Reviewed, UniProtKB/Swiss-Prot P0C278 (FRDA_SHEFR)

Names and origin

Protein names

Recommended name:
    Fumarate reductase flavoprotein subunit
    EC=1.3.99.1
Alternative name(s):
    Flavocytochrome c
    Flavocytochrome c3
      Short name=Fcc3

Gene names

Name:	fccA
Synonyms:	fcc3

Organism

Shewanella frigidimarina

Taxonomic identifier

56812 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Alteromonadales › Shewanellaceae › Shewanella

Protein attributes

Sequence length	571 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	Catalyzes fumarate reduction using artificial electron donors such as methyl viologen. The physiological reductant is unknown, but evidence indicates that flavocytochrome c participates in electron transfer from formate to fumarate and possibly also to trimethylamine oxide (TMAO). This enzyme is essentially unidirectional.
Catalytic activity	Succinate + acceptor = fumarate + reduced acceptor.
Cofactor	Binds 1 FAD per subunit.
Subunit structure	Monomer.
Subcellular location	Periplasm.
Induction	By anaerobiosis and fumarate.
Sequence similarities	In the C-terminal section; belongs to the FAD-dependent oxidoreductase 2 family. FRD/SDH subfamily. Contains 1 cytochrome c domain.
Caution	The N-terminal sequence has been extracted from PDB entry 1LJ1.
Mass spectrometry	Molecular mass is 63033±10 Da from positions 1 - 571. Determined by ESI. Ref.7

Ontologies

Keywords
Biological process	Electron transport Transport
Cellular component	Periplasm
Ligand	FAD Flavoprotein Heme Iron Metal-binding
Molecular function	Oxidoreductase
Technical term	3D-structure
Gene Ontology (GO)
Biological process	anaerobic electron transport chain Non-traceable author statement. Source: UniProtKB anaerobic respiration Non-traceable author statement. Source: UniProtKB transport Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	outer membrane-bounded periplasmic space Non-traceable author statement. Source: UniProtKB
Molecular function	electron carrier activity Non-traceable author statement. Source: UniProtKB iron ion binding Inferred from electronic annotation. Source: UniProtKB-KW succinate dehydrogenase activity Inferred from electronic annotation. Source: EC
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 571

571

Fumarate reductase flavoprotein subunit

PRO_0000010344

Regions

Domain

1 – 117

117

Cytochrome c

Nucleotide binding

132 – 143

12

FAD

Nucleotide binding

156 – 157

2

FAD

Nucleotide binding

164 – 165

2

FAD

Nucleotide binding

169 – 171

3

FAD

Nucleotide binding

549 – 550

2

FAD

Region

118 – 571

454

Flavoprotein-like

Sites

Active site

402

1

Proton donor

Metal binding

8

1

Iron (heme 2 axial ligand)

Metal binding

18

1

Iron (heme 1 axial ligand)

Metal binding

40

1

Iron (heme 2 axial ligand)

Metal binding

58

1

Iron (heme 3 axial ligand)

Metal binding

61

1

Iron (heme 4 axial ligand)

Metal binding

72

1

Iron (heme 3 axial ligand)

Metal binding

75

1

Iron (heme 1 axial ligand)

Metal binding

86

1

Iron (heme 4 axial ligand)

Binding site

14

1

Heme 1 (covalent)

Binding site

17

1

Heme 1 (covalent)

Binding site

36

1

Heme 2 (covalent)

Binding site

39

1

Heme 2 (covalent)

Binding site

68

1

Heme 3 (covalent)

Binding site

71

1

Heme 3 (covalent)

Binding site

82

1

Heme 4 (covalent)

Binding site

85

1

Heme 4 (covalent)

Binding site

365

1

Substrate

Binding site

377

1

Substrate

Binding site

504

1

Substrate

Binding site

544

1

Substrate

Experimental info

Mutagenesis

61

1

H → A: Reduces catalytic activity 10-fold. Reduces affinity for fumarate. Ref.7

Mutagenesis

61

1

H → M: Reduces catalytic activity 5-fold. Reduces affinity for fumarate. Ref.7

Mutagenesis

365

1

H → A: Reduces catalytic activity by over 75%. Ref.3

Mutagenesis

378

1

E → D: Strongly reduced affinity for substrate. Reduces activity 10000-fold. Ref.9

Mutagenesis

381

1

R → M: Strongly reduced catalytic activity. No effect on substrate affinity. Ref.9

Mutagenesis

402

1

R → A: Loss of activity. Ref.3 Ref.4

Mutagenesis

402

1

R → K or Y: Reduces activity 10000-fold. Ref.3 Ref.4

Mutagenesis

504

1

H → A: Reduces catalytic activity by over 64%. Ref.3

Secondary structure

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571

Helix Strand Turn

Details...

