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Q56223 (NQO3_THET8) Reviewed, UniProtKB/Swiss-Prot

Last modified February 19, 2014. Version 114. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
NADH-quinone oxidoreductase subunit 3

EC=1.6.99.5
Alternative name(s):
NADH dehydrogenase I chain 3
NDH-1 subunit 3
Gene names
Name:nqo3
Ordered Locus Names:TTHA0090
OrganismThermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) [Reference proteome] [HAMAP]
Taxonomic identifier300852 [NCBI]
Taxonomic lineageBacteriaDeinococcus-ThermusDeinococciThermalesThermaceaeThermus

Protein attributes

Sequence length783 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

NDH-1 shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is menaquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient required for the synthesis of ATP.

Catalytic activity

NADH + quinone = NAD+ + quinol.

Cofactor

Binds 1 2Fe-2S cluster per subunit. The 2Fe-2S cluster 1 is referred to as N1b.

Binds 3 4Fe-4S clusters per subunit. The 4Fe-4S clusters 2, 3, and 4 are referred to as N5, N4, and N7, respectively. The 4Fe-4S cluster 4 is too far away from the main redox chain to participate in electron transfer but probably confers structural stability.

Subunit structure

NDH-1 is composed of 15 different subunits, nqo1 to nqo15. The complex has a L-shaped structure, with the hydrophobic arm (subunits nqo7, nqo8 and nqo10 to nqo14) embedded in the membrane and the hydrophilic peripheral arm (subunits nqo1 to nqo6, nqo9 and nqo15) protruding into the bacterial cytoplasm. The hydrophilic domain contains all the redox centers. Ref.4 Ref.5

Subcellular location

Cell membrane; Peripheral membrane protein; Cytoplasmic side.

Domain

The subunit comprises two main parts, an N-terminal [FeFe]-hydrogenase-like domain (residues 1 to 240) that coordinates clusters 1, 2 and 3, and a domain similar to molybdopterin-containing enzymes (residues 241 to 767) whose first subdomain coordinates cluster 4.

Sequence similarities

Belongs to the complex I 75 kDa subunit family.

Contains 1 2Fe-2S ferredoxin-type domain.

Contains 1 4Fe-4S Mo/W bis-MGD-type domain.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 783783NADH-quinone oxidoreductase subunit 3
PRO_0000118541

Regions

Domain1 – 99992Fe-2S ferredoxin-type
Domain249 – 305574Fe-4S Mo/W bis-MGD-type

Sites

Metal binding341Iron-sulfur 1 (2Fe-2S)
Metal binding451Iron-sulfur 1 (2Fe-2S)
Metal binding481Iron-sulfur 1 (2Fe-2S)
Metal binding831Iron-sulfur 1 (2Fe-2S)
Metal binding1151Iron-sulfur 2 (4Fe-4S); via tele nitrogen
Metal binding1191Iron-sulfur 2 (4Fe-4S)
Metal binding1221Iron-sulfur 2 (4Fe-4S)
Metal binding1281Iron-sulfur 2 (4Fe-4S)
Metal binding1811Iron-sulfur 3 (4Fe-4S)
Metal binding1841Iron-sulfur 3 (4Fe-4S)
Metal binding1871Iron-sulfur 3 (4Fe-4S)
Metal binding2301Iron-sulfur 3 (4Fe-4S)
Metal binding2561Iron-sulfur 4 (4Fe-4S)
Metal binding2591Iron-sulfur 4 (4Fe-4S)
Metal binding2631Iron-sulfur 4 (4Fe-4S)
Metal binding2911Iron-sulfur 4 (4Fe-4S)

Experimental info

Mutagenesis2561C → A: Decreases amount and stability of iron-sulfur center 4. Ref.3
Mutagenesis2591C → A: Decreases amount and stability of iron-sulfur center 4. Ref.3
Mutagenesis2631C → A: Decreases amount and stability of iron-sulfur center 4. Ref.3
Mutagenesis2911C → A: Decreases amount and stability of iron-sulfur center 4. Ref.3
Sequence conflict3321G → S in AAA97944. Ref.1

Secondary structure

...................................................................................................................................... 783
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Q56223 [UniParc].

