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Q56223

- NQO3_THET8

UniProt

Q56223 - NQO3_THET8

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Protein
NADH-quinone oxidoreductase subunit 3
Gene
nqo3, TTHA0090
Organism
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

Functioni

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 activityi

NADH + quinone = NAD+ + quinol.

Cofactori

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.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi34 – 341Iron-sulfur 1 (2Fe-2S)
Metal bindingi45 – 451Iron-sulfur 1 (2Fe-2S)
Metal bindingi48 – 481Iron-sulfur 1 (2Fe-2S)
Metal bindingi83 – 831Iron-sulfur 1 (2Fe-2S)
Metal bindingi115 – 1151Iron-sulfur 2 (4Fe-4S); via tele nitrogen
Metal bindingi119 – 1191Iron-sulfur 2 (4Fe-4S)
Metal bindingi122 – 1221Iron-sulfur 2 (4Fe-4S)
Metal bindingi128 – 1281Iron-sulfur 2 (4Fe-4S)
Metal bindingi181 – 1811Iron-sulfur 3 (4Fe-4S)
Metal bindingi184 – 1841Iron-sulfur 3 (4Fe-4S)
Metal bindingi187 – 1871Iron-sulfur 3 (4Fe-4S)
Metal bindingi230 – 2301Iron-sulfur 3 (4Fe-4S)
Metal bindingi256 – 2561Iron-sulfur 4 (4Fe-4S)
Metal bindingi259 – 2591Iron-sulfur 4 (4Fe-4S)
Metal bindingi263 – 2631Iron-sulfur 4 (4Fe-4S)
Metal bindingi291 – 2911Iron-sulfur 4 (4Fe-4S)

GO - Molecular functioni

  1. 2 iron, 2 sulfur cluster binding Source: UniProtKB-KW
  2. 4 iron, 4 sulfur cluster binding Source: UniProtKB-KW
  3. NADH dehydrogenase (ubiquinone) activity Source: InterPro
  4. electron carrier activity Source: InterPro
  5. molybdenum ion binding Source: InterPro
  6. quinone binding Source: UniProtKB-KW

GO - Biological processi

  1. ATP synthesis coupled electron transport Source: InterPro
Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Ligandi

2Fe-2S, 4Fe-4S, Iron, Iron-sulfur, Metal-binding, NAD

Enzyme and pathway databases

BioCyciTTHE300852:GH8R-94-MONOMER.

Protein family/group databases

TCDBi3.D.1.3.1. the h(+) or na(+)-translocating nadh dehydrogenase (ndh) family.

Names & Taxonomyi

Protein namesi
Recommended name:
NADH-quinone oxidoreductase subunit 3 (EC:1.6.99.5)
Alternative name(s):
NADH dehydrogenase I chain 3
NDH-1 subunit 3
Gene namesi
Name:nqo3
Ordered Locus Names:TTHA0090
OrganismiThermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Taxonomic identifieri300852 [NCBI]
Taxonomic lineageiBacteriaDeinococcus-ThermusDeinococciThermalesThermaceaeThermus
ProteomesiUP000000532: Chromosome

Subcellular locationi

GO - Cellular componenti

  1. plasma membrane Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Cell membrane, Membrane

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi256 – 2561C → A: Decreases amount and stability of iron-sulfur center 4. 1 Publication
Mutagenesisi259 – 2591C → A: Decreases amount and stability of iron-sulfur center 4. 1 Publication
Mutagenesisi263 – 2631C → A: Decreases amount and stability of iron-sulfur center 4. 1 Publication
Mutagenesisi291 – 2911C → A: Decreases amount and stability of iron-sulfur center 4. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 783783NADH-quinone oxidoreductase subunit 3
PRO_0000118541Add
BLAST

Keywords - PTMi

Quinone

Interactioni

Subunit structurei

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.2 Publications

Protein-protein interaction databases

DIPiDIP-59261N.
STRINGi300852.TTHA0090.

