Riboflavin biosynthesis protein ribD - Buchnera aphidicola subsp. Baizongia pistaciae

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Reviewed, UniProtKB/Swiss-Prot Q89AB0 (RIBD_BUCBP)

Last modified June 16, 2009. Version 43. History...

Clusters with 100%, 90%, 50% identity |

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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 ribD
Including the following 2 domains:
    1- Recommended name:
            Diaminohydroxyphosphoribosylaminopyrimidine deaminase
                Short name=DRAP deaminase
              EC=3.5.4.26
        Alternative name(s):
            Riboflavin-specific deaminase
    2- Recommended name:
            5-amino-6-(5-phosphoribosylamino)uracil reductase
              EC=1.1.1.193
        Alternative name(s):
            HTP reductase

Gene names

Name:	ribD
Ordered Locus Names:	bbp_408

Organism

Buchnera aphidicola subsp. Baizongia pistaciae [Complete proteome] [HAMAP]

Taxonomic identifier

135842 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Buchnera

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Protein attributes

Sequence length	372 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Inferred from homology.

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General annotation (Comments)

Function	Converts 2,5-diamino-6-(ribosylamino)-4(3h)-pyrimidinone 5'-phosphate into 5-amino-6-(ribosylamino)-2,4(1h,3h)-pyrimidinedione 5'-phosphate By similarity.
Catalytic activity	2,5-diamino-6-hydroxy-4-(5-phosphoribosylamino)pyrimidine + H₂O = 5-amino-6-(5-phosphoribosylamino)uracil + NH₃. 5-amino-6-(5-phosphoribitylamino)uracil + NADP⁺ = 5-amino-6-(5-phosphoribosylamino)uracil + NADPH.
Cofactor	Binds 1 zinc ion By similarity.
Pathway	Cofactor biosynthesis; riboflavin biosynthesis; 6,7-dimethyl-8-(1-D-ribityl)lumazine from GTP: step 2/4. Cofactor biosynthesis; riboflavin biosynthesis; 6,7-dimethyl-8-(1-D-ribityl)lumazine from GTP: step 3/4.
Sequence similarities	In the N-terminal section; belongs to the cytidine and deoxycytidylate deaminase family. In the C-terminal section; belongs to the HTP reductase family.

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Ontologies

Keywords
Biological process	Riboflavin biosynthesis
Ligand	Metal-binding NADP Zinc
Molecular function	Hydrolase Oxidoreductase
Technical term	Complete proteome Multifunctional enzyme
Gene Ontology (GO)
Biological process	oxidation reduction Inferred from electronic annotation. Source: UniProtKB-KW riboflavin biosynthetic process Inferred from electronic annotation. Source: UniProtKB-KW
Molecular function	5-amino-6-(5-phosphoribosylamino)uracil reductase activity Inferred from electronic annotation. Source: EC NADP or NADPH binding Inferred from electronic annotation. Source: InterPro diaminohydroxyphosphoribosylaminopyrimidine deaminase activity Inferred from electronic annotation. Source: EC 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

Chain

1 – 372

372

Riboflavin biosynthesis protein ribD

PRO_0000171716

Regions

Nucleotide binding

303 – 309

NADP By similarity

Region

1 – 145

145

Deaminase

Region

146 – 372

227

Reductase

Sites

Active site

Proton donor By similarity

Metal binding

Zinc; catalytic By similarity

Metal binding

Zinc; catalytic By similarity

Metal binding

Zinc; catalytic By similarity

Binding site

154

NADP; via amide nitrogen and carbonyl oxygen By similarity

Binding site

168

Substrate By similarity

Binding site

170

NADP By similarity

Binding site

184

Substrate By similarity

Binding site

196

NADP By similarity

Binding site

200

NADP By similarity

Binding site

204

Substrate; via amide nitrogen By similarity

Binding site

207

Substrate By similarity

Binding site

236

NADP By similarity

Binding site

301

Substrate By similarity

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Sequences

Sequence

Length

Mass (Da)

Tools

Q89AB0-1 [UniParc].

Last modified June 1, 2003. Version 1.
Checksum: 6BB07CE7E9016C7A
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FASTA

372

41,598

        10         20         30         40         50         60 
MKDIFYMKKA IKLAKKGSLT TSPNPNVGCI IVNNNIIVGS GWHKKTGMKH AEIYALKTSG 

        70         80         90        100        110        120 
EKAKGATAYI TLEPCSHFGK TPPCCVALTK YGISRVVIAT LDPNPKVSGN GVKWLKKHGI 

       130        140        150        160        170        180 
LVTIGTLSKE SIKINKGFFQ RMTTGIPWIK LKLASSIDGR TALNNGKSKW ITSDKARHDV 

       190        200        210        220        230        240 
QHVREKSDAI ISSSETILFD NPLLTVRNTN NNDNNQKLLK HSKTFLKQPI RVIIDSKNRI 

       250        260        270        280        290        300 
TPSHKCIKQP GLLFLIRIHS DNNIWPSHIK QIILNNKSKK IDLIDLVKML AKYQINNILI 

       310        320        330        340        350        360 
EAGPSLSSSF LKLNIINELI IYIAPKILGN YAKPLFFLEN YSNLSDVPQF KFEKITQIGK 

       370 
DLKLILTKHN SS

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References

[1]

"Reductive genome evolution in Buchnera aphidicola."
van Ham R.C.H.J., Kamerbeek J., Palacios C., Rausell C., Abascal F., Bastolla U., Fernandez J.M., Jimenez L., Postigo M., Silva F.J., Tamames J., Viguera E., Latorre A., Valencia A., Moran F., Moya A.
Proc. Natl. Acad. Sci. U.S.A. 100:581-586(2003) [PubMed: 12522265] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].

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Cross-references

Sequence databases
	AE016826 Genomic DNA. Translation: AAO27119.1.
RefSeq	NP_778014.1.
3D structure databases
ModBase	Search...
Genome annotation databases
GeneID	1058488.
GenomeReviews	Gene locus bbp_408 in contig AE016826_GR.
KEGG	bab:bbp408.
Organism-specific databases
CMR	Search...
Phylogenomic databases
HOGENOM	Q89AB0.
OMA	Q89AB0. ECLRDAA.
Enzyme and pathway databases
BioCyc	BAPH224915:BBP_408-MON.
Family and domain databases
InterPro	IPR016192. APOBEC/CMP_deaminase_Zn-bd. IPR002125. CMP_dCMP_Zn_bd. IPR004794. Eubact_ribD. IPR011549. RibD_C. IPR002734. RibDG_C. [Graphical view]
PANTHER	PTHR11079:SF10. Eubact_ribD. 1 hit.
Pfam	PF00383. dCMP_cyt_deam_1. 1 hit. PF01872. RibD_C. 1 hit. [Graphical view]
TIGRFAMs	TIGR00326. eubact_ribD. 1 hit. TIGR00227. ribD_Cterm. 1 hit.
PROSITE	PS00903. CYT_DCMP_DEAMINASES. 1 hit. [Graphical view]
ProtoNet	Search...

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Entry information

Entry name

RIBD_BUCBP

Accession

Primary (citable) accession number: Q89AB0

Entry history

Integrated into UniProtKB/Swiss-Prot:	April 13, 2004
Last sequence update:	June 1, 2003
Last modified:	June 16, 2009
This is version 43 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)

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Relevant documents

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

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Family and domain databases

Entry information

Relevant documents