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Q56223

- NQO3_THET8

UniProt

Q56223 - NQO3_THET8

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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

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

Protein has several cofactor binding sites:
  • [2Fe-2S] clusterNote: Binds 1 [2Fe-2S] cluster per subunit. The [2Fe-2S] cluster 1 is referred to as N1b.
  • [4Fe-4S] clusterNote: 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
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-KW
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 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 – 54Combined sources
Beta strandi10 – 134Combined sources
Helixi19 – 257Combined sources
Beta strandi48 – 536Combined sources
Turni82 – 843Combined sources
Beta strandi89 – 979Combined sources
Helixi98 – 11215Combined sources
Turni119 – 1213Combined sources
Helixi125 – 1273Combined sources
Helixi129 – 1379Combined sources
Beta strandi167 – 1715Combined sources
Beta strandi174 – 1763Combined sources
Turni178 – 1803Combined sources
Helixi186 – 1938Combined sources
Helixi206 – 2083Combined sources
Turni221 – 2255Combined sources
Helixi226 – 2294Combined sources
Beta strandi231 – 2377Combined sources
Helixi238 – 2403Combined sources
Beta strandi241 – 2433Combined sources
Turni246 – 2483Combined sources
Beta strandi249 – 2557Combined sources
Beta strandi258 – 2614Combined sources
Beta strandi264 – 2707Combined sources
Beta strandi272 – 2798Combined sources
Helixi292 – 2965Combined sources
Turni297 – 3037Combined sources
Beta strandi310 – 31910Combined sources
Helixi322 – 33413Combined sources
Beta strandi340 – 3456Combined sources
Helixi353 – 36311Combined sources
Beta strandi364 – 3663Combined sources
Beta strandi369 – 3713Combined sources
Helixi379 – 3813Combined sources
Helixi387 – 3926Combined sources
Beta strandi396 – 4005Combined sources
Helixi402 – 4054Combined sources
Helixi408 – 41710Combined sources
Beta strandi447 – 4548Combined sources
Helixi457 – 4593Combined sources
Beta strandi463 – 4675Combined sources
Turni470 – 4723Combined sources
Helixi473 – 4819Combined sources
Helixi488 – 49912Combined sources
Beta strandi504 – 5074Combined sources
Helixi510 – 5134Combined sources
Helixi515 – 52713Combined sources
Beta strandi532 – 5343Combined sources
Helixi541 – 5444Combined sources
Helixi545 – 5473Combined sources
Beta strandi553 – 5553Combined sources
Beta strandi564 – 5707Combined sources
Helixi574 – 5774Combined sources
Beta strandi581 – 5855Combined sources
Turni592 – 5976Combined sources
Beta strandi599 – 6013Combined sources
Helixi607 – 6093Combined sources
Beta strandi612 – 6154Combined sources
Beta strandi619 – 6246Combined sources
Helixi637 – 64610Combined sources
Helixi657 – 66711Combined sources
Beta strandi691 – 6966Combined sources
Helixi701 – 7033Combined sources
Helixi708 – 7114Combined sources
Beta strandi715 – 7184Combined sources
Helixi720 – 7256Combined sources
Beta strandi733 – 7386Combined sources
Beta strandi741 – 7499Combined sources
Beta strandi758 – 7625Combined sources
Beta strandi768 – 7714Combined sources
Beta strandi774 – 7763Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
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

        10         20         30         40         50
MVRVKVNDRI VEVPPGTSVM DAVFHAGYDV PLFCSEKHLS PIGACRMCLV
60 70 80 90 100
RIGLPKKGPD GKPLLNEKGE PEIQWQPKLA ASCVTAVADG MVVDTLSDVV
110 120 130 140 150
REAQAGMVEF TLLNHPLDCP TCDKGGACEL QDRTVEYGLY EKYYQKGPLE
160 170 180 190 200
LPVYTRFEFT RRHVDKHHPL SPFVILDRER CIHCKRCVRY FEEVPGDEVL
210 220 230 240 250
DFIERGVHTF IGTMDFGLPS GFSGNITDIC PVGALLDLTA RFRARNWEME
260 270 280 290 300
ETPTTCALCP VGCGITADTR SGELLRIRAR EVPEVNEIWI CDAGRFGHEW
310 320 330 340 350
ADQNRLKTPL VRKEGRLVEA TWEEAFLALK EGLKEARGEE VGLYLAHDAT
360 370 380 390 400
LEEGLLASEL AKALKTPHLD FQGRTAAPAS LFPPASLEDL LQADFALVLG
410 420 430 440 450
DPTEEAPILH LRLSEFVRDL KPPHRYNHGT PFADLQIKER MPRRTDKMAL
460 470 480 490 500
FAPYRAPLMK WAAIHEVHRP GEEREILLAL LGDKEGSEMV AKAKEAWEKA
510 520 530 540 550
KNPVLILGAG VLQDTVAAER ARLLAERKGA KVLAMTPAAN ARGLEAMGVL
560 570 580 590 600
PGAKGASWDE PGALYAYYGF VPPEEALKGK RFVVMHLSHL HPLAERYAHV
610 620 630 640 650
VLPAPTFYEK RGHLVNLEGR VLPLSPAPIE NGEAEGALQV LALLAEALGV
660 670 680 690 700
RPPFRLHLEA QKALKARKVP EAMGRLSFRL KELRPKERKG AFYLRPTMWK
710 720 730 740 750
AHQAVGKAQE AARAELWAHP ETARAEALPE GAQVAVETPF GRVEARVVHR
760 770 780
EDVPKGHLYL SALGPAAGLR VEGRVLVPAG GEA
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:
EMBLi
GenBanki
DDBJi
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:
EMBLi
GenBanki
DDBJi
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:
PDBei
RCSB PDBi
PDBji
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: November 26, 2014
This is version 120 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