Structurei

Secondary structure

Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi2 – 54
Beta strandi10 – 134
Helixi19 – 257
Beta strandi48 – 536
Turni82 – 843
Beta strandi89 – 979
Helixi98 – 11215
Turni119 – 1213
Helixi125 – 1273
Helixi129 – 1379
Beta strandi167 – 1715
Beta strandi174 – 1763
Turni178 – 1803
Helixi186 – 1938
Helixi206 – 2083
Turni221 – 2255
Helixi226 – 2294
Beta strandi231 – 2377
Helixi238 – 2403
Beta strandi241 – 2433
Turni246 – 2483
Beta strandi249 – 2557
Beta strandi258 – 2614
Beta strandi264 – 2707
Beta strandi272 – 2798
Helixi292 – 2965
Turni297 – 3037
Beta strandi310 – 31910
Helixi322 – 33413
Beta strandi340 – 3456
Helixi353 – 36311
Beta strandi364 – 3663
Beta strandi369 – 3713
Helixi379 – 3813
Helixi387 – 3926
Beta strandi396 – 4005
Helixi402 – 4054
Helixi408 – 41710
Beta strandi447 – 4548
Helixi457 – 4593
Beta strandi463 – 4675
Turni470 – 4723
Helixi473 – 4819
Helixi488 – 49912
Beta strandi504 – 5074
Helixi510 – 5134
Helixi515 – 52713
Beta strandi532 – 5343
Helixi541 – 5444
Helixi545 – 5473
Beta strandi553 – 5553
Beta strandi564 – 5707
Helixi574 – 5774
Beta strandi581 – 5855
Turni592 – 5976
Beta strandi599 – 6013
Helixi607 – 6093
Beta strandi612 – 6154
Beta strandi619 – 6246
Helixi637 – 64610
Helixi657 – 66711
Beta strandi691 – 6966
Helixi701 – 7033
Helixi708 – 7114
Beta strandi715 – 7184
Helixi720 – 7256
Beta strandi733 – 7386
Beta strandi741 – 7499
Beta strandi758 – 7625
Beta strandi768 – 7714
Beta strandi774 – 7763

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
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[»]
ProteinModelPortaliQ56223.
SMRiQ56223. Positions 1-767.

Miscellaneous databases

EvolutionaryTraceiQ56223.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini1 – 99992Fe-2S ferredoxin-type
Add
BLAST
Domaini249 – 305574Fe-4S Mo/W bis-MGD-type
Add
BLAST

Domaini

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 similaritiesi

Phylogenomic databases

eggNOGiCOG1034.
HOGENOMiHOG000099655.
KOiK00336.
OMAiSGNITDI.
OrthoDBiEOG6CVV7G.
PhylomeDBiQ56223.

Family and domain databases

Gene3Di3.10.20.30. 1 hit.
3.40.50.1220. 1 hit.
InterProiIPR001041. 2Fe-2S_ferredoxin-type.
IPR009010. Asp_de-COase-like_dom.
IPR012675. Beta-grasp_dom.
IPR029035. DHS-like_NAD/FAD-binding_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]
PfamiPF00111. 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]
SMARTiSM00926. Molybdop_Fe4S4. 1 hit.
SM00929. NADH-G_4Fe-4S_3. 1 hit.
[Graphical view]
SUPFAMiSSF50692. SSF50692. 1 hit.
SSF54292. SSF54292. 1 hit.
TIGRFAMsiTIGR01973. NuoG. 1 hit.
PROSITEiPS51085. 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]

Sequencei

Sequence statusi: Complete.

