Riboflavin biosynthesis protein ribD

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Reviewed, UniProtKB/Swiss-Prot Q9Z735 (RIBD_CHLPN)

Last modified June 16, 2009. Version 68. 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 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
Synonyms:	ribG
Ordered Locus Names:	CPn_0871, CP_0998, CpB0900

Organism

Chlamydia pneumoniae (Chlamydophila pneumoniae) [Complete proteome] [HAMAP]

Taxonomic identifier

83558 [NCBI]

Taxonomic lineage

Bacteria › Chlamydiae › Chlamydiales › Chlamydiaceae › Chlamydophila

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Protein attributes

Sequence length	376 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.
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 – 376

376

Riboflavin biosynthesis protein ribD

PRO_0000171718

Regions

Nucleotide binding

302 – 308

NADP By similarity

Region

1 – 150

150

Deaminase

Region

151 – 376

226

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

159

NADP; via amide nitrogen and carbonyl oxygen By similarity

Binding site

173

Substrate By similarity

Binding site

175

NADP By similarity

Binding site

189

Substrate By similarity

Binding site

201

NADP By similarity

Binding site

205

NADP By similarity

Binding site

209

Substrate; via amide nitrogen By similarity

Binding site

212

Substrate By similarity

Binding site

230

NADP By similarity

Binding site

300

Substrate By similarity

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Sequences

Sequence

Length

Mass (Da)

Tools

Q9Z735-1 [UniParc].

Last modified May 1, 1999. Version 1.
Checksum: A05F069E0F127B07
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FASTA

376

41,209

        10         20         30         40         50         60 
MEDFSEQQLF FMRRAIEIGE KGRITAPPNP WVGCVVVQEN RIIGEGFHAY AGGPHAEELA 

        70         80         90        100        110        120 
IQNASMPISG SDVYVSLEPC SHFGSCPPCA NLLIKHKVSR VFVALVDPDP KVAGQGIAML 

       130        140        150        160        170        180 
RQAGIQVYVG IGESEAQASL QPYLYQRTHN FPWTILKSAA SVDGQVADSQ GKSQWITCPE 

       190        200        210        220        230        240 
ARHDVGKLRA ESQAILVGSR TVLSDDPWLT ARQPQGMLYP KQPLRVVLDS RGSVPPTSKV 

       250        260        270        280        290        300 
FDKTSPTLYV TTERCPENYI KVLDSLDVPV LLTESTPSGV DLHKVYEYLA QKKILQVLVE 

       310        320        330        340        350        360 
GGTTLHTSLL KERFVNSLVL YSGPMILGDQ KRPLVGVLGN LLESASPLTL KSSQILGNSL 

       370 
KVVWEISPQV FEPIRN

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References

[1]	"Comparative genomes of Chlamydia pneumoniae and C. trachomatis." Kalman S., Mitchell W.P., Marathe R., Lammel C.J., Fan J., Hyman R.W., Olinger L., Grimwood J., Davis R.W., Stephens R.S. Nat. Genet. 21:385-389(1999) [PubMed: 10192388] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: CWL029.
[2]	"Genome sequences of Chlamydia trachomatis MoPn and Chlamydia pneumoniae AR39." Read T.D., Brunham R.C., Shen C., Gill S.R., Heidelberg J.F., White O., Hickey E.K., Peterson J.D., Utterback T.R., Berry K.J., Bass S., Linher K.D., Weidman J.F., Khouri H.M., Craven B., Bowman C., Dodson R.J., Gwinn M.L. Fraser C.M. Nucleic Acids Res. 28:1397-1406(2000) [PubMed: 10684935] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: AR39.
[3]	"Comparison of whole genome sequences of Chlamydia pneumoniae J138 from Japan and CWL029 from USA." Shirai M., Hirakawa H., Kimoto M., Tabuchi M., Kishi F., Ouchi K., Shiba T., Ishii K., Hattori M., Kuhara S., Nakazawa T. Nucleic Acids Res. 28:2311-2314(2000) [PubMed: 10871362] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: J138.
[4]	"The genome sequence of Chlamydia pneumoniae TW183 and comparison with other Chlamydia strains based on whole genome sequence analysis." Geng M.M., Schuhmacher A., Muehldorfer I., Bensch K.W., Schaefer K.P., Schneider S., Pohl T., Essig A., Marre R., Melchers K. Submitted (MAY-2002) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: TW-183.

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Cross-references

Sequence databases
	AE001363 Genomic DNA. Translation: AAD19009.1. AE002161 Genomic DNA. Translation: AAF38776.1. BA000008 Genomic DNA. Translation: BAA99079.1. AE017160 Genomic DNA. Translation: AAP98829.1.
PIR	E86599. G72026.
RefSeq	NP_225066.1. NP_300928.1. NP_445535.1. NP_877172.1.
3D structure databases
ModBase	Search...
Genome annotation databases
GeneID	1467579. 895231. 919634. 963471.
GenomeReviews	Gene locus CPn_0871 in contig AE001363_GR. Gene locus CP_0998 in contig AE002161_GR. Gene locus CpB0900 in contig AE009440_GR. Gene locus ribD in contig BA000008_GR.
KEGG	cpa:CP0998. cpn:CPn0871. cpt:CpB0900.
TIGR	CP_0998.
Phylogenomic databases
HOGENOM	Q9Z735.
OMA	Q9Z735. CAVLTGI.
Enzyme and pathway databases
BioCyc	CPNE115711:CP_0998-MON. CPNE115713:CPN0871-MON. CPNE138677:CPJ0871-MON. CPNE182082:CPB0900-MON.
BRENDA	1.1.1.193. 264832. 3.5.4.26. 264832.
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_CHLPN

Accession

Primary (citable) accession number: Q9Z735
Secondary accession number(s): Q9JQ54

Entry history

Integrated into UniProtKB/Swiss-Prot:	May 30, 2000
Last sequence update:	May 1, 1999
Last modified:	June 16, 2009
This is version 68 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

Phylogenomic databases

Enzyme and pathway databases

Family and domain databases

Entry information

Relevant documents