Reviewed, UniProtKB/Swiss-Prot P29915 (NQO3_PARDE)

Names and origin

Protein names

Recommended name:
    NADH-quinone oxidoreductase chain 3
    EC=1.6.99.5
Alternative name(s):
    NADH dehydrogenase I, chain 3
    NDH-1, chain 3

Gene names

Name:

nqo3

Organism

Paracoccus denitrificans

Taxonomic identifier

266 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Alphaproteobacteria › Rhodobacterales › Rhodobacteraceae › Paracoccus

Protein attributes

Sequence length	673 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
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 believed to be ubiquinone. 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.
Catalytic activity	NADH + quinone = NAD+ + quinol.
Cofactor	Binds 1 2Fe-2S cluster per subunit. The 2Fe-2S cluster is known as N1b. Binds 2 4Fe-4S clusters per subunit. The 4Fe-4S cluster 1 is known as N5 and 4Fe-4S cluster 2 as N4.
Subunit structure	NDH-1 is composed of at least 14 different subunits, nqo1 to nqo14. The complex has a L-shaped structure, with the hydrophobic arm (subunits nqo7, nqo8, nqo10 to nqo14) embedded in the inner membrane and the hydrophilic peripheral arm (subunits nqo1 to nqo6, nqo9) protruding into the bacterial cytoplasm. The hydrophilic domain contains all the redox centers.
Subcellular location	Cell inner membrane; Peripheral membrane protein.
Sequence similarities	Belongs to the complex I 75 kDa subunit family. Contains 1 2Fe-2S ferredoxin-type domain.

Ontologies

Keywords
Cellular component	Cell inner membrane Cell membrane Membrane
Ligand	2Fe-2S 4Fe-4S Iron Iron-sulfur Metal-binding NAD Ubiquinone
Molecular function	Oxidoreductase
PTM	Quinone
Technical term	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 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
	Initiator methionine	1	1	Removed Ref.1
	Chain	2 – 673	672	NADH-quinone oxidoreductase chain 3		PRO_0000118540
Regions
	Domain	5 – 90	86	2Fe-2S ferredoxin-type
Sites
	Metal binding	37	1	Iron-sulfur 1 (2Fe-2S) Potential
	Metal binding	48	1	Iron-sulfur 1 (2Fe-2S) Potential
	Metal binding	51	1	Iron-sulfur 1 (2Fe-2S) Potential
	Metal binding	66	1	Iron-sulfur 1 (2Fe-2S) Potential
	Metal binding	106	1	Iron-sulfur 2 (4Fe-4S); via pros nitrogen Probable
	Metal binding	110	1	Iron-sulfur 2 (4Fe-4S) Potential
	Metal binding	113	1	Iron-sulfur 2 (4Fe-4S) Potential
	Metal binding	119	1	Iron-sulfur 2 (4Fe-4S) Potential
	Metal binding	158	1	Iron-sulfur 3 (4Fe-4S) Potential
	Metal binding	161	1	Iron-sulfur 3 (4Fe-4S) Potential
	Metal binding	164	1	Iron-sulfur 3 (4Fe-4S) Potential
	Metal binding	208	1	Iron-sulfur 3 (4Fe-4S) Potential
Experimental info
	Mutagenesis	106	1	H → A: Very little incorporation of iron-sulfur centers into protein in E.coli. Ref.4
	Mutagenesis	106	1	H → C: Alters the EPR signal of the N5 cluster; all 3 iron-sulfur clusters are less stable in E.coli. Ref.4

