2JLN | pdb_00002jln

Structure of Mhp1, a nucleobase-cation-symport-1 family transporter

• PDB DOI: https://doi.org/10.2210/pdb2JLN/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Microbacterium maritypicum
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 2008-09-11 Released: 2008-10-28 
• Deposition Author(s): Weyand, S., Shimamura, T., Yajima, S., Suzuki, S., Mirza, O., Krusong, K., Carpenter, E.P., Rutherford, N.G., Hadden, J.M., O'Reilly, J., Ma, P., Saidijam, M., Patching, S.G., Hope, R.J., Norbertczak, H.T., Roach, P.C.J., Iwata, S., Henderson, P.J.F., Cameron, A.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free: 
  0.281 (Depositor), 0.228 (DCC) 
• R-Value Work: 
  0.234 (Depositor), 0.224 (DCC) 
• R-Value Observed: 
  0.236 (Depositor) 

Literature

Structure and Molecular Mechanism of a Nucleobase-Cation-Symport-1 Family Transporter.

Weyand, S., Shimamura, T., Yajima, S., Suzuki, S., Mirza, O., Krusong, K., Carpenter, E.P., Rutherford, N.G., Hadden, J.M., O'Reilly, J., Ma, P., Saidijam, M., Patching, S.G., Hope, R.J., Norbertczak, H.T., Roach, P.C.J., Iwata, S., Henderson, P.J.F., Cameron, A.D.

(2008) Science 322: 709

• PubMed: 18927357 
• DOI: https://doi.org/10.1126/science.1164440
• Primary Citation Related Structures: 
  2JLN


• PubMed Abstract: 
  

  The nucleobase-cation-symport-1 (NCS1) transporters are essential components of salvage pathways for nucleobases and related metabolites. Here, we report the 2.85-angstrom resolution structure of the NCS1 benzyl-hydantoin transporter, Mhp1, from Microbacterium liquefaciens. Mhp1 contains 12 transmembrane helices, 10 of which are arranged in two inverted repeats of five helices. The structures of the outward-facing open and substrate-bound occluded conformations were solved, showing how the outward-facing cavity closes upon binding of substrate. Comparisons with the leucine transporter LeuT(Aa) and the galactose transporter vSGLT reveal that the outward- and inward-facing cavities are symmetrically arranged on opposite sides of the membrane. The reciprocal opening and closing of these cavities is synchronized by the inverted repeat helices 3 and 8, providing the structural basis of the alternating access model for membrane transport.

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Organizational Affiliation: 
• Membrane Protein Laboratory, Diamond Light Source Limited, Harwell Science and Innovation Campus, Chilton, Didcot, Oxfordshire OX11 0DE, UK.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 54.84 kDa 
• Atom Count: 3,571 
• Modeled Residue Count: 464 
• Deposited Residue Count: 501 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MHP1	A	501	Microbacterium maritypicum	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for D6R8X8 (Microbacterium maritypicum) Explore D6R8X8  Go to UniProtKB:  D6R8X8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HG	C [auth A]	MERCURY (II) ION Hg BQPIGGFYSBELGY-UHFFFAOYSA-N
NA	B [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free:  0.281 (Depositor), 0.228 (DCC) 
• R-Value Work:  0.234 (Depositor), 0.224 (DCC) 
• R-Value Observed: 0.236 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.7	α = 90
b = 109.14	β = 90
c = 113.82	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-10-28 
Deposition Author(s): Weyand, S., Shimamura, T., Yajima, S., Suzuki, S., Mirza, O., Krusong, K., Carpenter, E.P., Rutherford, N.G., Hadden, J.M., O'Reilly, J., Ma, P., Saidijam, M., Patching, S.G., Hope, R.J., Norbertczak, H.T., Roach, P.C.J., Iwata, S., Henderson, P.J.F., Cameron, A.D.

Revision History  

• Version 1.0: 2008-10-28
  Type: Initial release
  
• Version 1.1: 2011-05-07
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-05-08
  Changes: Data collection, Database references, Derived calculations, Other