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Structure paper

TitleDissecting the conformational complexity and mechanism of a bacterial heme transporter.
Journal, issue, pagesNat Chem Biol, Vol. 19, Issue 8, Page 992-991003, Year 2023
Publish dateApr 24, 2023
AuthorsDi Wu / Ahmad R Mehdipour / Franziska Finke / Hojjat G Goojani / Roan R Groh / Tamara N Grund / Thomas M B Reichhart / Rita Zimmermann / Sonja Welsch / Dirk Bald / Mark Shepherd / Gerhard Hummer / Schara Safarian /
PubMed AbstractIron-bound cyclic tetrapyrroles (hemes) are redox-active cofactors in bioenergetic enzymes. However, the mechanisms of heme transport and insertion into respiratory chain complexes remain unclear. ...Iron-bound cyclic tetrapyrroles (hemes) are redox-active cofactors in bioenergetic enzymes. However, the mechanisms of heme transport and insertion into respiratory chain complexes remain unclear. Here, we used cellular, biochemical, structural and computational methods to characterize the structure and function of the heterodimeric bacterial ABC transporter CydDC. We provide multi-level evidence that CydDC is a heme transporter required for functional maturation of cytochrome bd, a pharmaceutically relevant drug target. Our systematic single-particle cryogenic-electron microscopy approach combined with atomistic molecular dynamics simulations provides detailed insight into the conformational landscape of CydDC during substrate binding and occlusion. Our simulations reveal that heme binds laterally from the membrane space to the transmembrane region of CydDC, enabled by a highly asymmetrical inward-facing CydDC conformation. During the binding process, heme propionates interact with positively charged residues on the surface and later in the substrate-binding pocket of the transporter, causing the heme orientation to rotate 180°.
External linksNat Chem Biol / PubMed:37095238 / PubMed Central
MethodsEM (single particle)
Resolution2.71 - 3.89 Å
Structure data

14636

7zd5

EMDB-14636, PDB-7zd5:
IF(apo/as isolated) conformation of CydDC (Dataset-1)
Method: EM (single particle) / Resolution: 3.17 Å

EMDB-14638: IF(heme/confined) conformation of CydDC (Dataset-1)
Method: EM (single particle) / Resolution: 3.05 Å

14639

7zda

EMDB-14639, PDB-7zda:
IF(apo/asym) conformation of CydDC in ADP+Pi(CydC)/ATP(CydD) bound state (Dataset-2)
Method: EM (single particle) / Resolution: 3.17 Å

14640

7zdb

EMDB-14640, PDB-7zdb:
IF(heme/bound) conformation of CydDC in ADP+Pi(CydC)/ATP(CydD) bound state (Dataset-2)
Method: EM (single particle) / Resolution: 3.35 Å

EMDB-14641: IF(apo/as isolated) conformation of CydDC in ADP(CydD) bound state (Dataset-3)
Method: EM (single particle) / Resolution: 3.65 Å

14642

7zdc

EMDB-14642, PDB-7zdc:
IF(heme/confined) conformation of CydDC in ADP(CydD) bound state (Dataset-3)
Method: EM (single particle) / Resolution: 3.13 Å

14643

7zde

EMDB-14643, PDB-7zde:
IF(apo/as isolated) conformation of CydDC in AMP-PNP(CydD) bound state (Dataset-4)
Method: EM (single particle) / Resolution: 3.17 Å

14644

7zdf

EMDB-14644, PDB-7zdf:
IF(heme/confined) conformation of CydDC in AMP-PNP(CydD) bound state (Dataset-4)
Method: EM (single particle) / Resolution: 2.94 Å

14645

7zdg

EMDB-14645, PDB-7zdg:
IF(heme/confined) conformation of CydDC (Dataset-5)
Method: EM (single particle) / Resolution: 2.77 Å

EMDB-14646: IF(heme/confined) conformation of CydDC in AMP-PNP(CydD) bound state (Dataset-6)
Method: EM (single particle) / Resolution: 3.09 Å

EMDB-14647: IF(apo/asym) conformation of CydDC (Dataset-7)
Method: EM (single particle) / Resolution: 3.49 Å

EMDB-14649: IF(heme/coordinated) conformation of CydDC (Dataset-7)
Method: EM (single particle) / Resolution: 3.49 Å

14652

7zdk

EMDB-14652, PDB-7zdk:
IF(apo/asym) conformation of CydDC in AMP-PNP(CydC)/AMP-PNP(CydD) bound state (Dataset-8)
Method: EM (single particle) / Resolution: 3.01 Å

14653

7zdl

EMDB-14653, PDB-7zdl:
IF(heme/coordinated) conformation of CydDC in AMP-PNP(CydC)/AMP-PNP(CydD) bound state (Dataset-8)
Method: EM (single particle) / Resolution: 3.35 Å

EMDB-14654: IF(heme/coordinated) conformation of CydDC in AMP-PNP(CydC)/AMP-PNP(CydD) bound state (Dataset-9)
Method: EM (single particle) / Resolution: 3.42 Å

EMDB-14655: IF(apo/as isolated) conformation of CydDC in AMP-PNP(CydD) bound state (Dataset-10)
Method: EM (single particle) / Resolution: 3.26 Å

EMDB-14656: IF(heme/confined) conformation of CydDC in AMP-PNP(CydD) bound state (Dataset-10)
Method: EM (single particle) / Resolution: 3.35 Å

