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Protein

Riboflavin biosynthesis protein RibBA

Gene

ribBA

Organism
Desulfomicrobium baculatum (strain DSM 4028 / VKM B-1378) (Desulfovibrio baculatus)
Status
Unreviewed-Annotation score: Annotation score: 4 out of 5-Protein inferred from homologyi

Functioni

Catalyzes the conversion of D-ribulose 5-phosphate to formate and 3,4-dihydroxy-2-butanone 4-phosphate.UniRule annotationSAAS annotation
Catalyzes the conversion of GTP to 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate (DARP), formate and pyrophosphate.UniRule annotation

Catalytic activityi

D-ribulose 5-phosphate = formate + L-3,4-dihydroxybutan-2-one 4-phosphate.UniRule annotation
GTP + 3 H2O = formate + 2,5-diamino-6-hydroxy-4-(5-phospho-D-ribosylamino)pyrimidine + diphosphate.UniRule annotationSAAS annotation

Cofactori

Mg2+UniRule annotation, Mn2+UniRule annotationNote: Binds 2 divalent metal cations per subunit. Magnesium or manganese.UniRule annotation

Pathwayi: riboflavin biosynthesis

This protein is involved in step 1 of the subpathway that synthesizes 2-hydroxy-3-oxobutyl phosphate from D-ribulose 5-phosphate.UniRule annotation
Proteins known to be involved in this subpathway in this organism are:
  1. 3,4-dihydroxy-2-butanone 4-phosphate synthase (ribB), Riboflavin biosynthesis protein RibBA (ribBA)
This subpathway is part of the pathway riboflavin biosynthesis, which is itself part of Cofactor biosynthesis.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes 2-hydroxy-3-oxobutyl phosphate from D-ribulose 5-phosphate, the pathway riboflavin biosynthesis and in Cofactor biosynthesis.

Pathwayi: riboflavin biosynthesis

This protein is involved in step 1 of the subpathway that synthesizes 5-amino-6-(D-ribitylamino)uracil from GTP.SAAS annotation
Proteins known to be involved in the 4 steps of the subpathway in this organism are:
  1. Riboflavin biosynthesis protein RibBA (ribBA)
  2. Riboflavin biosynthesis protein RibD (Dbac_0062)
  3. Riboflavin biosynthesis protein RibD (Dbac_0062)
  4. no protein annotated in this organism
This subpathway is part of the pathway riboflavin biosynthesis, which is itself part of Cofactor biosynthesis.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes 5-amino-6-(D-ribitylamino)uracil from GTP, the pathway riboflavin biosynthesis and in Cofactor biosynthesis.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi28Magnesium or manganese 1UniRule annotation1
Metal bindingi28Magnesium or manganese 2UniRule annotation1
Binding sitei32D-ribulose 5-phosphateUniRule annotation1
Sitei126Essential for DHBP synthase activityUniRule annotation1
Binding sitei164D-ribulose 5-phosphateUniRule annotation1
Sitei164Essential for DHBP synthase activityUniRule annotation1
Metal bindingi257Zinc; catalyticUniRule annotation1
Metal bindingi268Zinc; catalyticUniRule annotation1
Metal bindingi270Zinc; catalyticUniRule annotation1
Binding sitei273GTPUniRule annotation1
Binding sitei317GTPUniRule annotation1
Active sitei329Proton acceptor; for GTP cyclohydrolase activityUniRule annotation1
Active sitei331Nucleophile; for GTP cyclohydrolase activityUniRule annotation1
Binding sitei352GTPUniRule annotation1
Binding sitei357GTPUniRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi252 – 256GTPUniRule annotation5
Nucleotide bindingi295 – 297GTPUniRule annotation3

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

HydrolaseUniRule annotationImported, LyaseUniRule annotationSAAS annotation

Keywords - Biological processi

Riboflavin biosynthesisUniRule annotationSAAS annotation

Keywords - Ligandi

GTP-bindingUniRule annotationSAAS annotation, MagnesiumUniRule annotation, ManganeseUniRule annotation, Metal-bindingUniRule annotationSAAS annotation, Nucleotide-binding, ZincUniRule annotationSAAS annotation

Enzyme and pathway databases

UniPathwayiUPA00275; UER00399.
UPA00275; UER00400.

Names & Taxonomyi

Protein namesi
Recommended name:
Riboflavin biosynthesis protein RibBAUniRule annotationSAAS annotation
Gene namesi
Name:ribBAUniRule annotation
Ordered Locus Names:Dbac_0060Imported
OrganismiDesulfomicrobium baculatum (strain DSM 4028 / VKM B-1378) (Desulfovibrio baculatus)Imported
Taxonomic identifieri525897 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaDeltaproteobacteriaDesulfovibrionalesDesulfomicrobiaceaeDesulfomicrobium
Proteomesi
  • UP000002216 Componenti: Chromosome

Interactioni

Protein-protein interaction databases

STRINGi525897.Dbac_0060.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini208 – 372GTP_cyclohydro2InterPro annotationAdd BLAST165

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni1 – 201DHBP synthaseUniRule annotationAdd BLAST201
Regioni27 – 28D-ribulose 5-phosphate bindingUniRule annotation2
Regioni202 – 404GTP cyclohydrolase IIUniRule annotationAdd BLAST203

Sequence similaritiesi

In the C-terminal section; belongs to the GTP cyclohydrolase II family.UniRule annotationSAAS annotation
In the N-terminal section; belongs to the DHBP synthase family.UniRule annotationSAAS annotation

Phylogenomic databases

eggNOGiENOG4105C66. Bacteria.
COG0108. LUCA.
COG0807. LUCA.
HOGENOMiHOG000115440.
KOiK14652.
OMAiLMVDRNT.
OrthoDBiPOG091H008U.

