Q7Z859 (LCPS_PHARH) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Bifunctional lycopene cyclase/phytoene synthase

Including the following 2 domains:

1. Lycopene beta-cyclase
   EC=5.5.1.19
   Alternative name(s):
   Lycopene cyclase
2. Phytoene synthase
   EC=2.5.1.32

Gene names

Name:	crtYB
Synonyms:	pbs

Organism

Phaffia rhodozyma (Yeast) (Xanthophyllomyces dendrorhous)

Taxonomic identifier

5421 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Fungi › Dikarya › Basidiomycota › Agaricomycotina › Tremellomycetes › Cystofilobasidiales › Cystofilobasidiaceae › Xanthophyllomyces

Protein attributes

Sequence length	673 AA.
Sequence status	Complete.
Protein existence	Evidence at transcript level

General annotation (Comments)

Function	Bifunctional enzyme that catalyzes the reactions from geranylgeranyl diphosphate to phytoene (phytoene synthase) and lycopene to beta-carotene via the intermediate gamma-carotene (lycopene cyclase). The cyclase preferentially catalyzes the symmetric cyclization of both ends of the substrate to produce dicyclic carotenoids. Beta-carotene is further processed to the acidic carotenoid astaxanthin. Ref.1 Ref.4
Catalytic activity	Carotenoid psi-end group = carotenoid beta-end group. 2 geranylgeranyl diphosphate = 15-cis-phytoene + 2 diphosphate.
Pathway	Carotenoid biosynthesis; beta-carotene biosynthesis. Carotenoid biosynthesis; phytoene biosynthesis; all-trans-phytoene from geranylgeranyl diphosphate: step 1/1.
Subcellular location	Membrane; Multi-pass membrane protein Potential.
Induction	Down-regulated in stationary phase. Ref.3 Ref.5
Sequence similarities	In the N-terminal section; belongs to the lycopene beta-cyclase family. In the C-terminal section; belongs to the phytoene/squalene synthase family.

Ontologies

Keywords
Biological process	Carotenoid biosynthesis
Cellular component	Membrane
Coding sequence diversity	Alternative splicing
Domain	Transmembrane Transmembrane helix
Molecular function	Isomerase Transferase
Technical term	Multifunctional enzyme
Gene Ontology (GO)
Biological_process	carotenoid biosynthetic process Inferred from electronic annotation. Source: UniProtKB-KW
Cellular_component	integral to membrane Inferred from electronic annotation. Source: UniProtKB-KW
Molecular_function	geranylgeranyl-diphosphate geranylgeranyltransferase activity Inferred from direct assay Ref.1. Source: UniProtKB intramolecular lyase activity Inferred from electronic annotation. Source: InterPro lycopene beta cyclase activity Inferred from direct assay Ref.1. Source: UniProtKB phytoene synthase activity Inferred from direct assay Ref.1. Source: UniProtKB
Complete GO annotation...

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]

Isoform 1 (identifier: Q7Z859-1)

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

Isoform 2 (identifier: Q7Z859-2)

The sequence of this isoform differs from the canonical sequence as follows:
     1-46: MTALAYYQIHLIYTLPILGLLGLLTSPILTKFDIYKISILVFIAFS → MSPYLFFVLHTTHVCICV

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 673	673	Bifunctional lycopene cyclase/phytoene synthase		PRO_0000409239
Regions
	Transmembrane	9 – 29	21	Helical; Potential
	Transmembrane	36 – 56	21	Helical; Potential
	Transmembrane	81 – 101	21	Helical; Potential
	Transmembrane	117 – 137	21	Helical; Potential
	Transmembrane	157 – 177	21	Helical; Potential
	Transmembrane	187 – 207	21	Helical; Potential
	Transmembrane	226 – 246	21	Helical; Potential
	Region	1 – 251	251	Lycopene beta-cyclase
	Region	258 – 673	416	Phytoene synthase
	Compositional bias	367 – 405	39	Pro-rich
Natural variations
	Alternative sequence	1 – 46	46	MTALA…FIAFS → MSPYLFFVLHTTHVCICV in isoform 2.		VSP_041283
	Natural variant	307	1	E → K in strain: CBS 6938 / CCRC 22365 / VKM Y-2793.

