Riboflavin biosynthesis protein ribBA, chloroplastic precursor

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Reviewed, UniProtKB/Swiss-Prot P47924 (RIBBA_ARATH)

Last modified November 3, 2009. Version 73. History...

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Names and origin · Protein attributes · General annotation (Comments) · Ontologies · Sequence annotation (Features) · Sequences · References · Cross-references · Entry information · Relevant documents

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Names and origin

Protein names

Recommended name:
    Riboflavin biosynthesis protein ribBA, chloroplastic
Including the following 2 domains:
    1- Recommended name:
            3,4-dihydroxy-2-butanone 4-phosphate synthase
                Short name=DHBP synthase
              EC=4.1.99.12
    2- Recommended name:
            GTP cyclohydrolase-2
              EC=3.5.4.25
        Alternative name(s):
            GTP cyclohydrolase II

Gene names

Name:	RIBBA
Synonyms:	RIBA
Ordered Locus Names:	At5g64300
ORF Names:	MSJ1.14

Organism

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

Taxonomic identifier

3702 [NCBI]

Taxonomic lineage

Eukaryota › Viridiplantae › Streptophyta › Embryophyta › Tracheophyta › Spermatophyta › Magnoliophyta › eudicotyledons › core eudicotyledons › rosids › eurosids II › Brassicales › Brassicaceae › Arabidopsis

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Protein attributes

Sequence length	543 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at transcript level.

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General annotation (Comments)

Function	Catalyzes the conversion of D-ribulose 5-phosphate to formate and 3,4-dihydroxy-2-butanone 4-phosphate By similarity. Catalyzes the conversion of GTP to 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate (DARP), formate and pyrophosphate By similarity.
Catalytic activity	D-ribulose 5-phosphate = formate + L-3,4-dihydroxybutan-2-one 4-phosphate. GTP + 3 H₂O = formate + 2,5-diamino-6-hydroxy-4-(5-phosphoribosylamino)pyrimidine + diphosphate.
Cofactor	Binds 2 divalent metal cations per subunit. Magnesium or manganese By similarity. Binds 1 zinc ion per subunit By similarity.
Pathway	Cofactor biosynthesis; riboflavin biosynthesis; 2-hydroxy-3-oxobutyl phosphate from D-ribulose 5-phosphate: step 1/1. Cofactor biosynthesis; riboflavin biosynthesis; 5-amino-6-(D-ribitylamino)uracil from GTP: step 1/4.
Subcellular location	Plastid › chloroplast Potential.
Sequence similarities	In the N-terminal section; belongs to the DHBP synthase family. In the C-terminal section; belongs to the GTP cyclohydrolase II family.

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Ontologies

Keywords
Biological process	Riboflavin biosynthesis
Cellular component	Chloroplast Plastid
Domain	Transit peptide
Ligand	GTP-binding Magnesium Manganese Metal-binding Nucleotide-binding Zinc
Molecular function	Hydrolase Lyase
Technical term	Complete proteome Multifunctional enzyme
Gene Ontology (GO)
Biological process	riboflavin biosynthetic process Ref.1 Ref.3 Inferred from genetic interaction. Source: TAIR
Cellular component	chloroplast Inferred from direct assay. Source: TAIR membrane Inferred from direct assay. Source: TAIR
Molecular function	3,4-dihydroxy-2-butanone-4-phosphate synthase activity Ref.1 Inferred from genetic interaction. Source: TAIR GTP binding Inferred from electronic annotation. Source: UniProtKB-KW GTP cyclohydrolase II activity Ref.1 Ref.3 Inferred from genetic interaction. Source: TAIR magnesium ion binding Inferred from electronic annotation. Source: UniProtKB-KW manganese ion binding Inferred from electronic annotation. Source: UniProtKB-KW zinc ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

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Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Transit peptide

1 – 56

Chloroplast Potential

Chain

57 – 543

487

Riboflavin biosynthesis protein ribBA, chloroplastic

PRO_0000030436

Regions

Nucleotide binding

379 – 383

GTP By similarity

Nucleotide binding

423 – 425

GTP By similarity

Region

57 – 328

272

DHBP synthase

Region

152 – 153

D-ribulose 5-phosphate binding By similarity

Region

267 – 271

D-ribulose 5-phosphate binding By similarity

Region

329 – 543

215

GTP cyclohydrolase II

Sites

Active site

457

Proton acceptor; for GTP cyclohydrolase activity Potential

Active site

459

Nucleophile; for GTP cyclohydrolase activity By similarity

Metal binding

153

Magnesium or manganese 1 By similarity

Metal binding

153

Magnesium or manganese 2 By similarity

Metal binding

270

Magnesium or manganese 2 By similarity

Metal binding

384

Zinc; catalytic By similarity

Metal binding

395

Zinc; catalytic By similarity

Metal binding

397

Zinc; catalytic By similarity

Binding site

157

D-ribulose 5-phosphate By similarity

Binding site

291

D-ribulose 5-phosphate By similarity

Binding site

400

GTP By similarity

Binding site

445

GTP By similarity

Binding site

480

GTP By similarity

Binding site

485

GTP By similarity

Site

253

Essential for DHBP synthase activity By similarity

Site

291

Essential for DHBP synthase activity By similarity

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Sequences

Sequence

Length

Mass (Da)

Tools

P47924-1 [UniParc].

