2EIL

Cadmium ion binding structure of bovine heart cytochrome C oxidase in the fully oxidized state

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.199 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

A histidine residue acting as a controlling site for dioxygen reduction and proton pumping by cytochrome c oxidase

Muramoto, K., Hirata, K., Shinzawa-Itoh, K., Yoko-O, S., Yamashita, E., Aoyama, H., Tsukihara, T., Yoshikawa, S.

(2007) Proc Natl Acad Sci U S A 104: 7881-7886

  • DOI: 10.1073/pnas.0610031104
  • Primary Citation of Related Structures:  
    2EIM, 2EIL, 2EIK, 2EIJ, 2EIN

  • PubMed Abstract: 

    • Cytochrome c oxidase transfers electrons and protons for dioxygen reduction coupled with proton pumping. These electron and proton transfers are tightly coupled with each other for the effective energy transduction by various unknown mechanisms. Here, we ...

    Cytochrome c oxidase transfers electrons and protons for dioxygen reduction coupled with proton pumping. These electron and proton transfers are tightly coupled with each other for the effective energy transduction by various unknown mechanisms. Here, we report a coupling mechanism by a histidine (His-503) at the entrance of a proton transfer pathway to the dioxygen reduction site (D-pathway) of bovine heart cytochrome c oxidase. In the reduced state, a water molecule is fixed by hydrogen bonds between His-503 and Asp-91 of the D-pathway and is linked via two water arrays extending to the molecular surface. The microenvironment of Asp-91 appears in the x-ray structure to have a proton affinity as high as that of His-503. Thus, Asp-91 and His-503 cooperatively trap, on the fixed water molecule, the proton that is transferred through the water arrays from the molecular surface. On oxidation, the His-503 imidazole plane rotates by 180 degrees to break the hydrogen bond to the protonated water and releases the proton to Asp-91. On reduction, Asp-91 donates the proton to the dioxygen reduction site through the D-pathway. The proton collection controlled by His-503 was confirmed by partial electron transfer inhibition by binding of Zn2+ and Cd2+ to His-503 in the x-ray structures. The estimated Kd for Zn2+ binding to His-503 in the x-ray structure is consistent with the reported Kd for complete proton-pumping inhibition by Zn2+ [Kannt A, Ostermann T, Muller H, Ruitenberg M (2001) FEBS Lett 503:142-146]. These results suggest that His-503 couples the proton transfer for dioxygen reduction with the proton pumping.

    Organizational Affiliation: 

    Department of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori, Ako, Hyogo 678-1297, Japan.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 1 A, N514Bos taurusMutation(s): 0 
Gene Names: MT-CO1, COI, COXI, MTCO1
EC: 1.9.3.1 (PDB Primary Data), 7.1.1.9 (UniProt)
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 2 B, O227Bos taurusMutation(s): 0 
Gene Names: MT-CO2, COII, COX2, COXII, MTCO2
EC: 1.9.3.1 (PDB Primary Data), 7.1.1.9 (UniProt)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 3 C, P261Bos taurusMutation(s): 0 
Gene Names: MT-CO3, COIII, COXIII, MTCO3
EC: 1.9.3.1 (PDB Primary Data), 7.1.1.9 (UniProt)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 4 isoform 1 D, Q147Bos taurusMutation(s): 0 
Gene Names: COX4I1, COX4
EC: 1.9.3.1
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase polypeptide Va E, R109Bos taurusMutation(s): 0 
Gene Names: COX5A
EC: 1.9.3.1
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase polypeptide Vb F, S98Bos taurusMutation(s): 0 
Gene Names: COX5B
EC: 1.9.3.1
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase polypeptide VIa-heart G, T85Bos taurusMutation(s): 0 
Gene Names: COX6A2, COX6A
EC: 1.9.3.1
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit VIb isoform 1 H, U85Bos taurusMutation(s): 0 
Gene Names: COX6B1, COX6B
EC: 1.9.3.1
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase polypeptide VIc I, V73Bos taurusMutation(s): 0 
Gene Names: COX6C
EC: 1.9.3.1
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase polypeptide VIIa-heart J, W59Bos taurusMutation(s): 0 
Gene Names: COX7A1, COX7A, COX7AH
EC: 1.9.3.1
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Entity ID: 11
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Cytochrome c oxidase polypeptide VIIb K, X56Bos taurusMutation(s): 0 
Gene Names: COX7B
EC: 1.9.3.1
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase polypeptide VIIc L, Y47Bos taurusMutation(s): 0 
Gene Names: COX7C, COX7CP1
EC: 1.9.3.1
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase polypeptide VIII-heart M, Z46Bos taurusMutation(s): 0 
Gene Names: COX8B, COX8H
EC: 1.9.3.1
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  • Reference Sequence
Small Molecules
Ligands 14 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL
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C, G, P, T
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L		 Ligand Interaction
TGL
Query on TGL
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A, D, L, N, Q
TRISTEAROYLGLYCEROL
C57 H110 O6
DCXXMTOCNZCJGO-UHFFFAOYSA-N		 Ligand Interaction
HEA
Query on HEA
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A, N
HEME-A
C49 H56 Fe N4 O6
ZGGYGTCPXNDTRV-PRYGPKJJSA-L		 Ligand Interaction
PEK
Query on PEK
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C, G, P, T
(1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE
C43 H78 N O8 P
ANRKEHNWXKCXDB-BHFWLYLHSA-N		 Ligand Interaction
PSC
Query on PSC
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B, O
(7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE
C42 H81 N O8 P
JLPULHDHAOZNQI-AUSZDXHESA-O		 Ligand Interaction
PGV
Query on PGV
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A, C, N, P, Z
(1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE
C40 H77 O10 P
ADYWCMPUNIVOEA-GPJPVTGXSA-N		 Ligand Interaction
DMU
Query on DMU
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C, M, P, Z
DECYL-BETA-D-MALTOPYRANOSIDE
C22 H42 O11
WOQQAWHSKSSAGF-WXFJLFHKSA-N		 Ligand Interaction
CHD
Query on CHD
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B, C, J, O, P, W
CHOLIC ACID
C24 H40 O5
BHQCQFFYRZLCQQ-OELDTZBJSA-N		 Ligand Interaction
CUA
Query on CUA
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B, O
DINUCLEAR COPPER ION
Cu2
ALKZAGKDWUSJED-UHFFFAOYSA-N		 Ligand Interaction
CD
Query on CD
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A, C, P
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N		 Ligand Interaction
ZN
Query on ZN
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F, S
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
CU
Query on CU
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A, N
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N		 Ligand Interaction
MG
Query on MG
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A, N
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
NA
Query on NA
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A, N
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N		 Ligand Interaction
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
FME
Query on FME		A,NL-PEPTIDE LINKINGC6 H11 N O3 SMET
TPO
Query on TPO		G,TL-PEPTIDE LINKINGC4 H10 N O6 PTHR
SAC
Query on SAC		I,VL-PEPTIDE LINKINGC5 H9 N O4SER
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.199 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 183.379α = 90
b = 205.898β = 90
c = 178.182γ = 90
Software Package:
Software NamePurpose
X-PLORrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-05-29
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance