G07411ON

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PGV Query on PGV Download Ideal Coordinates CCD File SDF format, chain H [auth F] SDF format, chain I [auth F] SDF format, chain J [auth F] SDF format, chain K [auth F] SDF format, chain L [auth G] SDF format, chain M [auth G] SDF format, chain N [auth G] SDF format, chain O [auth G] SDF format, chain P [auth G] SDF format, chain Q [auth G] MOL2 format, chain H [auth F] MOL2 format, chain I [auth F] MOL2 format, chain J [auth F] MOL2 format, chain K [auth F] MOL2 format, chain L [auth G] MOL2 format, chain M [auth G] MOL2 format, chain N [auth G] MOL2 format, chain O [auth G] MOL2 format, chain P [auth G] MOL2 format, chain Q [auth G] mmCIF format, chain H [auth F] mmCIF format, chain I [auth F] mmCIF format, chain J [auth F] mmCIF format, chain K [auth F] mmCIF format, chain L [auth G] mmCIF format, chain M [auth G] mmCIF format, chain N [auth G] mmCIF format, chain O [auth G] mmCIF format, chain P [auth G] mmCIF format, chain Q [auth G]	H [auth F] I [auth F] J [auth F] K [auth F] L [auth G] H [auth F], I [auth F], J [auth F], K [auth F], L [auth G], M [auth G], N [auth G], O [auth G], P [auth G], Q [auth G]	(1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE C₄₀ H₇₇ O₁₀ P ADYWCMPUNIVOEA-GPJPVTGXSA-N		Interactions Focus chain H [auth F] Focus chain I [auth F] Focus chain J [auth F] Focus chain K [auth F] Focus chain L [auth G] Focus chain M [auth G] Focus chain N [auth G] Focus chain O [auth G] Focus chain P [auth G] Focus chain Q [auth G] Interactions & Density Focus chain H [auth F] Focus chain I [auth F] Focus chain J [auth F] Focus chain K [auth F] Focus chain L [auth G] Focus chain M [auth G] Focus chain N [auth G] Focus chain O [auth G] Focus chain P [auth G] Focus chain Q [auth G]
UMQ Query on UMQ Download Ideal Coordinates CCD File SDF format, chain G [auth E] MOL2 format, chain G [auth E] mmCIF format, chain G [auth E]	G [auth E]	UNDECYL-MALTOSIDE C₂₃ H₄₄ O₁₁ UYEMNFYVTFDKRG-ZNGNCRBCSA-N		Interactions Focus chain G [auth E] Interactions & Density Focus chain G [auth E]
ADP Query on ADP Download Ideal Coordinates CCD File SDF format, chain S [auth A] SDF format, chain V [auth B] MOL2 format, chain S [auth A] MOL2 format, chain V [auth B] mmCIF format, chain S [auth A] mmCIF format, chain V [auth B]	S [auth A], V [auth B]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain S [auth A] Focus chain V [auth B] Interactions & Density Focus chain S [auth A] Focus chain V [auth B]
BEF Query on BEF Download Ideal Coordinates CCD File SDF format, chain T [auth A] SDF format, chain W [auth B] MOL2 format, chain T [auth A] MOL2 format, chain W [auth B] mmCIF format, chain T [auth A] mmCIF format, chain W [auth B]	T [auth A], W [auth B]	BERYLLIUM TRIFLUORIDE ION Be F₃ OGIAHMCCNXDTIE-UHFFFAOYSA-K		Interactions Focus chain T [auth A] Focus chain W [auth B] Interactions & Density Focus chain T [auth A] Focus chain W [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain R [auth A] SDF format, chain U [auth B] MOL2 format, chain R [auth A] MOL2 format, chain U [auth B] mmCIF format, chain R [auth A] mmCIF format, chain U [auth B]	R [auth A], U [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain R [auth A] Focus chain U [auth B] Interactions & Density Focus chain R [auth A] Focus chain U [auth B]

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 5
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900001 Query on PRD_900001	F [auth C]	alpha-maltose	Oligosaccharide / Nutrient		Interactions Focus chain F [auth C] Interactions & Density Focus chain F [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.265
R-Value Work: 0.228
R-Value Observed: 0.230
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.13	α = 85.58
b = 97.34	β = 78.98
c = 112.84	γ = 72.25

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2011-08-10

Deposition Author(s):

Oldham, M.L.

Chen, J.

Revision History (Full details and data files)

Version 1.0: 2011-08-10
Type: Initial release
Version 1.1: 2011-09-28
Changes: Database references
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
Version 2.1: 2023-09-06
Changes: Data collection, Database references, Refinement description, Structure summary