4IN7

(M)L214N mutant of the Rhodobacter sphaeroides Reaction Center


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.174 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Role of Rhodobacter sphaeroides photosynthetic reaction center residue M214 in the composition, absorbance properties, and conformations of H(A) and B(A) cofactors.

Saer, R.G.Hardjasa, A.Rosell, F.I.Mauk, A.G.Murphy, M.E.Beatty, J.T.

(2013) Biochemistry 52: 2206-2217

  • DOI: 10.1021/bi400207m
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • In the native reaction center (RC) of Rhodobacter sphaeroides, the side chain of (M)L214 projects orthogonally toward the plane and into the center of the A branch bacteriopheophytin (BPhe) macrocycle. The possibility that this side chain is responsi ...

    In the native reaction center (RC) of Rhodobacter sphaeroides, the side chain of (M)L214 projects orthogonally toward the plane and into the center of the A branch bacteriopheophytin (BPhe) macrocycle. The possibility that this side chain is responsible for the dechelation of the central Mg(2+) of bacteriochlorophyll (BChl) was investigated by replacement of (M)214 with residues possessing small, nonpolar side chains that can neither coordinate nor block access to the central metal ion. The (M)L214 side chain was also replaced with Cys, Gln, and Asn to evaluate further the requirements for assembly of the RC with BChl in the HA pocket. Photoheterotrophic growth studies showed no difference in growth rates of the (M)214 nonpolar mutants at a low light intensity, but the growth of the amide-containing mutants was impaired. The absorbance spectra of purified RCs indicated that although absorbance changes are associated with the nonpolar mutations, the nonpolar mutant RC pigment compositions are the same as in the wild-type protein. Crystal structures of the (M)L214G, (M)L214A, and (M)L214N mutants were determined (determined to 2.2-2.85 Å resolution), confirming the presence of BPhe in the HA pocket and revealing alternative conformations of the phytyl tail of the accessory BChl in the BA site of these nonpolar mutants. Our results demonstrate that (i) BChl is converted to BPhe in a manner independent of the aliphatic side chain length of nonpolar residues replacing (M)214, (ii) BChl replaces BPhe if residue (M)214 has an amide-bearing side chain, (iii) (M)214 side chains containing sulfur are not sufficient to bind BChl in the HA pocket, and (iv) the (M)214 side chain influences the conformation of the phytyl tail of the BA BChl.


    Organizational Affiliation

    Department of Microbiology and Immunology, The University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC, Canada V6T 1Z3.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Reaction center protein H chain
H
266Rhodobacter sphaeroidesGene Names: puhA
Find proteins for P0C0Y7 (Rhodobacter sphaeroides)
Go to UniProtKB:  P0C0Y7
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Reaction center protein L chain
L
282Rhodobacter sphaeroidesGene Names: pufL
Find proteins for P0C0Y8 (Rhodobacter sphaeroides)
Go to UniProtKB:  P0C0Y8
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Reaction center protein M chain
M
307Rhodobacter sphaeroidesMutations: N215L
Gene Names: pufM
Find proteins for P0C0Y9 (Rhodobacter sphaeroides)
Go to UniProtKB:  P0C0Y9
Small Molecules
Ligands 14 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

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H
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
GGD
Query on GGD

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H
NONADEC-10-ENOIC ACID 2-[3,4-DIHYDROXY-6-HYDROXYMETHYL-5-(3,4,5-TRIHYDROXY-6-HYDROXYMETHYL-TETRAHYDRO-PYRAN-2-YLOXY)-TETRAHYDRO-PYRAN-2-YLOXY]-1-OCTADEC-9-ENOYLOXYMETHYL-ETHYL ESTER
GLUCOSYL-GALACTOSYL DIACYL-GLYCEROL
C52 H94 O15
OGKQOSUHVSQNSH-IQXSWRQFSA-N
 Ligand Interaction
PO4
Query on PO4

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L
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
U10
Query on U10

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L, M
UBIQUINONE-10
Coenzyme Q10
C59 H90 O4
ACTIUHUUMQJHFO-UPTCCGCDSA-N
 Ligand Interaction
CDL
Query on CDL

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M
CARDIOLIPIN
DIPHOSPHATIDYL GLYCEROL; BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
 Ligand Interaction
PC1
Query on PC1

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M
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
3-SN-PHOSPHATIDYLCHOLINE
C44 H88 N O8 P
NRJAVPSFFCBXDT-HUESYALOSA-N
 Ligand Interaction
GOL
Query on GOL

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H, L
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
BCL
Query on BCL

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L, M
BACTERIOCHLOROPHYLL A
C55 H74 Mg N4 O6
DSJXIQQMORJERS-RUUWGSCADZ
 Ligand Interaction
LDA
Query on LDA

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L, M
LAURYL DIMETHYLAMINE-N-OXIDE
C14 H31 N O
SYELZBGXAIXKHU-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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M
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
FE
Query on FE

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M
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
HTO
Query on HTO

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L
HEPTANE-1,2,3-TRIOL
C7 H16 O3
HXYCHJFUBNTKQR-RNFRBKRXSA-N
 Ligand Interaction
BPH
Query on BPH

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M
BACTERIOPHEOPHYTIN A
C55 H76 N4 O6
KWOZSBGNAHVCKG-SZQBJALDSA-N
 Ligand Interaction
SPO
Query on SPO

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M
SPHEROIDENE
C41 H60 O
FJOCMTHZSURUFA-KXCOHNEYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.174 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 139.138α = 90.00
b = 139.138β = 90.00
c = 185.140γ = 120.00
Software Package:
Software NamePurpose
XSCALEdata scaling
PDB_EXTRACTdata extraction
REFMACrefinement
SCALAdata scaling
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-06-05
    Type: Initial release
  • Version 1.1: 2017-11-15
    Type: Refinement description