6A2J

Crystal structure of heme A synthase from Bacillus subtilis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.206 

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This is version 1.1 of the entry. See complete history

Literature

Crystal structure of heme A synthase fromBacillus subtilis.

Niwa, S.Takeda, K.Kosugi, M.Tsutsumi, E.Mogi, T.Miki, K.

(2018) Proc. Natl. Acad. Sci. U.S.A. 115: 11953-11957

  • DOI: 10.1073/pnas.1813346115
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Heme A is an essential cofactor for respiratory terminal oxidases and vital for respiration in aerobic organisms. The final step of heme A biosynthesis is formylation of the C-8 methyl group of heme molecule by heme A synthase (HAS). HAS is a heme-co ...

    Heme A is an essential cofactor for respiratory terminal oxidases and vital for respiration in aerobic organisms. The final step of heme A biosynthesis is formylation of the C-8 methyl group of heme molecule by heme A synthase (HAS). HAS is a heme-containing integral membrane protein, and its structure and reaction mechanisms have remained unknown. Thus, little is known about HAS despite of its importance. Here we report the crystal structure of HAS from Bacillus subtilis at 2.2-Å resolution. The N- and C-terminal halves of HAS consist of four-helix bundles and they align in a pseudo twofold symmetry manner. Each bundle contains a pair of histidine residues and forms a heme-binding domain. The C-half domain binds a cofactor-heme molecule, while the N-half domain is vacant. Many water molecules are found in the transmembrane region and around the substrate-binding site, and some of them interact with the main chain of transmembrane helix. Comparison of these two domain structures enables us to construct a substrate-heme binding state structure. This structure implies that a completely conserved glutamate, Glu57 in B. subtilis , is the catalytic residue for the formylation reaction. These results provide valuable suggestions of the substrate-heme binding mechanism. Our results present significant insight into the heme A biosynthesis.


    Organizational Affiliation

    School of International Health, Graduate School of Medicine, University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.,Department of Chemistry, Graduate School of Science, Kyoto University, 606-8502 Kyoto, Japan; miki@kuchem.kyoto-u.ac.jp.,Department of Chemistry, Graduate School of Science, Kyoto University, 606-8502 Kyoto, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Heme A synthase
A
309Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: ctaA
EC: 1.3.-.-
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex IV (Cytochrome C Oxidase)
Protein: 
Heme A synthase (HAS)
Find proteins for P12946 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P12946
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OLC
Query on OLC

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Download CCD File 
A
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
1-Oleoyl-R-glycerol
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
 Ligand Interaction
SO4
Query on SO4

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Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
HEM
Query on HEM

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Download CCD File 
A
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
CU
Query on CU

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Download CCD File 
A
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.206 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 90.465α = 90.00
b = 90.465β = 90.00
c = 147.309γ = 120.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
XDSdata scaling
SOLVEphasing
XDSdata reduction
PHENIXrefinement

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japan--
Japan Society for the Promotion of ScienceJapan15J02413

Revision History 

  • Version 1.0: 2018-11-21
    Type: Initial release
  • Version 1.1: 2018-12-12
    Type: Data collection, Database references