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Protein

Riboflavin biosynthesis protein RibBA

Gene

ribBA

Organism
Mycobacterium tuberculosis (strain ATCC 25177 / H37Ra)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the conversion of D-ribulose 5-phosphate to formate and 3,4-dihydroxy-2-butanone 4-phosphate.UniRule 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 annotation

Cofactori

Protein has several cofactor binding sites:
  • Mg2+UniRule annotation, Mn2+UniRule annotationNote: Binds 2 divalent metal cations per subunit. Magnesium or manganese.UniRule annotation
  • Zn2+UniRule annotationNote: Binds 1 zinc ion per subunit.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. 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.UniRule annotation
Proteins known to be involved in the 4 steps of the subpathway in this organism are:
  1. Riboflavin biosynthesis protein RibBA (ribBA)
  2. no protein annotated in this organism
  3. no protein annotated in this organism
  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)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi29 – 291Magnesium or manganese 1UniRule annotation
Metal bindingi29 – 291Magnesium or manganese 2UniRule annotation
Binding sitei33 – 331D-ribulose 5-phosphateUniRule annotation
Sitei127 – 1271Essential for DHBP synthase activityUniRule annotation
Metal bindingi144 – 1441Magnesium or manganese 2UniRule annotation
Binding sitei165 – 1651D-ribulose 5-phosphateUniRule annotation
Sitei165 – 1651Essential for DHBP synthase activityUniRule annotation
Metal bindingi264 – 2641Zinc; catalyticUniRule annotation
Metal bindingi275 – 2751Zinc; catalyticUniRule annotation
Metal bindingi277 – 2771Zinc; catalyticUniRule annotation
Binding sitei280 – 2801GTPUniRule annotation
Binding sitei325 – 3251GTPUniRule annotation
Active sitei337 – 3371Proton acceptor; for GTP cyclohydrolase activityUniRule annotation
Active sitei339 – 3391Nucleophile; for GTP cyclohydrolase activityUniRule annotation
Binding sitei360 – 3601GTPUniRule annotation
Binding sitei365 – 3651GTPUniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi259 – 2635GTPUniRule annotation
Nucleotide bindingi303 – 3053GTPUniRule annotation

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Hydrolase, Lyase

Keywords - Biological processi

Riboflavin biosynthesis

Keywords - Ligandi

GTP-binding, Magnesium, Manganese, Metal-binding, Nucleotide-binding, Zinc

Enzyme and pathway databases

BioCyciMTUB419947:GJ8N-1471-MONOMER.
BRENDAi4.1.99.12. 3445.
UniPathwayiUPA00275; UER00399.
UPA00275; UER00400.

Names & Taxonomyi

Protein namesi
Recommended name:
Riboflavin biosynthesis protein RibBAUniRule annotation
Including the following 2 domains:
3,4-dihydroxy-2-butanone 4-phosphate synthaseUniRule annotation (EC:4.1.99.12UniRule annotation)
Short name:
DHBP synthaseUniRule annotation
GTP cyclohydrolase-2UniRule annotation (EC:3.5.4.25UniRule annotation)
Alternative name(s):
GTP cyclohydrolase IIUniRule annotation
Gene namesi
Name:ribBAUniRule annotation
Ordered Locus Names:MRA_1424
OrganismiMycobacterium tuberculosis (strain ATCC 25177 / H37Ra)
Taxonomic identifieri419947 [NCBI]
Taxonomic lineageiBacteriaActinobacteriaCorynebacterialesMycobacteriaceaeMycobacteriumMycobacterium tuberculosis complex
Proteomesi
  • UP000001988 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 425425Riboflavin biosynthesis protein RibBAPRO_1000067426Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi419947.MtubH3_010100010626.

Structurei

Secondary structure

1
425
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi7 – 159Combined sources
Beta strandi20 – 267Combined sources
Beta strandi33 – 375Combined sources
Helixi38 – 403Combined sources
Helixi43 – 5210Combined sources
Beta strandi53 – 553Combined sources
Beta strandi58 – 614Combined sources
Helixi63 – 686Combined sources
Beta strandi90 – 956Combined sources
Beta strandi97 – 993Combined sources
Helixi102 – 11312Combined sources
Helixi119 – 1213Combined sources
Beta strandi122 – 13211Combined sources
Helixi137 – 1393Combined sources
Helixi144 – 15411Combined sources
Beta strandi159 – 1679Combined sources
Beta strandi169 – 1713Combined sources
Helixi178 – 18811Combined sources
Beta strandi191 – 1944Combined sources
Helixi195 – 20410Combined sources
Beta strandi209 – 21911Combined sources
Beta strandi222 – 23110Combined sources
Beta strandi237 – 2448Combined sources
Beta strandi255 – 2628Combined sources
Helixi265 – 2684Combined sources
Helixi277 – 29115Combined sources
Beta strandi294 – 2996Combined sources
Helixi343 – 3508Combined sources
Beta strandi354 – 3596Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3MGZX-ray2.07A1-206[»]
3MIOX-ray1.80A/B1-206[»]
3MK5X-ray2.06A1-206[»]
4I14X-ray3.00A/B1-425[»]
ProteinModelPortaliA5U2B7.
SMRiA5U2B7. Positions 1-383.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiA5U2B7.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni1 – 204204DHBP synthaseAdd
BLAST
Regioni28 – 292D-ribulose 5-phosphate bindingUniRule annotation
Regioni141 – 1455D-ribulose 5-phosphate bindingUniRule annotation
Regioni205 – 425221GTP cyclohydrolase IIAdd
BLAST