Sequences

	Sequence		Length	Mass (Da)
	Isoform 1 [UniParc]. Last modified October 1, 2003. Version 1. Checksum: ECAB54AF256240A2	FASTA	673	74,736
	10 20 30 40 50 60 MTALAYYQIH LIYTLPILGL LGLLTSPILT KFDIYKISIL VFIAFSATTP WDSWIIRNGA 70 80 90 100 110 120 WTYPSAESGQ GVFGTFLDVP YEEYAFFVIQ TVITGLVYVL ATRHLLPSLA LPKTRSSALS 130 140 150 160 170 180 LALKALIPLP IIYLFTAHPS PSPDPLVTDH YFYMRALSLL ITPPTMLLAA LSGEYAFDWK 190 200 210 220 230 240 SGRAKSTIAA IMIPTVYLIW VDYVAVGQDS WSINDEKIVG WRLGGVLPIE EAMFFLLTNL 250 260 270 280 290 300 MIVLGLSACD HTQALYLLHG RTIYGNKKMP SSFPLITPPV LSLFFSSRPY SSQPKRDLEL 310 320 330 340 350 360 AVKLLEEKSR SFFVASAGFP SEVRERLVGL YAFCRVTDDL IDSPEVSSNP HATIDMVSDF 370 380 390 400 410 420 LTLLFGPPLH PSQPDKILSS PLLPPSHPSR PTGMYPLPPP PSLSPAELVQ FLTERVPVQY 430 440 450 460 470 480 HFAFRLLAKL QGLIPRYPLD ELLRGYTTDL IFPLSTEAVQ ARKTPIETTA DLLDYGLCVA 490 500 510 520 530 540 GSVAELLVYV SWASAPSQVP ATIEEREAVL VASREMGTAL QLVNIARDIK GDATEGRFYL 550 560 570 580 590 600 PLSFFGLRDE SKLAIPTDWT EPRPQDFDKL LSLSPSSTLP SSNASESFRF EWKTYSLPLV 610 620 630 640 650 660 AYAEDLAKHS YKGIDRLPTE VQAGMRAACA SYLLIGREIK VVWKGDVGER RTVAGWRRVR 670 KVLSVVMSGW EGQ
	Isoform 2 [UniParc]. Checksum: 72B51B9CEB84904C	FASTA	645	71,643
	10 20 30 40 50 60 MSPYLFFVLH TTHVCICVAT TPWDSWIIRN GAWTYPSAES GQGVFGTFLD VPYEEYAFFV 70 80 90 100 110 120 IQTVITGLVY VLATRHLLPS LALPKTRSSA LSLALKALIP LPIIYLFTAH PSPSPDPLVT 130 140 150 160 170 180 DHYFYMRALS LLITPPTMLL AALSGEYAFD WKSGRAKSTI AAIMIPTVYL IWVDYVAVGQ 190 200 210 220 230 240 DSWSINDEKI VGWRLGGVLP IEEAMFFLLT NLMIVLGLSA CDHTQALYLL HGRTIYGNKK 250 260 270 280 290 300 MPSSFPLITP PVLSLFFSSR PYSSQPKRDL ELAVKLLEEK SRSFFVASAG FPSEVRERLV 310 320 330 340 350 360 GLYAFCRVTD DLIDSPEVSS NPHATIDMVS DFLTLLFGPP LHPSQPDKIL SSPLLPPSHP 370 380 390 400 410 420 SRPTGMYPLP PPPSLSPAEL VQFLTERVPV QYHFAFRLLA KLQGLIPRYP LDELLRGYTT 430 440 450 460 470 480 DLIFPLSTEA VQARKTPIET TADLLDYGLC VAGSVAELLV YVSWASAPSQ VPATIEEREA 490 500 510 520 530 540 VLVASREMGT ALQLVNIARD IKGDATEGRF YLPLSFFGLR DESKLAIPTD WTEPRPQDFD 550 560 570 580 590 600 KLLSLSPSST LPSSNASESF RFEWKTYSLP LVAYAEDLAK HSYKGIDRLP TEVQAGMRAA 610 620 630 640 CASYLLIGRE IKVVWKGDVG ERRTVAGWRR VRKVLSVVMS GWEGQ

