P50861 (RIB4_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
6,7-dimethyl-8-ribityllumazine synthase
Short name=DMRL synthase
Short name=Lumazine synthase
EC=2.5.1.9

Alternative name(s):
Riboflavin synthase beta chain

Gene names

Name:	RIB4
Ordered Locus Names:	YOL143C

Organism

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

Eukaryota › Fungi › Dikarya › Ascomycota › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces

Protein attributes

Sequence length	169 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Condensation of 5-amino-6-(1'-D)-ribityl-amino-2,4(1H,3H)-pyrimidinedione with L-3,4-dihydroxy-2-butanone 4-phosphate to produce 6,7-dimethyl-8-(1-D-ribityl)lumazine.
Catalytic activity	2 6,7-dimethyl-8-(1-D-ribityl)lumazine = riboflavin + 4-(1-D-ribitylamino)-5-amino-2,6-dihydroxypyrimidine.
Pathway	Cofactor biosynthesis; riboflavin biosynthesis; riboflavin from 2-hydroxy-3-oxobutyl phosphate and 5-amino-6-(D-ribitylamino)uracil: step 2/2.
Subunit structure	Homopentamer.
Miscellaneous	Present with 3260 molecules/cell in log phase SD medium. Ref.5
Sequence similarities	Belongs to the DMRL synthase family.

Ontologies

Keywords
Biological process	Riboflavin biosynthesis
Molecular function	Transferase
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological process	riboflavin biosynthetic process Inferred from mutant phenotype Ref.1. Source: SGD
Cellular component	cytoplasm Inferred from direct assay. Source: SGD nucleus Inferred from direct assay. Source: SGD riboflavin synthase complex Inferred from electronic annotation. Source: InterPro
Molecular function	6,7-dimethyl-8-ribityllumazine synthase activity Inferred from genetic interaction Ref.1. Source: SGD riboflavin synthase activity Inferred from electronic annotation. Source: EC
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 169

169

6,7-dimethyl-8-ribityllumazine synthase

PRO_0000134857

Experimental info

Sequence conflict

44

1

A → V in CAA79744. Ref.1

Sequence conflict

51

1

N → K in CAA79744. Ref.1

Secondary structure

1

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

169

Helix Strand Turn

Details...

Beta strand

20 – 24

5

Helix

29 – 45

17

Helix

50 – 52

3

Beta strand

53 – 57

5

Helix

61 – 63

3

Helix

64 – 77

14

Beta strand

83 – 92

10

Beta strand

95 – 97

3

Helix

98 – 117

20

Beta strand

124 – 130

7

Helix

131 – 137

7

Helix

149 – 164

16

Sequences

	Sequence		Length	Mass (Da)
	P50861 [UniParc]. Last modified May 30, 2000. Version 2. Checksum: 574E847FA6F2860E	FASTA	169	18,556
	10 20 30 40 50 60 MAVKGLGKPD QVYDGSKIRV GIIHARWNRV IIDALVKGAI ERMASLGVEE NNIIIETVPG 70 80 90 100 110 120 SYELPWGTKR FVDRQAKLGK PLDVVIPIGV LIKGSTMHFE YISDSTTHAL MNLQEKVDMP 130 140 150 160 VIFGLLTCMT EEQALARAGI DEAHSMHNHG EDWGAAAVEM AVKFGKNAF

