Q93W20 (NIFU2_ARATH) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
NifU-like protein 2, chloroplastic
Short name=AtCNfu2
Short name=AtCnfU-V

Gene names

Name:	NIFU2
Synonyms:	CNFU2, NFU2
Ordered Locus Names:	At5g49940
ORF Names:	K9P8.16

Organism

Arabidopsis thaliana (Mouse-ear cress) [Reference proteome]

Taxonomic identifier

3702 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Viridiplantae › Streptophyta › Streptophytina › Embryophyta › Tracheophyta › Euphyllophyta › Spermatophyta › Magnoliophyta › eudicotyledons › core eudicotyledons › rosids › malvids › Brassicales › Brassicaceae › Camelineae › Arabidopsis

Protein attributes

Sequence length	235 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	Molecular scaffold for [Fe-S] cluster assembly of chloroplastic iron-sulfur proteins. Required for biogenesis of ferredoxin, a major photosynthetic electron carrier containing [2Fe-2S] cluster. Required for the assembly of photosystem I complex. Ref.7 Ref.8
Cofactor	Binds 1 [2Fe-2S] cluster per subunit. Ref.7
Subunit structure	Homodimer; disulfide-linked. Ref.7 Ref.9
Subcellular location	Plastid › chloroplast stroma Ref.1 Ref.7.
Tissue specificity	Predominantly expressed in leaves and floral stalks. Ubiquitous (at protein level). Ref.1 Ref.7
Disruption phenotype	Plants are dwarf with faint pale-green leaves, decreased amount of ferredoxin and impaired photosystem I accumulation. Ref.7
Sequence similarities	Belongs to the NifU family.
Sequence caution	The sequence BAA97015.1 differs from that shown. Reason: Erroneous gene model prediction. The predicted gene At5g49940 has been split into 2 genes: At5g49940 and At5g49945.

Ontologies

Keywords
Cellular component	Chloroplast Plastid
Coding sequence diversity	Alternative splicing
Domain	Transit peptide
Ligand	2Fe-2S Iron Iron-sulfur Metal-binding
PTM	Disulfide bond
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	chloroplast organization Inferred from mutant phenotype Ref.7. Source: TAIR iron-sulfur cluster assembly Inferred from mutant phenotype Ref.7. Source: TAIR
Cellular_component	chloroplast stroma Inferred from direct assay PubMed 20061580. Source: TAIR
Molecular_function	2 iron, 2 sulfur cluster binding Inferred from electronic annotation. Source: UniProtKB-KW iron ion binding Inferred from electronic annotation. Source: InterPro structural molecule activity Traceable author statement Ref.1. Source: TAIR
Complete GO annotation...

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]

Isoform 1 (identifier: Q93W20-1)

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

Isoform 2 (identifier: Q93W20-2)

The sequence of this isoform differs from the canonical sequence as follows:
     175-185: LEEIRPYLIGT → KFWCWKKSGLT
     186-235: Missing.

Note: May be due to a competing donor splice site. No experimental confirmation available.

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Transit peptide

1 – 16

16

Chloroplast Potential

Chain

17 – 235

219

NifU-like protein 2, chloroplastic

PRO_0000247613

Amino acid modifications

Disulfide bond

126

Interchain (with C-129) Ref.9

Disulfide bond

129

Interchain (with C-126) Ref.9

Natural variations

Alternative sequence

175 – 185

11

LEEIRPYLIGT → KFWCWKKSGLT in isoform 2.

VSP_040522

Alternative sequence

186 – 235

50

Missing in isoform 2.

VSP_040523

Secondary structure

1

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

235

Helix Strand Turn

Details...

Helix

87 – 103

17

Beta strand

106 – 114

9

Beta strand

117 – 123

7

Helix

124 – 127

4

Helix

130 – 132

3

Helix

133 – 147

15

Beta strand

153 – 156

4

Helix

168 – 178

11

Helix

179 – 181

3

Helix

184 – 186

3

Beta strand

189 – 196

8

Beta strand

199 – 206

8

Helix

207 – 210

4

Helix

213 – 225

13

Beta strand

231 – 234

4

Sequences

	Sequence		Length	Mass (Da)
	Isoform 1 [UniParc]. Last modified December 1, 2001. Version 1. Checksum: 6443A3A407D8A3A8	FASTA	235	25,620
	10 20 30 40 50 60 MQLLTLNPAA ISRTPPQAID PSSSSSLLLP FPQILSSQRA LGLVARPCNP LRRGLSRFLS 70 80 90 100 110 120 SRQLFRRSKV VKAVATPDPI LEVPLTEENV ESVLDEIRPY LMSDGGNVAL HEIDGNIVRV 130 140 150 160 170 180 KLQGACGSCP SSTMTMKMGI ERRLMEKIPE IVAVEALPDE ETGLELNEEN IEKVLEEIRP 190 200 210 220 230 YLIGTADGSL DLVEIEDPIV KIRITGPAAG VMTVRVAVTQ KLREKIPSIA AVQLI
	Isoform 2 [UniParc]. Checksum: 46069648F7D039D3	FASTA	185	20,422
	10 20 30 40 50 60 MQLLTLNPAA ISRTPPQAID PSSSSSLLLP FPQILSSQRA LGLVARPCNP LRRGLSRFLS 70 80 90 100 110 120 SRQLFRRSKV VKAVATPDPI LEVPLTEENV ESVLDEIRPY LMSDGGNVAL HEIDGNIVRV 130 140 150 160 170 180 KLQGACGSCP SSTMTMKMGI ERRLMEKIPE IVAVEALPDE ETGLELNEEN IEKVKFWCWK KSGLT