References

[1]	"Isolation and functional characterisation of a novel type of carotenoid biosynthetic gene from Xanthophyllomyces dendrorhous." Verdoes J.C., Krubasik K.P., Sandmann G., van Ooyen A.J. Mol. Gen. Genet. 262:453-461(1999) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION. Strain: CBS 6938 / CCRC 22365 / VKM Y-2793.
[2]	"Alternative splicing of transcripts from crtI and crtYB genes of Xanthophyllomyces dendrorhous." Lodato P., Alcaino J., Barahona S., Retamales P., Cifuentes V. Appl. Environ. Microbiol. 69:4676-4682(2003) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS 1 AND 2). Strain: ATCC 24230 / UCD 67-385.
[3]	"Genomic organization of the structural genes controlling the astaxanthin biosynthesis pathway of Xanthophyllomyces dendrorhous." Niklitschek M., Alcaino J., Barahona S., Sepulveda D., Lozano C., Carmona M., Marcoleta A., Martinez C., Lodato P., Baeza M., Cifuentes V. Biol. Res. 41:93-108(2008) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], INDUCTION. Strain: ATCC 24230 / UCD 67-385.
[4]	"The biotechnological potential of the al-2 gene from Neurospora crassa for the production of monocyclic keto hydroxy carotenoids." Sandmann G., Zhu C., Krubasik P., Fraser P.D. Biochim. Biophys. Acta 1761:1085-1092(2006) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[5]	"Expression of the carotenoid biosynthesis genes in Xanthophyllomyces dendrorhous." Lodato P., Alcaino J., Barahona S., Niklitschek M., Carmona M., Wozniak A., Baeza M., Jimenez A., Cifuentes V. Biol. Res. 40:73-84(2007) [PubMed] [Europe PMC] [Abstract] Cited for: INDUCTION. Strain: ATCC 24230 / UCD 67-385.

Cross-references

Sequence databases
EMBL GenBank DDBJ	AJ133646 Genomic DNA. Translation: CAB51949.1. AY174117 mRNA. Translation: AAO73816.1. AY177204 mRNA. Translation: AAO47570.1. DQ016503 Genomic DNA. Translation: AAY33923.1.
3D structure databases
ProteinModelPortal	Q7Z859.
ModBase	Search...
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Enzyme and pathway databases
BioCyc	MetaCyc:MONOMER-17247.
UniPathway	UPA00799; UER00773. UPA00802.
Family and domain databases
Gene3D	1.10.600.10. 3 hits.
InterPro	IPR017825. Lycopene_cyclase_dom. IPR002060. Squ/phyt_synthse. IPR019845. Squalene/phytoene_synthase_CS. IPR008949. Terpenoid_synth. [Graphical view]
Pfam	PF00494. SQS_PSY. 1 hit. [Graphical view]
SUPFAM	SSF48576. Terpenoid_synth. 1 hit.
TIGRFAMs	TIGR03462. CarR_dom_SF. 2 hits.
PROSITE	PS01045. SQUALEN_PHYTOEN_SYN_2. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

LCPS_PHARH

Accession

Primary (citable) accession number: Q7Z859
Secondary accession number(s): Q7Z856, Q9UUQ0

Entry history

Integrated into UniProtKB/Swiss-Prot:	May 31, 2011
Last sequence update:	October 1, 2003
Last modified:	April 3, 2013
This is version 38 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program