EMDB-14657: IF(apo/as isolated) conformation of CydDC in AMP-PNP(CydD) bound state (Dataset-11)
Method: EM (single particle) / Resolution: 3.44 Å

EMDB-14659: IF(heme/confined) conformation of CydDC in AMP-PNP(CydD) bound state (Dataset-12)
Method: EM (single particle) / Resolution: 3.44 Å

EMDB-14660: IF(apo/asym) conformation of CydDC in AMP-PNP(CydC)/AMP-PNP(CydD) bound state (Dataset-13)
Method: EM (single particle) / Resolution: 3.26 Å

EMDB-14662: IF(heme/coordinated) conformation of CydDC in AMP-PNP(CydC)/AMP-PNP(CydD) bound state (Dataset-13)
Method: EM (single particle) / Resolution: 3.17 Å

EMDB-14663: IF(heme/coordinated) conformation of CydDC in AMP-PNP(CydC)/AMP-PNP(CydD) bound state (Dataset-14)
Method: EM (single particle) / Resolution: 3.05 Å

EMDB-14665: IF(heme/confined) conformation of CydDC in AMP-PNP(CydD) bound state (Dataset-14)
Method: EM (single particle) / Resolution: 2.87 Å

14667

7zdr

EMDB-14667, PDB-7zdr:
IF(apo/as isolated) conformation of CydDC mutant (H85A.C) in AMP-PNP(CydD) bound state (Dataset-16)
Method: EM (single particle) / Resolution: 3.05 Å

14668

7zds

EMDB-14668, PDB-7zds:
IF(apo/as isolated) conformation of CydDC mutant (E500Q.C) (Dataset-18)
Method: EM (single particle) / Resolution: 3.26 Å

14669

7zdt

EMDB-14669, PDB-7zdt:
Occ(apo/return) conformation of CydDC mutant (E500Q.C) in ATP(CydC) bound state (Dataset-18)
Method: EM (single particle) / Resolution: 2.71 Å

14670

7zdu

EMDB-14670, PDB-7zdu:
Occ(apo/return) conformation of CydDC mutant (E500Q.C) in ATP(CydC)/ATP(CydD) bound state (Dataset-19)
Method: EM (single particle) / Resolution: 2.98 Å

14671

7zdv

EMDB-14671: IF(apo/as isolated) conformation of CydDC mutant (E500Q.C) in AMP-PNP(CydD) bound state (Dataset-19)
PDB-7zdv: IF(apo/as isolated) conformation of CydDC mutant (E500Q.C) in AMP-PNP(CydD) bound state (Dataset-20)
Method: EM (single particle) / Resolution: 3.05 Å

EMDB-14672: Occ(apo/return) conformation of CydDC mutant (E500Q.C) in ATP(CydC)/AMP-PNP(CydD) bound state (Dataset-20)
Method: EM (single particle) / Resolution: 3.89 Å

EMDB-14673: IF(heme/confined) conformation of CydDC mutant (E500Q.C) (Dataset-21)
Method: EM (single particle) / Resolution: 3.77 Å

EMDB-14674: Occ(apo/return) conformation of CydDC mutant (E500Q.C) in ATP(CydC) bound state (Dataset-21)
Method: EM (single particle) / Resolution: 3.17 Å

14675

7zdw

EMDB-14675, PDB-7zdw:
IF(heme/confined) conformation of CydDC mutant (E500Q.C) in AMP-PNP(CydD) bound state (Dataset-22)
Method: EM (single particle) / Resolution: 3.35 Å

EMDB-14676: Occ(apo/return) conformation of CydDC mutant (E500Q.C) in ATP(CydC)/AMP-PNP(CydD) bound state (Dataset-22)
Method: EM (single particle) / Resolution: 3.35 Å

14684

7ze5

EMDB-14684, PDB-7ze5:
Occ(apo/return) conformation of CydDC mutant (E500Q.C) in ATP(CydC)/AMP-PNP(CydD) bound state (Dataset-23)
Method: EM (single particle) / Resolution: 2.94 Å

14689

7zec

EMDB-14689, PDB-7zec:
IF(heme/confined) conformation of CydDC in ATP(CydD) bound state (Dataset-15)
Method: EM (single particle) / Resolution: 3.05 Å

EMDB-15264: IF(apo/as isolated) conformation of CydDC mutant (H85A.C) in AMP-PNP(CydD) bound state (Dataset-17)
Method: EM (single particle) / Resolution: 3.26 Å

EMDB-15265: IF(heme/coordinated) conformation of CydDC mutant (E500Q.C) in AMP-PNP(CydC)/AMP-PNP(CydD) bound state (Dataset-23)
Method: EM (single particle) / Resolution: 3.65 Å

Chemicals

ChemComp-MG:
Unknown entry

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM / Adenosine diphosphate

ChemComp-PO3:
PHOSPHITE ION / Phosphite ester

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM / Adenosine triphosphate

ChemComp-HEB:
HEME B/C

ChemComp-ANP:
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP, energy-carrying molecule analogue*YM

ChemComp-ISW:
{3,3'-[(9S)-8,13-diethenyl-3,7,12,17-tetramethyl-9,10-dihydroporphyrin-2,18-diyl-kappa~4~N~21~,N~22~,N~23~,N~24~]dipropanoato(2-)}iron

Source
  • Escherichia coli (E. coli)
  • escherichia coli k-12 (bacteria)
KeywordsMEMBRANE PROTEIN / ABC transporter / CydDC / Heme transporter

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