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"The Saccharomyces cerevisiae RIB4 gene codes for 6,7-dimethyl-8-ribityllumazine synthase involved in riboflavin biosynthesis. Molecular characterization of the gene and purification of the encoded protein." Garcia-Ramirez J.J., Santos M.A., Revuelta J.L. J. Biol. Chem. 270:23801-23807(1995) [PubMed: 7559556] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"The nucleotide sequence of Saccharomyces cerevisiae chromosome XV." Dujon B., Albermann K., Aldea M., Alexandraki D., Ansorge W., Arino J., Benes V., Bohn C., Bolotin-Fukuhara M., Bordonne R., Boyer J., Camasses A., Casamayor A., Casas C., Cheret G., Cziepluch C., Daignan-Fornier B., Dang V.-D. , de Haan M., Delius H., Durand P., Fairhead C., Feldmann H., Gaillon L., Galisson F., Gamo F.-J., Gancedo C., Goffeau A., Goulding S.E., Grivell L.A., Habbig B., Hand N.J., Hani J., Hattenhorst U., Hebling U., Hernando Y., Herrero E., Heumann K., Hiesel R., Hilger F., Hofmann B., Hollenberg C.P., Hughes B., Jauniaux J.-C., Kalogeropoulos A., Katsoulou C., Kordes E., Lafuente M.J., Landt O., Louis E.J., Maarse A.C., Madania A., Mannhaupt G., Marck C., Martin R.P., Mewes H.-W., Michaux G., Paces V., Parle-McDermott A.G., Pearson B.M., Perrin A., Pettersson B., Poch O., Pohl T.M., Poirey R., Portetelle D., Pujol A., Purnelle B., Ramezani Rad M., Rechmann S., Schwager C., Schweizer M., Sor F., Sterky F., Tarassov I.A., Teodoru C., Tettelin H., Thierry A., Tobiasch E., Tzermia M., Uhlen M., Unseld M., Valens M., Vandenbol M., Vetter I., Vlcek C., Voet M., Volckaert G., Voss H., Wambutt R., Wedler H., Wiemann S., Winsor B., Wolfe K.H., Zollner A., Zumstein E., Kleine K. Nature 387:98-102(1997) [PubMed: 9169874] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 96604 / S288c / FY1679.
[3]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: ATCC 204508 / S288c.
[4]	"Approaching a complete repository of sequence-verified protein-encoding clones for Saccharomyces cerevisiae." Hu Y., Rolfs A., Bhullar B., Murthy T.V.S., Zhu C., Berger M.F., Camargo A.A., Kelley F., McCarron S., Jepson D., Richardson A., Raphael J., Moreira D., Taycher E., Zuo D., Mohr S., Kane M.F., Williamson J. , Simpson A.J.G., Bulyk M.L., Harlow E., Marsischky G., Kolodner R.D., LaBaer J. Genome Res. 17:536-543(2007) [PubMed: 17322287] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: ATCC 204508 / S288c.
[5]	"Global analysis of protein expression in yeast." Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N., O'Shea E.K., Weissman J.S. Nature 425:737-741(2003) [PubMed: 14562106] [Abstract] Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
[6]	"The atomic structure of pentameric lumazine synthase from Saccharomyces cerevisiae at 1.85 A resolution reveals the binding mode of a phosphonate intermediate analogue." Meining W., Moertl S., Fischer M., Cushman M., Bacher A., Ladenstein R. J. Mol. Biol. 299:181-197(2000) [PubMed: 10860731] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.85 ANGSTROMS).
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

Z21620 Genomic DNA. Translation: CAA79744.1.
Z74885 Genomic DNA. Translation: CAA99164.1.
AY558430 Genomic DNA. Translation: AAS56756.1.
BK006948 Genomic DNA. Translation: DAA10642.1.

PIR

S61871.

RefSeq

NP_014498.1. NM_001183397.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1EJB	X-ray	1.85	A/B/C/D/E	2-169	[»]

ProteinModelPortal

P50861.

SMR

P50861. Positions 2-169.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-1931N.

IntAct

P50861. 8 interactions.

MINT

MINT-397811.

STRING

P50861.

Proteomic databases

PeptideAtlas

P50861.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblFungi

YOL143C; YOL143C; YOL143C.

GeneID

854022.

KEGG

sce:YOL143C.

NMPDR

fig|4932.3.peg.5584.

Organism-specific databases

CYGD

YOL143c.

SGD

S000005503. RIB4.

Phylogenomic databases

eggNOG

fuNOG10195.

GeneTree

EFGT00050000004551.

HOGENOM

HBG311126.

OMA

DYVCNEA.

OrthoDB

EOG49S9GR.

Enzyme and pathway databases

BioCyc

MetaCyc:YOL143C-MONOMER.

Gene expression databases

ArrayExpress

P50861.

Genevestigator

P50861.

GermOnline

YOL143C. Saccharomyces cerevisiae.

Family and domain databases

InterPro

IPR002180. DMRL_synthase.
[Graphical view]

Gene3D

G3DSA:3.40.50.960. DMRL_synthase. 1 hit.

KO

K00794.

PANTHER

PTHR21058. DMRL_synthase. 1 hit.

Pfam

PF00885. DMRL_synthase. 1 hit.
[Graphical view]

SUPFAM

SSF52121. DMRL_synthase. 1 hit.

TIGRFAMs

TIGR00114. Lumazine-synth. 1 hit.

ProtoNet

Search...

Other

NextBio

975556.

Entry information

Entry name

RIB4_YEAST

Accession

Primary (citable) accession number: P50861
Secondary accession number(s): D6W1S6, Q08286

Entry history

Integrated into UniProtKB/Swiss-Prot:	October 1, 1996
Last sequence update:	May 30, 2000
Last modified:	December 14, 2011
This is version 108 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program