Q56223-1 [UniParc]FASTAAdd to Basket

« Hide

MVRVKVNDRI VEVPPGTSVM DAVFHAGYDV PLFCSEKHLS PIGACRMCLV    50
RIGLPKKGPD GKPLLNEKGE PEIQWQPKLA ASCVTAVADG MVVDTLSDVV 100
REAQAGMVEF TLLNHPLDCP TCDKGGACEL QDRTVEYGLY EKYYQKGPLE 150
LPVYTRFEFT RRHVDKHHPL SPFVILDRER CIHCKRCVRY FEEVPGDEVL 200
DFIERGVHTF IGTMDFGLPS GFSGNITDIC PVGALLDLTA RFRARNWEME 250
ETPTTCALCP VGCGITADTR SGELLRIRAR EVPEVNEIWI CDAGRFGHEW 300
ADQNRLKTPL VRKEGRLVEA TWEEAFLALK EGLKEARGEE VGLYLAHDAT 350
LEEGLLASEL AKALKTPHLD FQGRTAAPAS LFPPASLEDL LQADFALVLG 400
DPTEEAPILH LRLSEFVRDL KPPHRYNHGT PFADLQIKER MPRRTDKMAL 450
FAPYRAPLMK WAAIHEVHRP GEEREILLAL LGDKEGSEMV AKAKEAWEKA 500
KNPVLILGAG VLQDTVAAER ARLLAERKGA KVLAMTPAAN ARGLEAMGVL 550
PGAKGASWDE PGALYAYYGF VPPEEALKGK RFVVMHLSHL HPLAERYAHV 600
VLPAPTFYEK RGHLVNLEGR VLPLSPAPIE NGEAEGALQV LALLAEALGV 650
RPPFRLHLEA QKALKARKVP EAMGRLSFRL KELRPKERKG AFYLRPTMWK 700
AHQAVGKAQE AARAELWAHP ETARAEALPE GAQVAVETPF GRVEARVVHR 750
EDVPKGHLYL SALGPAAGLR VEGRVLVPAG GEA 783
Length:783
Mass (Da):86,529
Last modified:March 29, 2005 - v2
Checksum:i19A56201A20F9B82
GO

Sequence conflict

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti332 – 3321G → S in AAA97944. 1 Publication

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
U52917 Genomic DNA. Translation: AAA97944.1.
AP008226 Genomic DNA. Translation: BAD69913.1.
PIRiT11904.
RefSeqiYP_143356.1. NC_006461.1.

Genome annotation databases

EnsemblBacteriaiBAD69913; BAD69913; BAD69913.
GeneIDi3168388.
KEGGittj:TTHA0090.
PATRICi23955111. VBITheThe93045_0088.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
U52917 Genomic DNA. Translation: AAA97944.1 .
AP008226 Genomic DNA. Translation: BAD69913.1 .
PIRi T11904.
RefSeqi YP_143356.1. NC_006461.1.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
2FUG X-ray 3.30 3/C/L/U 1-783 [» ]
2YBB electron microscopy 19.00 3 1-783 [» ]
3I9V X-ray 3.10 3/C 1-783 [» ]
3IAM X-ray 3.10 3/C 1-783 [» ]
3IAS X-ray 3.15 3/C/L/U 1-783 [» ]
3M9S X-ray 4.50 3/C 1-783 [» ]
4HEA X-ray 3.30 3/D 1-783 [» ]
ProteinModelPortali Q56223.
SMRi Q56223. Positions 1-767.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

DIPi DIP-59261N.
STRINGi 300852.TTHA0090.

Protein family/group databases

TCDBi 3.D.1.3.1. the h(+) or na(+)-translocating nadh dehydrogenase (ndh) family.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai BAD69913 ; BAD69913 ; BAD69913 .
GeneIDi 3168388.
KEGGi ttj:TTHA0090.
PATRICi 23955111. VBITheThe93045_0088.

Phylogenomic databases

eggNOGi COG1034.
HOGENOMi HOG000099655.
KOi K00336.
OMAi SGNITDI.
OrthoDBi EOG6CVV7G.
PhylomeDBi Q56223.

Enzyme and pathway databases

BioCyci TTHE300852:GH8R-94-MONOMER.

Miscellaneous databases

EvolutionaryTracei Q56223.

Family and domain databases

Gene3Di 3.10.20.30. 1 hit.
3.40.50.1220. 1 hit.
InterProi IPR001041. 2Fe-2S_ferredoxin-type.
IPR009010. Asp_de-COase-like_dom.
IPR012675. Beta-grasp_dom.
IPR029035. DHS-like_NAD/FAD-binding_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 ]
Pfami PF00111. 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 ]
SMARTi SM00926. Molybdop_Fe4S4. 1 hit.
SM00929. NADH-G_4Fe-4S_3. 1 hit.
[Graphical view ]
SUPFAMi SSF50692. SSF50692. 1 hit.
SSF54292. SSF54292. 1 hit.
TIGRFAMsi TIGR01973. NuoG. 1 hit.
PROSITEi PS51085. 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 ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  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.

Entry informationi

Entry nameiNQO3_THET8
AccessioniPrimary (citable) accession number: Q56223
Secondary accession number(s): Q5SM53
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: March 29, 2005
Last modified: July 9, 2014
This is version 117 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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