Last modified March 29, 2005. Version 2.
Checksum: 19A56201A20F9B82

FASTA78386,529
        10         20         30         40         50         60 
MVRVKVNDRI VEVPPGTSVM DAVFHAGYDV PLFCSEKHLS PIGACRMCLV RIGLPKKGPD 

        70         80         90        100        110        120 
GKPLLNEKGE PEIQWQPKLA ASCVTAVADG MVVDTLSDVV REAQAGMVEF TLLNHPLDCP 

       130        140        150        160        170        180 
TCDKGGACEL QDRTVEYGLY EKYYQKGPLE LPVYTRFEFT RRHVDKHHPL SPFVILDRER 

       190        200        210        220        230        240 
CIHCKRCVRY FEEVPGDEVL DFIERGVHTF IGTMDFGLPS GFSGNITDIC PVGALLDLTA 

       250        260        270        280        290        300 
RFRARNWEME ETPTTCALCP VGCGITADTR SGELLRIRAR EVPEVNEIWI CDAGRFGHEW 

       310        320        330        340        350        360 
ADQNRLKTPL VRKEGRLVEA TWEEAFLALK EGLKEARGEE VGLYLAHDAT LEEGLLASEL 

       370        380        390        400        410        420 
AKALKTPHLD FQGRTAAPAS LFPPASLEDL LQADFALVLG DPTEEAPILH LRLSEFVRDL 

       430        440        450        460        470        480 
KPPHRYNHGT PFADLQIKER MPRRTDKMAL FAPYRAPLMK WAAIHEVHRP GEEREILLAL 

       490        500        510        520        530        540 
LGDKEGSEMV AKAKEAWEKA KNPVLILGAG VLQDTVAAER ARLLAERKGA KVLAMTPAAN 

       550        560        570        580        590        600 
ARGLEAMGVL PGAKGASWDE PGALYAYYGF VPPEEALKGK RFVVMHLSHL HPLAERYAHV 

       610        620        630        640        650        660 
VLPAPTFYEK RGHLVNLEGR VLPLSPAPIE NGEAEGALQV LALLAEALGV RPPFRLHLEA 

       670        680        690        700        710        720 
QKALKARKVP EAMGRLSFRL KELRPKERKG AFYLRPTMWK AHQAVGKAQE AARAELWAHP 

       730        740        750        760        770        780 
ETARAEALPE GAQVAVETPF GRVEARVVHR EDVPKGHLYL SALGPAAGLR VEGRVLVPAG 