Helix

4 – 9

6

Helix

14 – 16

3

Helix

30 – 40

11

Helix

43 – 47

5

Helix

68 – 70

3

Beta strand

74 – 76

3

Helix

81 – 84

4

Helix

107 – 111

5

Helix

112 – 120

9

Beta strand

124 – 132

9

Helix

136 – 147

12

Beta strand

152 – 155

4

Beta strand

157 – 161

5

Helix

165 – 167

3

Helix

178 – 182

5

Helix

189 – 199

11

Turn

200 – 202

3

Helix

206 – 225

20

Beta strand

232 – 234

3

Beta strand

244 – 247

4

Turn

248 – 250

3

Helix

253 – 267

15

Beta strand

271 – 283

13

Beta strand

289 – 296

8

Turn

297 – 299

3

Beta strand

300 – 311

12

Helix

320 – 326

7

Helix

328 – 330

3

Helix

344 – 351

8

Beta strand

362 – 369

8

Turn

370 – 372

3

Helix

379 – 382

4

Beta strand

386 – 388

3

Helix

402 – 410

9

Helix

413 – 415

3

Beta strand

417 – 422

6

Helix

423 – 428

6

Helix

431 – 438

8

Beta strand

443 – 446

4

Helix

447 – 454

8

Helix

458 – 473

16

Turn

478 – 480

3

Beta strand

494 – 506

13

Beta strand

509 – 512

4

Beta strand

517 – 519

3

Beta strand

525 – 531

7

Beta strand

536 – 540

5

Helix

548 – 567

20

Sequences

	Sequence		Length	Mass (Da)
	P0C278-1 [UniParc]. Last modified December 12, 2006. Version 1. Checksum: D2E4FC43C9A6484C	FASTA	571	60,621
	10 20 30 40 50 60 ADNLAEFHVQ NQECDSCHTP DGELSNDSLT YENTQCVSCH GTLEEVAETT KHEHYNAHAS 70 80 90 100 110 120 HFPGEVACTS CHSAHEKSMV YCDSCHSFDF NMPYAKKWQR DEPTIAELAK DKSERQAALA 130 140 150 160 170 180 SAPHDTVDVV VVGSGGAGFS AAISATDSGA KVILIEKEPV IGGNAKLAAG GMNAAWTDQQ 190 200 210 220 230 240 KAKKITDSPE LMFEDTMKGG QNINDPALVK VLSSHSKDSV DWMTAMGADL TDVGMMGGAS 250 260 270 280 290 300 VNRAHRPTGG AGVGAHVVQV LYDNAVKRNI DLRMNTRGIE VLKDDKGTVK GILVKGMYKG 310 320 330 340 350 360 YYWVKADAVI LATGGFAKNN ERVAKLDPSL KGFISTNQPG AVGDGLDVAE NAGGALKDMQ 370 380 390 400 410 420 YIQAHPTLSV KGGVMVTEAV RGNGAILVNR EGKRFVNEIT TRDKASAAIL AQTGKSAYLI 430 440 450 460 470 480 FDDSVRKSLS KIDKYIGLGV APTADSLVKL GKMEGIDGKA LTETVARYNS LVSSGKDTDF 490 500 510 520 530 540 ERPNLPRALN EGNYYAIEVT PGVHHTMGGV MIDTKAEVMN AKKQVIPGLY GAGEVTGGVH 550 560 570 GANRLGGNAI SDIITFGRLA GEEAAKYSKK N

