Reviewed, UniProtKB/Swiss-Prot Q56223 (NQO3_THET8)

Names and origin

Protein names

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 names

Name:	nqo3
Ordered Locus Names:	TTHA0090

Organism

Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) [Complete proteome] [HAMAP]

Taxonomic identifier

300852 [NCBI]

Taxonomic lineage

Bacteria › Deinococcus-Thermus › Deinococci › Thermales › Thermaceae › Thermus

Protein attributes

Sequence length	783 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Evidence 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.

Ontologies

Keywords
Cellular component	Cell membrane Membrane
Ligand	2Fe-2S 4Fe-4S Iron Iron-sulfur Metal-binding NAD
Molecular function	Oxidoreductase
PTM	Quinone
Technical term	3D-structure Complete proteome Direct protein sequencing
Gene Ontology (GO)
Biological process	ATP synthesis coupled electron transport Inferred from electronic annotation. Source: InterPro
Cellular component	plasma membrane Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular function	2 iron, 2 sulfur cluster binding Inferred from electronic annotation. Source: UniProtKB-KW 4 iron, 4 sulfur cluster binding Inferred from electronic annotation. Source: UniProtKB-KW NADH dehydrogenase (ubiquinone) activity Inferred from electronic annotation. Source: InterPro electron carrier activity Inferred from electronic annotation. Source: InterPro iron ion binding Inferred from electronic annotation. Source: UniProtKB-KW molybdenum ion binding Inferred from electronic annotation. Source: InterPro quinone binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 783

783

NADH-quinone oxidoreductase subunit 3

PRO_0000118541

Regions

Domain

1 – 99

99

2Fe-2S ferredoxin-type

Sites

Metal binding

34

1

Iron-sulfur 1 (2Fe-2S)

Metal binding

45

1

Iron-sulfur 1 (2Fe-2S)

Metal binding

48

1

Iron-sulfur 1 (2Fe-2S)

Metal binding

83

1

Iron-sulfur 1 (2Fe-2S)

Metal binding

115

1

Iron-sulfur 2 (4Fe-4S); via tele nitrogen

Metal binding

119

1

Iron-sulfur 2 (4Fe-4S)

Metal binding

122

1

Iron-sulfur 2 (4Fe-4S)

Metal binding

128

1

Iron-sulfur 2 (4Fe-4S)

Metal binding

181

1

Iron-sulfur 3 (4Fe-4S)

Metal binding

184

1

Iron-sulfur 3 (4Fe-4S)

Metal binding

187

1

Iron-sulfur 3 (4Fe-4S)

Metal binding

230

1

Iron-sulfur 3 (4Fe-4S)

Metal binding

256

1

Iron-sulfur 4 (4Fe-4S)

Metal binding

259

1

Iron-sulfur 4 (4Fe-4S)

Metal binding

263

1

Iron-sulfur 4 (4Fe-4S)

Metal binding

291

1

Iron-sulfur 4 (4Fe-4S)

Experimental info

Mutagenesis

256

1

C → A: Decreases amount and stability of iron-sulfur center 4. Ref.3

Mutagenesis

259

1

C → A: Decreases amount and stability of iron-sulfur center 4. Ref.3

Mutagenesis

263

1

C → A: Decreases amount and stability of iron-sulfur center 4. Ref.3

Mutagenesis

291

1

C → A: Decreases amount and stability of iron-sulfur center 4. Ref.3

Sequence conflict

332

1

G → S in AAA97944. Ref.1

Secondary structure

1

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783

Helix Strand Turn

Details...