Last modified January 10, 2003. Version 2.
Checksum: 31D89A500E42BF81
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FASTA

543

59,056

        10         20         30         40         50         60 
MSSINLSSSS PSTISLSRSR LSQSSTTLLH GLHRVTLPSN HPLSTFSIKT NTGKVKAAVI 

        70         80         90        100        110        120 
SREDDLLSFT NGNTPLSNGS LIDDRTEEPL EADSVSLGTL AADSAPAPAN GFVAEDDDFE 

       130        140        150        160        170        180 
LDLPTPGFSS IPEAIEDIRQ GKLVVVVDDE DRENEGDLVM AAQLATPEAM AFIVRHGTGI 

       190        200        210        220        230        240 
VCVSMKEDDL ERLHLPLMVN QKENEEKLST AFTVTVDAKH GTTTGVSARD RATTILSLAS 

       250        260        270        280        290        300 
RDSKPEDFNR PGHIFPLKYR EGGVLKRAGH TEASVDLTVL AGLDPVGVLC EIVDDDGSMA 

       310        320        330        340        350        360 
RLPKLREFAA ENNLKVVSIA DLIRYRRKRD KLVERASAAR IPTMWGPFTA YCYRSILDGI 

       370        380        390        400        410        420 
EHIAMVKGEI GDGQDILVRV HSECLTGDIF GSARCDCGNQ LALSMQQIEA TGRGVLVYLR 

       430        440        450        460        470        480 
GHEGRGIGLG HKLRAYNLQD AGRDTVEANE ELGLPVDSRE YGIGAQIIRD LGVRTMKLMT 

       490        500        510        520        530        540 
NNPAKYVGLK GYGLAIVGRV PLLSLITKEN KRYLETKRTK MGHMYGLKFK GDVVEKIESE 


SES

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References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Biosynthesis of riboflavin in plants. The ribA gene of Arabidopsis thaliana specifies a bifunctional GTP cyclohydrolase II/3,4-dihydroxy-2-butanone 4-phosphate synthase." Herz S.W., Eberhardt S., Bacher A. Phytochemistry 53:723-731(2000) [PubMed: 10783978] [Abstract] Cited for: NUCLEOTIDE SEQUENCE.
[2]	"Structural analysis of Arabidopsis thaliana chromosome 5. III. Sequence features of the regions of 1,191,918 bp covered by seventeen physically assigned P1 clones." Nakamura Y., Sato S., Kaneko T., Kotani H., Asamizu E., Miyajima N., Tabata S. DNA Res. 4:401-414(1997) [PubMed: 9501997] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: cv. Columbia.
[3]	"Isolation of cDNAs encoding GTP cyclohydrolase II from Arabidopsis thaliana." Kobayashi M., Sugiyama M., Yamamoto K. Gene 160:303-304(1995) [PubMed: 7642114] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 279-543.
+	Additional computationally mapped references.

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Cross-references

Sequence databases
	AJ000053 Genomic DNA. Translation: CAA03884.1. AB008268 Genomic DNA. Translation: BAB09861.1. D45165 mRNA. Translation: BAA08113.1. Different initiation.
IPI	IPI00522822.
PIR	JC4209.
RefSeq	NP_201235.4.
UniGene	At.49217
3D structure databases
HSSP	HSSP built from PDB template 1G58 based on UniProtKB P24199.
ModBase	Search...
Protein-protein interaction databases
STRING	P47924.
Proteomic databases
PRIDE	P47924.
Genome annotation databases
GeneID	836551.
GenomeReviews	Gene locus AT5G64300 in contig BA000015_GR.
KEGG	ath:AT5G64300.
Organism-specific databases
GeneFarm	2299. 254.
TAIR	At5g64300.
Phylogenomic databases
OMA	LRCDCRM.
Enzyme and pathway databases
BRENDA	3.5.4.25. 302. 4.1.99.12. 302.
Gene expression databases
ArrayExpress	P47924.
Genevestigator	P47924.
GermOnline	AT5G64300. Arabidopsis thaliana.
Family and domain databases
InterPro	IPR017945. DHBP_synth_RibB-like_a/b_dom. IPR000422. DHBP_synthase_RibB. IPR000926. GTP_CycHdrlase_II. [Graphical view]
Gene3D	G3DSA:3.90.870.10. DHBP_synth_RibB-like_a/b_dom. 1 hit.
Pfam	PF00926. DHBP_synthase. 1 hit. PF00925. GTP_cyclohydro2. 1 hit. [Graphical view]
ProDom	PD003034. DHBP_synthase. 1 hit. [Graphical view] [Entries sharing at least one domain]
TIGRFAMs	TIGR00505. ribA. 1 hit. TIGR00506. ribB. 1 hit.
ProtoNet	Search...

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Entry information

Entry name

RIBBA_ARATH

Accession

Primary (citable) accession number: P47924
Secondary accession number(s): Q9SBA8

Entry history

Integrated into UniProtKB/Swiss-Prot:	February 1, 1996
Last sequence update:	January 10, 2003
Last modified:	November 3, 2009
This is version 73 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

PPAP (Plant Proteome Annotation Project)

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Relevant documents

Arabidopsis thaliana

Arabidopsis thaliana: entries and gene names

PATHWAY comments

Index of metabolic and biosynthesis pathways

SIMILARITY comments

Index of protein domains and families

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Molecule processing

Regions

Sites

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Proteomic databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Gene expression databases

Family and domain databases

Entry information

Relevant documents