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Q56223

- NQO3_THET8

UniProt

Q56223 - NQO3_THET8

Protein

NADH-quinone oxidoreductase subunit 3

Gene

nqo3

Organism
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 118 (01 Oct 2014)
      Sequence version 2 (29 Mar 2005)
      Previous versions | rss
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    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. electron carrier activity Source: InterPro
    4. molybdenum ion binding Source: InterPro
    5. NADH dehydrogenase (ubiquinone) activity Source: InterPro
    6. quinone binding Source: UniProtKB-KW

    GO - Biological processi

    1. ATP synthesis coupled electron transport Source: InterPro

    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

    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 3PRO_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

    1
    783
    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.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ56223.

    Family & Domainsi

    Domains and Repeats

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

    Belongs to the complex I 75 kDa subunit family.Curated
    Contains 1 2Fe-2S ferredoxin-type domain.PROSITE-ProRule annotation
    Contains 1 4Fe-4S Mo/W bis-MGD-type domain.PROSITE-ProRule annotation

    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

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti332 – 3321G → S in AAA97944. (PubMed:9020134)Curated

    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

    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: October 1, 2014
    This is version 118 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