Beta strand

2 – 5

4

Beta strand

10 – 13

4

Helix

19 – 26

8

Beta strand

48 – 53

6

Turn

82 – 84

3

Beta strand

92 – 95

4

Helix

98 – 113

16

Turn

119 – 121

3

Helix

125 – 127

3

Helix

129 – 136

8

Beta strand

168 – 174

7

Helix

186 – 193

8

Helix

206 – 208

3

Helix

225 – 229

5

Beta strand

231 – 236

6

Helix

238 – 240

3

Beta strand

241 – 243

3

Turn

246 – 248

3

Beta strand

249 – 254

6

Beta strand

265 – 270

6

Beta strand

273 – 279

7

Helix

292 – 296

5

Helix

299 – 302

4

Beta strand

310 – 312

3

Beta strand

314 – 319

6

Helix

322 – 333

12

Beta strand

336 – 340

5

Beta strand

342 – 345

4

Helix

351 – 363

13

Beta strand

364 – 366

3

Beta strand

369 – 371

3

Helix

379 – 381

3

Helix

387 – 392

6

Beta strand

396 – 400

5

Helix

402 – 405

4

Helix

407 – 416

10

Turn

417 – 419

3

Helix

445 – 447

3

Beta strand

448 – 454

7

Helix

457 – 459

3

Beta strand

463 – 467

5

Helix

473 – 481

9

Beta strand

482 – 484

3

Helix

488 – 499

12

Beta strand

504 – 507

4

Helix

510 – 512

3

Helix

514 – 526

13

Beta strand

531 – 534

4

Helix

541 – 545

5

Turn

546 – 548

3

Beta strand

553 – 555

3

Beta strand

564 – 570

7

Helix

574 – 577

4

Beta strand

583 – 585

3

Helix

594 – 597

4

Beta strand

599 – 601

3

Helix

607 – 609

3

Beta strand

612 – 615

4

Beta strand

619 – 624

6

Helix

637 – 648

12

Helix

657 – 666

10

Beta strand

691 – 694

4

Helix

701 – 703

3

Helix

709 – 712

4

Beta strand

720 – 722

3

Turn

725 – 727

3

Beta strand

733 – 738

6

Beta strand

741 – 747

7

Beta strand

749 – 751

3

Sequences

	Sequence		Length	Mass (Da)
	Q56223-1 [UniParc]. Last modified March 29, 2005. Version 2. Checksum: 19A56201A20F9B82	FASTA	783	86,529
	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

References

	« Hide 'large scale' referencesShow '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: 9020134] [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].
[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: 11704668] [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: 16584177] [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: 16469879] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (3.3 ANGSTROMS), SUBUNIT, ELECTRON TRANSFER MECHANISM.

Cross-references

Sequence databases

EMBLGenBankDDBJ

U52917 Genomic DNA. Translation: AAA97944.1.
AP008226 Genomic DNA. Translation: BAD69913.1.

PIR

T11904.

RefSeq

YP_143356.1.

3D structure databases

PDBPDBe

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2FUG	X-ray	3.30	3/C/L/U	1-783	[»]

ModBase

Search...

Protein family/group databases

TCDB

3.D.1.3.1. proton-translocating NADH dehydrogenase (NDH) family.

Genome annotation databases

GeneID

3168388.

GenomeReviews

Gene locus TTHA0090 in contig AP008226_GR.

KEGG

ttj:TTHA0090.

NMPDR

fig|300852.3.peg.121.

Organism-specific databases

CMR

Search...

Phylogenomic databases

HOGENOM

Q56223.

OMA

Q56223. SDKTRYA.

Enzyme and pathway databases

BioCyc

TTHE300852:TTHA0090-MON.

Family and domain databases

InterPro

IPR006058. 2Fe2S_fd_BS.
IPR001041. Ferredoxin.
IPR006656. Mopterin_OxRdtase.
IPR006963. Mopterin_OxRdtase_Fe4S4.
IPR006657. MPT_dinuc_bd.
IPR000283. NADH_UbQ_OxRdtase_75KDa_su_CS.
IPR010228. NADH_UbQ_OxRdtase_Gsu.
IPR019574. NADH_UbQ_OxRdtase_Gsu_4Fe4S-bd.
[Graphical view]

Pfam

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]

TIGRFAMs

TIGR01973. NuoG. 1 hit.

PROSITE

PS00197. 2FE2S_FER_1. False negative.
PS51085. 2FE2S_FER_2. 1 hit.
PS00641. COMPLEX1_75K_1. 1 hit.
PS00642. COMPLEX1_75K_2. 1 hit.
PS00643. COMPLEX1_75K_3. 1 hit.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

NQO3_THET8

Accession

Primary (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:	June 16, 2009
This is version 79 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes)