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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: 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.2 Publications

Catalytic activityi

NADH + a quinone = NAD+ + a quinol.

Cofactori

Protein has several cofactor binding sites:
  • [2Fe-2S] cluster1 PublicationNote: Binds 1 [2Fe-2S] cluster per subunit. The [2Fe-2S] cluster 1 is referred to as N1b.1 Publication
  • [4Fe-4S] cluster1 PublicationNote: 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.1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi34Iron-sulfur 1 (2Fe-2S)1 Publication1
Metal bindingi45Iron-sulfur 1 (2Fe-2S)1 Publication1
Metal bindingi48Iron-sulfur 1 (2Fe-2S)1 Publication1
Metal bindingi83Iron-sulfur 1 (2Fe-2S)1 Publication1
Metal bindingi115Iron-sulfur 2 (4Fe-4S); via tele nitrogen1 Publication1
Metal bindingi119Iron-sulfur 2 (4Fe-4S)1 Publication1
Metal bindingi122Iron-sulfur 2 (4Fe-4S)1 Publication1
Metal bindingi128Iron-sulfur 2 (4Fe-4S)1 Publication1
Metal bindingi181Iron-sulfur 3 (4Fe-4S)1 Publication1
Metal bindingi184Iron-sulfur 3 (4Fe-4S)1 Publication1
Metal bindingi187Iron-sulfur 3 (4Fe-4S)1 Publication1
Metal bindingi230Iron-sulfur 3 (4Fe-4S)1 Publication1
Metal bindingi256Iron-sulfur 4 (4Fe-4S)1 Publication1
Metal bindingi259Iron-sulfur 4 (4Fe-4S)1 Publication1
Metal bindingi263Iron-sulfur 4 (4Fe-4S)1 Publication1
Metal bindingi291Iron-sulfur 4 (4Fe-4S)1 Publication1

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Ligandi

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

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:1.6.5.11)
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
Proteomesi
  • UP000000532 Componenti: Chromosome

Subcellular locationi

  • Cell membrane 1 Publication; Peripheral membrane protein 1 Publication; Cytoplasmic side 1 Publication

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cell membrane, Membrane

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi256C → A: Decreases amount and stability of iron-sulfur center 4. 1 Publication1
Mutagenesisi259C → A: Decreases amount and stability of iron-sulfur center 4. 1 Publication1
Mutagenesisi263C → A: Decreases amount and stability of iron-sulfur center 4. 1 Publication1
Mutagenesisi291C → A: Decreases amount and stability of iron-sulfur center 4. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001185411 – 783NADH-quinone oxidoreductase subunit 3Add BLAST783

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

1783
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi2 – 5Combined sources4
Beta strandi10 – 13Combined sources4
Helixi19 – 25Combined sources7
Beta strandi48 – 53Combined sources6
Turni82 – 84Combined sources3
Beta strandi89 – 97Combined sources9
Helixi98 – 112Combined sources15
Turni119 – 121Combined sources3
Helixi125 – 127Combined sources3
Helixi129 – 137Combined sources9
Beta strandi167 – 171Combined sources5
Beta strandi174 – 176Combined sources3
Turni178 – 180Combined sources3
Helixi186 – 193Combined sources8
Helixi206 – 208Combined sources3
Turni221 – 225Combined sources5
Helixi226 – 229Combined sources4
Beta strandi231 – 237Combined sources7
Helixi238 – 240Combined sources3
Beta strandi241 – 243Combined sources3
Turni246 – 248Combined sources3
Beta strandi249 – 255Combined sources7
Beta strandi258 – 261Combined sources4
Beta strandi264 – 270Combined sources7
Beta strandi272 – 279Combined sources8
Helixi292 – 296Combined sources5
Turni297 – 303Combined sources7
Beta strandi310 – 319Combined sources10
Helixi322 – 334Combined sources13
Beta strandi340 – 345Combined sources6
Helixi353 – 363Combined sources11
Beta strandi364 – 366Combined sources3
Beta strandi369 – 371Combined sources3
Helixi379 – 381Combined sources3
Helixi387 – 392Combined sources6
Beta strandi396 – 400Combined sources5
Helixi402 – 405Combined sources4
Helixi408 – 417Combined sources10
Beta strandi447 – 454Combined sources8
Helixi457 – 459Combined sources3
Beta strandi463 – 467Combined sources5
Turni470 – 472Combined sources3
Helixi473 – 481Combined sources9
Helixi488 – 499Combined sources12
Beta strandi504 – 507Combined sources4
Helixi510 – 513Combined sources4
Helixi515 – 527Combined sources13
Beta strandi532 – 534Combined sources3
Helixi541 – 544Combined sources4
Helixi545 – 547Combined sources3
Beta strandi553 – 555Combined sources3
Beta strandi564 – 570Combined sources7
Helixi574 – 577Combined sources4
Beta strandi581 – 585Combined sources5
Turni592 – 597Combined sources6
Beta strandi599 – 601Combined sources3
Helixi607 – 609Combined sources3
Beta strandi612 – 615Combined sources4
Beta strandi619 – 624Combined sources6
Helixi637 – 646Combined sources10
Helixi657 – 667Combined sources11
Beta strandi691 – 696Combined sources6
Helixi701 – 703Combined sources3
Helixi708 – 711Combined sources4
Beta strandi715 – 718Combined sources4
Helixi720 – 725Combined sources6
Beta strandi733 – 738Combined sources6
Beta strandi741 – 749Combined sources9
Beta strandi758 – 762Combined sources5
Beta strandi768 – 771Combined sources4
Beta strandi774 – 776Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ56223.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini1 – 992Fe-2S ferredoxin-typePROSITE-ProRule annotationAdd BLAST99
Domaini249 – 3054Fe-4S Mo/W bis-MGD-typePROSITE-ProRule annotationAdd BLAST57

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 4.1 Publication

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

eggNOGiENOG4108IEH. Bacteria.
COG1034. LUCA.
HOGENOMiHOG000099655.
KOiK00336.
OMAiAMTRCIS.
PhylomeDBiQ56223.

Family and domain databases

CDDicd00207. fer2. 1 hit.
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]
PfamiPF04879. 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)DescriptionActionsGraphical viewLength
Sequence conflicti332G → S in AAA97944 (PubMed:9020134).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U52917 Genomic DNA. Translation: AAA97944.1.
AP008226 Genomic DNA. Translation: BAD69913.1.
PIRiT11904.
RefSeqiWP_011227701.1. NC_006461.1.
YP_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.
PIRiT11904.
RefSeqiWP_011227701.1. NC_006461.1.
YP_143356.1. NC_006461.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-59261N.
STRINGi300852.TTHA0090.

Protein family/group databases

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

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Phylogenomic databases

eggNOGiENOG4108IEH. Bacteria.
COG1034. LUCA.
HOGENOMiHOG000099655.
KOiK00336.
OMAiAMTRCIS.
PhylomeDBiQ56223.

Miscellaneous databases

EvolutionaryTraceiQ56223.

Family and domain databases

CDDicd00207. fer2. 1 hit.
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]
PfamiPF04879. 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]
ProtoNetiSearch...

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 2, 2016
This is version 132 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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.