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiENOG4105C66. Bacteria.
COG0108. LUCA.
COG0807. LUCA.
HOGENOMiHOG000115440.
KOiK14652.
OMAiLMVDRNT.
OrthoDBiEOG679TK8.

Family and domain databases

Gene3Di3.90.870.10. 1 hit.
HAMAPiMF_00179. RibA.
MF_00180. RibB.
MF_01283. RibBA.
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.

A5U2B7-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTRLDSVERA VADIAAGKAV IVIDDEDREN EGDLIFAAEK ATPEMVAFMV
60 70 80 90 100
RYTSGYLCVP LDGAICDRLG LLPMYAVNQD KHGTAYTVTV DARNGIGTGI
110 120 130 140 150
SASDRATTMR LLADPTSVAD DFTRPGHVVP LRAKDGGVLR RPGHTEAAVD
160 170 180 190 200
LARMAGLQPA GAICEIVSQK DEGSMAHTDE LRVFADEHGL ALITIADLIE
210 220 230 240 250
WRRKHEKHIE RVAEARIPTR HGEFRAIGYT SIYEDVEHVA LVRGEIAGPN
260 270 280 290 300
ADGDDVLVRV HSECLTGDVF GSRRCDCGPQ LDAALAMVAR EGRGVVLYMR
310 320 330 340 350
GHEGRGIGLM HKLQAYQLQD AGADTVDANL KLGLPADARD YGIGAQILVD
360 370 380 390 400
LGVRSMRLLT NNPAKRVGLD GYGLHIIERV PLPVRANAEN IRYLMTKRDK
410 420
LGHDLAGLDD FHESVHLPGE FGGAL
Length:425
Mass (Da):46,017
Last modified:July 10, 2007 - v1
Checksum:iFA7F73868814591F
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000611 Genomic DNA. Translation: ABQ73167.1.
RefSeqiWP_003407334.1. NC_009525.1.

Genome annotation databases

EnsemblBacteriaiABQ73167; ABQ73167; MRA_1424.
KEGGimra:MRA_1424.
PATRICi18142767. VBIMycTub106795_1585.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000611 Genomic DNA. Translation: ABQ73167.1.
RefSeqiWP_003407334.1. NC_009525.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3MGZX-ray2.07A1-206[»]
3MIOX-ray1.80A/B1-206[»]
3MK5X-ray2.06A1-206[»]
4I14X-ray3.00A/B1-425[»]
ProteinModelPortaliA5U2B7.
SMRiA5U2B7. Positions 1-383.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi419947.MtubH3_010100010626.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABQ73167; ABQ73167; MRA_1424.
KEGGimra:MRA_1424.
PATRICi18142767. VBIMycTub106795_1585.

Phylogenomic databases

eggNOGiENOG4105C66. Bacteria.
COG0108. LUCA.
COG0807. LUCA.
HOGENOMiHOG000115440.
KOiK14652.
OMAiLMVDRNT.
OrthoDBiEOG679TK8.

Enzyme and pathway databases

UniPathwayiUPA00275; UER00399.
UPA00275; UER00400.
BioCyciMTUB419947:GJ8N-1471-MONOMER.
BRENDAi4.1.99.12. 3445.

Miscellaneous databases

EvolutionaryTraceiA5U2B7.

Family and domain databases

Gene3Di3.90.870.10. 1 hit.
HAMAPiMF_00179. RibA.
MF_00180. RibB.
MF_01283. RibBA.
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...

Publicationsi

  1. "Genetic basis of virulence attenuation revealed by comparative genomic analysis of Mycobacterium tuberculosis strain H37Ra versus H37Rv."
    Zheng H., Lu L., Wang B., Pu S., Zhang X., Zhu G., Shi W., Zhang L., Wang H., Wang S., Zhao G., Zhang Y.
    PLoS ONE 3:E2375-E2375(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 25177 / H37Ra.

Entry informationi

Entry nameiRIBBA_MYCTA
AccessioniPrimary (citable) accession number: A5U2B7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 5, 2008
Last sequence update: July 10, 2007
Last modified: February 17, 2016
This is version 71 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Multifunctional enzyme

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

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.