3RLF

Crystal structure of the maltose-binding protein/maltose transporter complex in an outward-facing conformation bound to MgAMPPNP

• PDB DOI: https://doi.org/10.2210/pdb3RLF/pdb

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


• Deposited: 2011-04-19 Released: 2011-08-10 
• Deposition Author(s): Oldham, M.L., Chen, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.254 
• R-Value Work: 0.223 
• R-Value Observed: 0.225 

Starting Model: experimental

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 
• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A2B1C1D1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 220.46 kDa 
• Atom Count: 15,268 
• Modelled Residue Count: 1,892 
• Deposited Residue Count: 1,952 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Maltose-binding periplasmic protein	A [auth E]	380	Escherichia coli K-12	Mutation(s): 0  Gene Names: malE, b4034, JW3994 Membrane Entity: Yes
UniProt
Find proteins for P0AEX9 (Escherichia coli (strain K12)) Explore P0AEX9  Go to UniProtKB:  P0AEX9

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: malF, b4033, JW3993 Membrane Entity: Yes
UniProt
Find proteins for P02916 (Escherichia coli (strain K12)) Explore P02916  Go to UniProtKB:  P02916

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: malG, b4032, JW3992 Membrane Entity: Yes
UniProt
Find proteins for P68183 (Escherichia coli (strain K12)) Explore P68183  Go to UniProtKB:  P68183

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: malK, b4035, JW3995 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

Oligosaccharides

Help

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
Glycosylation Resources
GlyTouCan:  G07411ON GlyCosmos:  G07411ON

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PGV	H [auth F], I [auth F], J [auth G], K [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
ANP	M [auth A], O [auth B]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C10 H17 N6 O12 P3 PVKSNHVPLWYQGJ-KQYNXXCUSA-N
UMQ	G [auth E]	UNDECYL-MALTOSIDE C23 H44 O11 UYEMNFYVTFDKRG-ZNGNCRBCSA-N
MG	L [auth A], N [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.254 
• R-Value Work: 0.223 
• R-Value Observed: 0.225 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.098	α = 86.7
b = 95.812	β = 82.68
c = 109.983	γ = 76.4

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-08-10 
Deposition Author(s): Oldham, M.L., Chen, J.

Revision History  

• Version 1.0: 2011-08-10
  Type: Initial release
  
• Version 1.1: 2011-08-24
  Changes: Database references
• Version 1.2: 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: 2023-09-13
  Changes: Data collection, Database references, Refinement description, Structure summary