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Iron-sulphur cluster assembly in plants: distinct NFU proteins in mitochondria and plastids from Arabidopsis thaliana." Leon S., Touraine B., Ribot C., Briat J.-F., Lobreaux S. Biochem. J. 371:823-830(2003) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), TISSUE SPECIFICITY, SUBCELLULAR LOCATION, GENE FAMILY. Strain: cv. Columbia.
[2]	"Structural analysis of Arabidopsis thaliana chromosome 5. X. Sequence features of the regions of 3,076,755 bp covered by sixty P1 and TAC clones." Sato S., Nakamura Y., Kaneko T., Katoh T., Asamizu E., Kotani H., Tabata S. DNA Res. 7:31-63(2000) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: cv. Columbia.
[3]	The Arabidopsis Information Resource (TAIR) Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: cv. Columbia.
[4]	"Functional annotation of a full-length Arabidopsis cDNA collection." Seki M., Narusaka M., Kamiya A., Ishida J., Satou M., Sakurai T., Nakajima M., Enju A., Akiyama K., Oono Y., Muramatsu M., Hayashizaki Y., Kawai J., Carninci P., Itoh M., Ishii Y., Arakawa T., Shibata K., Shinagawa A., Shinozaki K. Science 296:141-145(2002) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1). Strain: cv. Columbia.
[5]	"Empirical analysis of transcriptional activity in the Arabidopsis genome." Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M., Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G., Liu S.X., Lam B., Sakano H., Wu T., Yu G. , Miranda M., Quach H.L., Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C., Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J., Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A., Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C., Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X., Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M., Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K., Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A., Ecker J.R. Science 302:842-846(2003) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1). Strain: cv. Columbia.
[6]	"Analysis of multiple occurrences of alternative splicing events in Arabidopsis thaliana using novel sequenced full-length cDNAs." Iida K., Fukami-Kobayashi K., Toyoda A., Sakaki Y., Kobayashi M., Seki M., Shinozaki K. DNA Res. 16:155-164(2009) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2). Strain: cv. Columbia.
[7]	"The Arabidopsis chloroplastic NifU-like protein CnfU, which can act as an iron-sulfur cluster scaffold protein, is required for biogenesis of ferredoxin and photosystem I." Yabe T., Morimoto K., Kikuchi S., Nishio K., Terashima I., Nakai M. Plant Cell 16:993-1007(2004) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, COFACTOR, SUBUNIT, SUBCELLULAR LOCATION, TISSUE SPECIFICITY, DISRUPTION PHENOTYPE.
[8]	"Nfu2: a scaffold protein required for [4Fe-4S] and ferredoxin iron-sulphur cluster assembly in Arabidopsis chloroplasts." Touraine B., Boutin J.-P., Marion-Poll A., Briat J.-F., Peltier G., Lobreaux S. Plant J. 40:101-111(2004) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[9]	"Structural analysis of Arabidopsis CnfU protein: an iron-sulfur cluster biosynthetic scaffold in chloroplasts." Yabe T., Yamashita E., Kikuchi A., Morimoto K., Nakagawa A., Tsukihara T., Nakai M. J. Mol. Biol. 381:160-173(2008) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.35 ANGSTROMS) OF 83-235, SUBUNIT, DISULFIDE BONDS.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

AJ512934 mRNA. Translation: CAD55559.1.
AB024032 Genomic DNA. Translation: BAA97015.1. Sequence problems.
CP002688 Genomic DNA. Translation: AED95873.1.
CP002688 Genomic DNA. Translation: AED95874.1.
AK316745 mRNA. Translation: BAH19468.1.
AF370353 mRNA. Translation: AAK44168.1.
AF428399 mRNA. Translation: AAL16167.1.
AY062984 mRNA. Translation: AAL34158.1.
AK118652 mRNA. Translation: BAC43248.1.

IPI

IPI00517598.
IPI00846628.

RefSeq

NP_001078739.1. NM_001085270.2.
NP_568715.1. NM_124372.4.

UniGene

At.26219.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2Z51	X-ray	1.35	A	83-235	[»]

ProteinModelPortal

Q93W20.

SMR

Q93W20. Positions 83-235.

ModBase

Search...

Protein-protein interaction databases

STRING

3702.AT5G49940.1-P.

Proteomic databases

PaxDb

Q93W20.

PRIDE

Q93W20.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblPlants

AT5G49940.1; AT5G49940.1; AT5G49940.

GeneID

835057.

KEGG

ath:AT5G49940.

Organism-specific databases

GeneFarm

3943. 402.

TAIR

At5g49940.

Phylogenomic databases

eggNOG

COG0694.

HOGENOM

HOG000006174.

InParanoid

Q93W20.

OMA

LEFVTIE.

PhylomeDB

Q93W20.

ProtClustDB

CLSN2720187.

Gene expression databases

Genevestigator

Q93W20.

GermOnline

AT5G49940. Arabidopsis thaliana.

Family and domain databases

InterPro

IPR001075. NIF_FeS_clus_asmbl_NifU_C.
[Graphical view]

Pfam

PF01106. NifU. 2 hits.
[Graphical view]

ProDom

PD002830. NIF_FeS_clus_asmbl_NifU_C. 2 hits.
[Graphical view] [Entries sharing at least one domain]

ProtoNet

Search...

Other

EvolutionaryTrace

Q93W20.

Entry information

Entry name

NIFU2_ARATH

Accession

Primary (citable) accession number: Q93W20
Secondary accession number(s): A8MS35, Q9LTX6

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 25, 2006
Last sequence update:	December 1, 2001
Last modified:	May 1, 2013
This is version 69 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Plant Protein Annotation Program