Q56224 (NQO9_THET8) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
NADH-quinone oxidoreductase subunit 9
EC=1.6.99.5

Alternative name(s):
NADH dehydrogenase I subunit 9
NDH-1 subunit 9

Gene names

Name:	nqo9
Ordered Locus Names:	TTHA0092

Organism

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

Taxonomic identifier

300852 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Deinococcus-Thermus › Deinococci › Thermales › Thermaceae › Thermus › Thermus thermophilus

Protein attributes

Sequence length	182 AA.
Sequence status	Complete.
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. The role of the nqo9 subunit appears to provide a 'connecting chain' of two clusters between cluster N5 and the terminal cluster N2, and to stabilize the structure of the complex by interacting with other subunits. HAMAP-Rule MF_01351
Catalytic activity	NADH + quinone = NAD+ + quinol. HAMAP-Rule MF_01351
Cofactor	Binds 2 4Fe-4S clusters per subunit. The 4Fe-4S clusters are referred to as N6a and N6b.
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.3 Ref.4
Subcellular location	Cell membrane; Peripheral membrane protein; Cytoplasmic side HAMAP-Rule MF_01351.
Sequence similarities	Belongs to the complex I 23 kDa subunit family. Contains 2 4Fe-4S ferredoxin-type domains.

Ontologies

Keywords
Cellular component	Cell membrane Membrane
Domain	Repeat
Ligand	4Fe-4S Iron Iron-sulfur Metal-binding NAD
Molecular function	Oxidoreductase
PTM	Quinone
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	photosynthesis, light reaction Inferred from electronic annotation. Source: HAMAP
Cellular_component	plasma membrane Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	4 iron, 4 sulfur cluster binding Inferred from electronic annotation. Source: UniProtKB-KW NADH dehydrogenase (quinone) activity Inferred from electronic annotation. Source: HAMAP electron carrier activity Inferred from electronic annotation. Source: InterPro iron ion binding Inferred from electronic annotation. Source: HAMAP 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 – 182

182

NADH-quinone oxidoreductase subunit 9 HAMAP-Rule MF_01351

PRO_0000118721

Regions

Domain

43 – 73

31

4Fe-4S ferredoxin-type 1

Domain

89 – 118

30

4Fe-4S ferredoxin-type 2

Sites

Metal binding

53

1

Iron-sulfur 1 (4Fe-4S)

Metal binding

56

1

Iron-sulfur 1 (4Fe-4S)

Metal binding

59

1

Iron-sulfur 1 (4Fe-4S)

Metal binding

63

1

Iron-sulfur 2 (4Fe-4S)

Metal binding

98

1

Iron-sulfur 2 (4Fe-4S)

Metal binding

101

1

Iron-sulfur 2 (4Fe-4S)

Metal binding

104

1

Iron-sulfur 2 (4Fe-4S)

Metal binding

108

1

Iron-sulfur 1 (4Fe-4S)

Secondary structure

1

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182

Helix Strand Turn

Details...

Helix

4 – 18

15

Turn

26 – 28

3

Beta strand

40 – 43

4

Helix

58 – 62

5

Beta strand

68 – 73

6

Beta strand

77 – 79

3

Beta strand

81 – 85

5

Beta strand

87 – 94

8

Turn

95 – 97

3

Helix

103 – 107

5

Beta strand

109 – 111

3

Beta strand

113 – 115

3

Beta strand

123 – 125

3

Helix

126 – 129

4

Beta strand

130 – 132

3

Helix

133 – 136

4

Helix

144 – 149

6

Turn

150 – 153

4

Beta strand

160 – 162

3

Helix

168 – 170

3

Sequences

	Sequence		Length	Mass (Da)
	Q56224 [UniParc]. Last modified November 1, 1997. Version 1. Checksum: 054A9F7942C64C66	FASTA	182	20,080
	10 20 30 40 50 60 MTLKALAQSL GITLKYLFSK PVTVPYPDAP VALKPRFHGR HVLTRHPNGL EKCIGCSLCA 70 80 90 100 110 120 AACPAYAIYV EPAENDPENP VSAGERYAKV YEINMLRCIF CGLCEEACPT GAIVLGYDFE 130 140 150 160 170 180 MADYEYSDLV YGKEDMLVDV VGTKPQRREA KRTGKPVKVG YVVPYVRPEL EGFKAPTEGG KR

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] [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]	"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: IDENTIFICATION BY MASS SPECTROMETRY, SUBUNIT.
[4]	"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.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

U52917 Genomic DNA. Translation: AAA97946.1.
AP008226 Genomic DNA. Translation: BAD69915.1.

PIR

T11906.

RefSeq

YP_143358.1. NC_006461.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2FUG	X-ray	3.30	9/G/P/Y	1-182	[»]
2YBB	electron microscopy	19.00	8	1-182	[»]
3I9V	X-ray	3.10	9/G	1-182	[»]
3IAM	X-ray	3.10	9/G	1-182	[»]
3IAS	X-ray	3.15	9/G/P/Y	1-182	[»]
3M9S	X-ray	4.50	9/G	1-182	[»]
4HEA	X-ray	3.30	9/O	1-182	[»]

ProteinModelPortal

Q56224.

SMR

Q56224. Positions 26-179.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-59267N.

STRING

300852.TTHA0092.

Protein family/group databases

TCDB

3.D.1.3.1. H+ or Na+-translocating NADH dehydrogenase (NDH) family.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

BAD69915; BAD69915; BAD69915.

GeneID

3167944.

KEGG

ttj:TTHA0092.

PATRIC

23955115. VBITheThe93045_0090.

Phylogenomic databases

eggNOG

COG1143.

HOGENOM

HOG000228291.

KO

K00338.

OMA

RGAWIGE.

ProtClustDB

CLSK445099.

Enzyme and pathway databases

BioCyc

TTHE300852:GH8R-96-MONOMER.

Family and domain databases

Gene3D

1.10.1060.10. 1 hit.

HAMAP

MF_01351. NDH1_NuoI.

InterPro

IPR001450. 4Fe4S-bd_dom.
IPR017896. 4Fe4S_Fe-S-bd.
IPR017900. 4Fe4S_Fe_S_CS.
IPR012285. Fum_reductase_C.
IPR010226. NADH_quinone_OxRdtase_chainI.
[Graphical view]

Pfam

PF00037. Fer4. 2 hits.
[Graphical view]

TIGRFAMs

TIGR01971. NuoI. 1 hit.

PROSITE

PS00198. 4FE4S_FER_1. 2 hits.
PS51379. 4FE4S_FER_2. 2 hits.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

Q56224.

Entry information

Entry name

NQO9_THET8

Accession

Primary (citable) accession number: Q56224
Secondary accession number(s): Q5SM51

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 1, 1997
Last sequence update:	November 1, 1997
Last modified:	May 29, 2013
This is version 108 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program