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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)DescriptionActionsGraphical viewLength
Metal bindingi29Magnesium or manganese 1UniRule annotation1
Metal bindingi29Magnesium or manganese 2UniRule annotation1
Binding sitei33D-ribulose 5-phosphateUniRule annotation1
Sitei127Essential for DHBP synthase activityUniRule annotation1
Metal bindingi144Magnesium or manganese 2UniRule annotation1
Binding sitei165D-ribulose 5-phosphateUniRule annotation1
Sitei165Essential for DHBP synthase activityUniRule annotation1
Metal bindingi264Zinc; catalyticUniRule annotation1
Metal bindingi275Zinc; catalyticUniRule annotation1
Metal bindingi277Zinc; catalyticUniRule annotation1
Binding sitei280GTPUniRule annotation1
Binding sitei325GTPUniRule annotation1
Active sitei337Proton acceptor; for GTP cyclohydrolase activityUniRule annotation1
Active sitei339Nucleophile; for GTP cyclohydrolase activityUniRule annotation1
Binding sitei360GTPUniRule annotation1
Binding sitei365GTPUniRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi259 – 263GTPUniRule annotation5
Nucleotide bindingi303 – 305GTPUniRule annotation3

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

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)DescriptionActionsGraphical viewLength
ChainiPRO_10000674261 – 425Riboflavin biosynthesis protein RibBAAdd BLAST425

Proteomic databases

PRIDEiA5U2B7.

Interactioni

Protein-protein interaction databases

STRINGi419947.MtubH3_010100010626.

Structurei

Secondary structure

1425
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi7 – 15Combined sources9
Beta strandi20 – 26Combined sources7
Beta strandi33 – 37Combined sources5
Helixi38 – 40Combined sources3
Helixi43 – 52Combined sources10
Beta strandi53 – 55Combined sources3
Beta strandi58 – 61Combined sources4
Helixi63 – 68Combined sources6
Beta strandi90 – 95Combined sources6
Beta strandi97 – 99Combined sources3
Helixi102 – 113Combined sources12
Helixi119 – 121Combined sources3
Beta strandi122 – 132Combined sources11
Helixi137 – 139Combined sources3
Helixi144 – 154Combined sources11
Beta strandi159 – 167Combined sources9
Beta strandi169 – 171Combined sources3
Helixi178 – 188Combined sources11
Beta strandi191 – 194Combined sources4
Helixi195 – 204Combined sources10
Beta strandi209 – 219Combined sources11
Beta strandi222 – 231Combined sources10
Beta strandi237 – 244Combined sources8
Beta strandi255 – 262Combined sources8
Helixi265 – 268Combined sources4
Helixi277 – 291Combined sources15
Beta strandi294 – 299Combined sources6
Helixi343 – 350Combined sources8
Beta strandi354 – 359Combined sources6

3D structure databases

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

Miscellaneous databases

EvolutionaryTraceiA5U2B7.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni1 – 204DHBP synthaseAdd BLAST204
Regioni28 – 29D-ribulose 5-phosphate bindingUniRule annotation2
Regioni141 – 145D-ribulose 5-phosphate bindingUniRule annotation5
Regioni205 – 425GTP cyclohydrolase IIAdd BLAST221

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.

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.

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
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3MGZX-ray2.07A1-206[»]
3MIOX-ray1.80A/B1-206[»]
3MK5X-ray2.06A1-206[»]
4I14X-ray3.00A/B1-425[»]
ProteinModelPortaliA5U2B7.
SMRiA5U2B7.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi419947.MtubH3_010100010626.

Proteomic databases

PRIDEiA5U2B7.

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.

Enzyme and pathway databases

UniPathwayiUPA00275; UER00399.
UPA00275; UER00400.
BRENDAi4.1.99.12. 3445.

Miscellaneous databases

EvolutionaryTraceiA5U2B7.

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 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: November 2, 2016
This is version 74 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.