1G29

MALK

• PDB DOI:  https://doi.org/10.2210/pdb1G29/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Thermococcus litoralis
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2000-10-18 Released: 2000-12-06 
• Deposition Author(s): Diederichs, K., Diez, J., Greller, G., Mueller, C., Breed, J., Schnell, C., Vonrhein, C., Boos, W., Welte, W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.247 
• R-Value Work: 0.211 

Literature

Crystal structure of MalK, the ATPase subunit of the trehalose/maltose ABC transporter of the archaeon Thermococcus litoralis.

Diederichs, K., Diez, J., Greller, G., Muller, C., Breed, J., Schnell, C., Vonrhein, C., Boos, W., Welte, W.

(2000) EMBO J 19: 5951-5961

• PubMed: 11080142 
• DOI: https://doi.org/10.1093/emboj/19.22.5951
• Primary Citation of Related Structures:  
  1G29


• PubMed Abstract: 
  

The members of the ABC transporter family transport a wide variety of molecules into or out of cells and cellular compartments. Apart from a translocation pore, each member possesses two similar nucleoside triphosphate-binding subunits or domains in order to couple the energy-providing reaction with transport. In the maltose transporter of several Gram-negative bacteria and the archaeon Thermo coccus litoralis, the nucleoside triphosphate-binding subunit contains a C-terminal regulatory domain. A dimer of the subunit is attached cytoplasmically to the translocation pore. Here we report the crystal structure of this dimer showing two bound pyrophosphate molecules at 1.9 A resolution. The dimer forms by association of the ATPase domains, with the two regulatory domains attached at opposite poles. Significant deviation from 2-fold symmetry is seen at the interface of the dimer and in the regions corresponding to those residues known to be in contact with the translocation pore. The structure and its relationship to function are discussed in the light of known mutations from the homologous Escherichia coli and Salmonella typhimurium proteins.

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Organizational Affiliation: 

Fachbereich Biologie, Universität Konstanz, M656, D-78457 Konstanz, Germany.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 2  

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 85.65 kDa 
• Atom Count: 6,362 
• Modelled Residue Count: 744 
• Deposited Residue Count: 744 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MALTOSE TRANSPORT PROTEIN MALK	A [auth 1], B [auth 2]	372	Thermococcus litoralis	Mutation(s): 0  Gene Names: malK EC: 7.5.2.1
UniProt
Find proteins for Q9YGA6 (Thermococcus litoralis (strain ATCC 51850 / DSM 5473 / JCM 8560 / NS-C)) Explore Q9YGA6  Go to UniProtKB:  Q9YGA6

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
POP	AA [auth 1], GB [auth 2]	PYROPHOSPHATE 2- H2 O7 P2 XPPKVPWEQAFLFU-UHFFFAOYSA-L
DIO	BA [auth 1], CA [auth 1], DA [auth 1]	1,4-DIETHYLENE DIOXIDE C4 H8 O2 RYHBNJHYFVUHQT-UHFFFAOYSA-N
CL	AB [auth 2], BB [auth 2], D [auth 1], E [auth 1], EB [auth 2], HA [auth 2], JA [auth 2], K [auth 1], MA [auth 2], U [auth 1]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	GA [auth 2], H [auth 1], KA [auth 2], N [auth 1], QA [auth 2], RA [auth 2], SA [auth 2], UA [auth 2], V [auth 1], W [auth 1], YA [auth 2]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA	CB [auth 2], DB [auth 2], F [auth 1], FB [auth 2], G [auth 1], I [auth 1], IA [auth 2], J [auth 1], L [auth 1], LA [auth 2], M [auth 1], NA [auth 2], O [auth 1], OA [auth 2], P [auth 1], PA [auth 2], Q [auth 1], R [auth 1], S [auth 1], T [auth 1], TA [auth 2], VA [auth 2], WA [auth 2], X [auth 1], XA [auth 2], Y [auth 1], Z [auth 1], ZA [auth 2]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N
NH4	C [auth 1], EA [auth 2], FA [auth 2]	AMMONIUM ION H4 N QGZKDVFQNNGYKY-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.247 
• R-Value Work: 0.211 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 190.718	α = 90
b = 65.705	β = 90
c = 77.912	γ = 90

Software Package:

Software Name	Purpose
SHARP	phasing
CNS	refinement
MAR345	data collection
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-12-06 
Deposition Author(s): Diederichs, K., Diez, J., Greller, G., Mueller, C., Breed, J., Schnell, C., Vonrhein, C., Boos, W., Welte, W.

Revision History  

• Version 1.0: 2000-12-06
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-04
  Changes: Refinement description