References

[1]	"Crystallization and preliminary X-ray analysis of flavocytochrome c(3), the fumarate reductase from Shewanella frigidimarina." Pealing S.L., Lysek D.A., Taylor P., Alexeev D., Reid G.A., Chapman S.K., Walkinshaw M.D. J. Struct. Biol. 127:76-78(1999) [PubMed: 10479620] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 11-571, CRYSTALLIZATION. Strain: ACAM591.
[2]	"Structural and mechanistic mapping of a unique fumarate reductase." Taylor P., Pealing S.L., Reid G.A., Chapman S.K., Walkinshaw M.D. Nat. Struct. Biol. 6:1108-1112(1999) [PubMed: 10581550] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS).
[3]	"Identification of the active site acid/base catalyst in a bacterial fumarate reductase: a kinetic and crystallographic study." Doherty M.K., Pealing S.L., Miles C.S., Moysey R., Taylor P., Walkinshaw M.D., Reid G.A., Chapman S.K. Biochemistry 39:10695-10701(2000) [PubMed: 10978153] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) OF MUTANTS ALA-365 AND ALA-504 IN COMPLEX WITH FAD; FUMARATE AND HEMES, MUTAGENESIS OF HIS-365; ARG-402 AND HIS-504.
[4]	"Kinetic and crystallographic analysis of the key active site acid/base arginine in a soluble fumarate reductase." Mowat C.G., Moysey R., Miles C.S., Leys D., Doherty M.K., Taylor P., Walkinshaw M.D., Reid G.A., Chapman S.K. Biochemistry 40:12292-12298(2001) [PubMed: 11591148] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF MUTANTS ALA-402; LYS-402 AND TYR-402, MUTAGENESIS OF ARG-402, ENZYME KINETICS.
[5]	"Role of His505 in the soluble fumarate reductase from Shewanella frigidimarina." Pankhurst K.L., Mowat C.G., Miles C.S., Leys D., Walkinshaw M.D., Reid G.A., Chapman S.K. Biochemistry 41:8551-8556(2002) [PubMed: 12093271] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) OF MUTANTS ALA-505 AND TYR-505, CHARACTERIZATION.
[6]	"Engineering water to act as an active site acid catalyst in a soluble fumarate reductase." Mowat C.G., Pankhurst K.L., Miles C.S., Leys D., Walkinshaw M.D., Reid G.A., Chapman S.K. Biochemistry 41:11990-11996(2002) [PubMed: 12356299] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) OF MUTANTS PHE-363 AND PHE-363/ALA-402, CHARACTERIZATION, MASS SPECTROMETRY.
[7]	"Histidine 61: an important heme ligand in the soluble fumarate reductase from Shewanella frigidimarina." Rothery E.L., Mowat C.G., Miles C.S., Walkinshaw M.D., Reid G.A., Chapman S.K. Biochemistry 42:13160-13169(2003) [PubMed: 14609326] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) OF MUTANTS ALA-61 AND MET-61 IN COMPLEXES WITH HEME; SUBSTRATE AND FAD, MASS SPECTROMETRY, MUTAGENESIS OF HIS-61.
[8]	"Probing domain mobility in a flavocytochrome." Rothery E.L., Mowat C.G., Miles C.S., Mott S., Walkinshaw M.D., Reid G.A., Chapman S.K. Biochemistry 43:4983-4989(2004) [PubMed: 15109257] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS) OF MUTANT CYS-251/CYS430.
[9]	"A proton delivery pathway in the soluble fumarate reductase from Shewanella frigidimarina." Pankhurst K.L., Mowat C.G., Rothery E.L., Hudson J.M., Jones A.K., Miles C.S., Walkinshaw M.D., Armstrong F.A., Reid G.A., Chapman S.K. J. Biol. Chem. 281:20589-20597(2006) [PubMed: 16699170] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) OF MUTANTS ASP-378 AND MET-381, MASS SPECTROMETRY, MUTAGENESIS OF GLU-378 AND ARG-381.

Cross-references

Sequence databases

EMBLGenBankDDBJ

AJ132010 Genomic DNA. Translation: CAB38558.1.

3D structure databases

PDBPDBe

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1E39	X-ray	1.80	A	1-571	[»]
1JRX	X-ray	2.00	A/B	1-571	[»]
1JRY	X-ray	2.00	A/B	1-571	[»]
1JRZ	X-ray	2.00	A/B	1-571	[»]
1KSS	X-ray	1.80	A	1-571	[»]
1KSU	X-ray	2.00	A/B	1-571	[»]
1LJ1	X-ray	2.00	A/B	1-571	[»]
1M64	X-ray	1.80	A/B	1-571	[»]
1P2E	X-ray	2.20	A	1-571	[»]
1P2H	X-ray	2.10	A	1-571	[»]
1Q9I	X-ray	1.60	A	1-571	[»]
1QJD	X-ray	1.80	A	1-571	[»]
1Y0P	X-ray	1.50	A	1-571	[»]
2B7R	X-ray	1.70	A	1-571	[»]
2B7S	X-ray	2.12	A	1-571	[»]

ModBase

Search...

Enzyme and pathway databases

BRENDA

1.3.99.1. 276222.

Family and domain databases

InterPro

IPR003953. FAD_bind2_N.
IPR010960. Flavocytochrome_c.
IPR011031. Multihaem_cyt.
[Graphical view]

Pfam

PF00890. FAD_binding_2. 1 hit.
[Graphical view]

TIGRFAMs

TIGR01813. flavo_cyto_c. 1 hit.

PROSITE

PS51008. MULTIHEME_CYTC. 1 hit.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

FRDA_SHEFR

Accession

Primary (citable) accession number: P0C278
Secondary accession number(s): Q02469, Q9X969

Entry history

Integrated into UniProtKB/Swiss-Prot:	December 12, 2006
Last sequence update:	December 12, 2006
Last modified:	June 16, 2009
This is version 16 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

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