GEA 

« Hide

References

« Hide 'large scale' references
[1]"The proton-translocating NADH-quinone oxidoreductase (NDH-1) of thermophilic bacterium Thermus thermophilus HB-8. Complete DNA sequence of the gene cluster and thermostable properties of the expressed NQO2 subunit."
Yano T., Chu S.S., Sled' V.D., Ohnishi T., Yagi T.
J. Biol. Chem. 272:4201-4211(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]"Complete genome sequence of Thermus thermophilus HB8."
Masui R., Kurokawa K., Nakagawa N., Tokunaga F., Koyama Y., Shibata T., Oshima T., Yokoyama S., Yasunaga T., Kuramitsu S.
Submitted (NOV-2004) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: HB8 / ATCC 27634 / DSM 579.
[3]"Characterization of the iron-sulfur cluster coordinated by a cysteine cluster motif (CXXCXXXCX27C) in the Nqo3 subunit in the proton-translocating NADH-quinone oxidoreductase (NDH-1) of Thermus thermophilus HB-8."
Nakamaru-Ogiso E., Yano T., Ohnishi T., Yagi T.
J. Biol. Chem. 277:1680-1688(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: EXPRESSION OF 240-324 FOR CHARACTERIZATION OF A FOURTH [4FE-4S] CENTER, MUTAGENESIS OF CYS-256; CYS-259; CYS-263 AND CYS-291.
[4]"Identification of a novel subunit of respiratory complex I from Thermus thermophilus."
Hinchliffe P., Carroll J., Sazanov L.A.
Biochemistry 45:4413-4420(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: PROTEIN SEQUENCE OF 1-8, IDENTIFICATION BY MASS SPECTROMETRY, EPR SPECTROSCOPY, SUBUNIT.
[5]"Structure of the hydrophilic domain of respiratory complex I from Thermus thermophilus."
Sazanov L.A., Hinchliffe P.
Science 311:1430-1436(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (3.3 ANGSTROMS), SUBUNIT, ELECTRON TRANSFER MECHANISM.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
U52917 Genomic DNA. Translation: AAA97944.1.
AP008226 Genomic DNA. Translation: BAD69913.1.
PIRT11904.
RefSeqYP_143356.1. NC_006461.1.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
2FUGX-ray3.303/C/L/U1-783[»]
2YBBelectron microscopy19.0031-783[»]
3I9VX-ray3.103/C1-783[»]
3IAMX-ray3.103/C1-783[»]
3IASX-ray3.153/C/L/U1-783[»]
3M9SX-ray4.503/C1-783[»]
4HEAX-ray3.303/D1-783[»]
ProteinModelPortalQ56223.
SMRQ56223. Positions 1-767.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

DIPDIP-59261N.
STRING300852.TTHA0090.

Protein family/group databases

TCDB3.D.1.3.1. the h(+) or na(+)-translocating nadh dehydrogenase (ndh) family.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaBAD69913; BAD69913; BAD69913.
GeneID3168388.
KEGGttj:TTHA0090.
PATRIC23955111. VBITheThe93045_0088.

Phylogenomic databases

eggNOGCOG1034.
HOGENOMHOG000099655.
KOK00336.
OMAGAMTLIQ.
OrthoDBEOG6CVV7G.
ProtClustDBCLSK497043.

Enzyme and pathway databases

BioCycTTHE300852:GH8R-94-MONOMER.

Family and domain databases

Gene3D3.10.20.30. 1 hit.
InterProIPR001041. 2Fe-2S_ferredoxin-type.
IPR009010. Asp_de-COase-like_dom.
IPR012675. Beta-grasp_dom.
IPR006657. MoPterin_dinucl-bd_dom.
IPR006656. Mopterin_OxRdtase.
IPR006963. Mopterin_OxRdtase_4Fe-4S_dom.
IPR000283. NADH_UbQ_OxRdtase_75kDa_su_CS.
IPR010228. NADH_UbQ_OxRdtase_Gsu.
IPR019574. NADH_UbQ_OxRdtase_Gsu_4Fe4S-bd.
[Graphical view]
PfamPF00111. Fer2. 1 hit.
PF04879. Molybdop_Fe4S4. 1 hit.
PF00384. Molybdopterin. 2 hits.
PF01568. Molydop_binding. 1 hit.
PF10588. NADH-G_4Fe-4S_3. 1 hit.
[Graphical view]
SMARTSM00926. Molybdop_Fe4S4. 1 hit.
SM00929. NADH-G_4Fe-4S_3. 1 hit.
[Graphical view]
SUPFAMSSF50692. SSF50692. 1 hit.
SSF54292. SSF54292. 1 hit.
TIGRFAMsTIGR01973. NuoG. 1 hit.
PROSITEPS51085. 2FE2S_FER_2. 1 hit.
PS51669. 4FE4S_MOW_BIS_MGD. 1 hit.
PS00641. COMPLEX1_75K_1. 1 hit.
PS00642. COMPLEX1_75K_2. 1 hit.
PS00643. COMPLEX1_75K_3. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceQ56223.

Entry information

Entry nameNQO3_THET8
AccessionPrimary (citable) accession number: Q56223
Secondary accession number(s): Q5SM53
Entry history
Integrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: March 29, 2005
Last modified: February 19, 2014
This is version 114 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references