Family and domain databases

CDDicd00641. GTP_cyclohydro2. 1 hit.
Gene3Di3.90.870.10. 1 hit.
HAMAPiMF_00179. RibA. 1 hit.
MF_00180. RibB. 1 hit.
MF_01283. RibBA. 1 hit.
InterProiIPR017945. DHBP_synth_RibB-like_a/b_dom.
IPR000422. DHBP_synthase_RibB.
IPR032677. GTP_cyclohydro_II.
IPR000926. RibA.
IPR016299. Riboflavin_synth_RibBA.
[Graphical view]
PfamiPF00926. DHBP_synthase. 1 hit.
PF00925. GTP_cyclohydro2. 1 hit.
[Graphical view]
SUPFAMiSSF142695. SSF142695. 1 hit.
SSF55821. SSF55821. 1 hit.
TIGRFAMsiTIGR00505. ribA. 1 hit.
TIGR00506. ribB. 1 hit.

Sequencei

Sequence statusi: Complete.

C7LSH6-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MHKCSAEEAI KEIKAGKMII LVDDEDRENE GDLTIAAEMV TPEAINFMAK
60 70 80 90 100
YGRGLICLAL EPALVDKLEL PLMARRNTSK FGTNFTVSIE AKQGVTTGIS
110 120 130 140 150
AHDRALTIQT AVADQTTPED LATPGHIFPL RAKPGGVLVR AGQTEGSVDL
160 170 180 190 200
ARLAGLKGAA VICEIMNDDG SMSRMPDLRK FAEEHDMKIA TIADLIAYRS
210 220 230 240 250
RKDSLVRRVA EARMPTCYGE FTIVAYENDI DSHTHIALVK GEINEETPVL
260 270 280 290 300
VRVHSECLTG DVFGSMRCDC GSQLQRAMQM VNDEGAGVIL YMRQEGRGIG
310 320 330 340 350
LGNKIKAYHL QDEGRDTVEA NLELGFAPDL RDYGLGAQIL VDLGVKRMRL
360 370 380 390 400
LTNNPKKIIG LEGYGLKVEE RISIEIPACD DNKCYLHTKH SKLGHLLQFE

AENK
Length:404
Mass (Da):44,379
Last modified:October 13, 2009 - v1
Checksum:iD4CB39048F1F5266
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001629 Genomic DNA. Translation: ACU88190.1.
RefSeqiWP_012805275.1. NC_013173.1.

Genome annotation databases

EnsemblBacteriaiACU88190; ACU88190; Dbac_0060.
KEGGidba:Dbac_0060.
PATRICi21702370. VBIDesBac69216_0058.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001629 Genomic DNA. Translation: ACU88190.1.
RefSeqiWP_012805275.1. NC_013173.1.

3D structure databases

ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi525897.Dbac_0060.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiACU88190; ACU88190; Dbac_0060.
KEGGidba:Dbac_0060.
PATRICi21702370. VBIDesBac69216_0058.

Phylogenomic databases

eggNOGiENOG4105C66. Bacteria.
COG0108. LUCA.
COG0807. LUCA.
HOGENOMiHOG000115440.
KOiK14652.
OMAiLMVDRNT.
OrthoDBiPOG091H008U.

Enzyme and pathway databases

UniPathwayiUPA00275; UER00399.
UPA00275; UER00400.

Family and domain databases

CDDicd00641. GTP_cyclohydro2. 1 hit.
Gene3Di3.90.870.10. 1 hit.
HAMAPiMF_00179. RibA. 1 hit.
MF_00180. RibB. 1 hit.
MF_01283. RibBA. 1 hit.
InterProiIPR017945. DHBP_synth_RibB-like_a/b_dom.
IPR000422. DHBP_synthase_RibB.
IPR032677. GTP_cyclohydro_II.
IPR000926. RibA.
IPR016299. Riboflavin_synth_RibBA.
[Graphical view]
PfamiPF00926. DHBP_synthase. 1 hit.
PF00925. GTP_cyclohydro2. 1 hit.
[Graphical view]
SUPFAMiSSF142695. SSF142695. 1 hit.
SSF55821. SSF55821. 1 hit.
TIGRFAMsiTIGR00505. ribA. 1 hit.
TIGR00506. ribB. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiC7LSH6_DESBD
AccessioniPrimary (citable) accession number: C7LSH6
Entry historyi
Integrated into UniProtKB/TrEMBL: October 13, 2009
Last sequence update: October 13, 2009
Last modified: November 30, 2016
This is version 56 of the entry and version 1 of the sequence. [Complete history]
Entry statusiUnreviewed (UniProtKB/TrEMBL)

Miscellaneousi

Keywords - Technical termi

Complete proteome, Multifunctional enzymeUniRule annotation, Reference proteomeImported

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.