Sequences

	Sequence		Length	Mass (Da)
	P29915-1 [UniParc]. Last modified January 23, 2007. Version 4. Checksum: 5778B4A77940CF1D	FASTA	673	73,159
	10 20 30 40 50 60 MADLRKIKID DTIIEVDPNM TLIQACEMAG IEVPRFCYHE RLSIAGNCRM CLVEVVGGPP 70 80 90 100 110 120 KPAASCAMQV KDLRPGPEGA PSEIRTNSPM VKKAREGVME FLLINHPLDC PICDQGGECD 130 140 150 160 170 180 LQDQAMAYGV DFSRYREPKR ATEDLNLGPL VETHMTRCIS CTRCVRFTTE VAGITQMGQT 190 200 210 220 230 240 GRGEDSEITS YLNQTLESNM QGNIIDLCPV GALVSKPYAF TARPWELTKT ESIDVMDALG 250 260 270 280 290 300 SSIRIDTKGR EVMRILPRNH DGVNEEWISD KTRFVWDGLR RQRLDRPYIR ENGRLRPASW 310 320 330 340 350 360 PEALEAAARA MKGKKIAGLI GDLVPAEAAF SLKQLVEGLG GKVECRVDGA RLPAGNRSAY 370 380 390 400 410 420 VGTARIEDID DAEMIQLIGT NPRDEAPVLN ARIRKAWSKG AKVGLVGEPV DLTYDYAHVG 430 440 450 460 470 480 TDRAALESLS SREISDETKA RPSIVIVGQG AIARRDGEAV LAHAMKLAEN SNSGLLILHT 490 500 510 520 530 540 AAGRVGAMDV GAVTEGGLLA AIDGAEVVYN LGADEVDIDQ GPFVIYQGSH GDRGAHRDII 550 560 570 580 590 600 LPGACYTEES GLFVNTEGRP QLAMRANFAP GEGKENWAIL RALSAELGAT QPWDSLAGLR 610 620 630 640 650 660 RKLVEAVPHL AQIDQVPQNE WQPLGRFDLG QASFRYAIRD FYLTNPIARS SPLMGELSAM 670 AAARKAPAPL AAE

References

[1]	"Structural features of the 66-kDa subunit of the energy-transducing NADH-ubiquinone oxidoreductase (NDH-1) of Paracoccus denitrificans." Xu X., Matsuno-Yagi A., Yagi T. Arch. Biochem. Biophys. 296:40-48(1992) [PubMed: 1605643] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 2-16. Strain: ATCC 13543 / NRRL B-3784.
[2]	"DNA sequencing of the seven remaining structural genes of the gene cluster encoding the energy-transducing NADH-quinone oxidoreductase of Paracoccus denitrificans." Xu X., Matsuno-Yagi A., Yagi T. Biochemistry 32:968-981(1993) [PubMed: 8422400] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 658-673.
[3]	"Expression and characterization of the 66-kilodalton (NQO3) iron-sulfur subunit of the proton-translocating NADH-quinone oxidoreductase of Paracoccus denitrificans." Yano T., Yagi T., Sled' V.D., Ohnishi T. J. Biol. Chem. 270:18264-18270(1995) [PubMed: 7629145] [Abstract] Cited for: IDENTIFICATION OF A [2FE--2S] AND A [4FE--4S] CLUSTER.
[4]	"Characterization of cluster N5 as a fast-relaxing [4Fe-4S] cluster in the Nqo3 subunit of the proton-translocating NADH-ubiquinone oxidoreductase from Paracoccus denitrificans." Yano T., Sklar J., Nakamaru-Ogiso E., Takahashi Y., Yagi T., Ohnishi T. J. Biol. Chem. 278:15514-15522(2003) [PubMed: 12600982] [Abstract] Cited for: IDENTIFICATION OF A SECOND [4FE--4S] CLUSTER, MUTAGENESIS OF HIS-106.

Cross-references

Sequence databases
EMBLGenBankDDBJ	M84572 Genomic DNA. Translation: AAA25587.1.
PIR	A45456. S23948.
3D structure databases
ModBase	Search...
Protein family/group databases
TCDB	3.D.1.2.1. proton-translocating NADH dehydrogenase (NDH) family.
Enzyme and pathway databases
BRENDA	1.6.99.5. 59.
Family and domain databases
InterPro	IPR006058. 2Fe2S_fd_BS. IPR001041. Ferredoxin. IPR006656. Mopterin_OxRdtase. IPR000283. NADH_UbQ_OxRdtase_75KDa_su_CS. IPR010228. NADH_UbQ_OxRdtase_Gsu. IPR019574. NADH_UbQ_OxRdtase_Gsu_4Fe4S-bd. IPR015405. NuoG_C. [Graphical view]
Pfam	PF09326. DUF1982. 1 hit. PF00111. Fer2. 1 hit. PF00384. Molybdopterin. 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_PARDE

Accession

Primary (citable) accession number: P29915

Entry history

Integrated into UniProtKB/Swiss-Prot:	April 1, 1993
Last sequence update:	January 23, 2007
Last modified:	June 16, 2009
This is version 75 of the entry and version 4 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

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