Q96I15 (SCLY_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Selenocysteine lyase
Short name=hSCL
EC=4.4.1.16

Gene names

Name:	SCLY
Synonyms:	SCL

Organism

Homo sapiens (Human)

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo

Protein attributes

Sequence length	445 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Catalyzes the decomposition of L-selenocysteine to L-alanine and elemental selenium By similarity.
Catalytic activity	L-selenocysteine + reduced acceptor = selenide + L-alanine + acceptor.
Cofactor	Pyridoxal phosphate.
Subunit structure	Homodimer By similarity.
Subcellular location	Cytoplasm › cytosol By similarity.
Induction	Up-regulated in acute glomerulonephritis. Regulated by JUN/AP-1. Ref.5
Sequence similarities	Belongs to the class-V pyridoxal-phosphate-dependent aminotransferase family.
Sequence caution	The sequence BAA91659.1 differs from that shown. Reason: Erroneous initiation.

Ontologies

Keywords
Cellular component	Cytoplasm
Coding sequence diversity	Alternative splicing Polymorphism
Ligand	Pyridoxal phosphate
Molecular function	Lyase Transferase
PTM	Acetylation
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological process	cellular amino acid metabolic process Traceable author statement. Source: ProtInc
Cellular component	cytosol Traceable author statement. Source: ProtInc
Molecular function	pyridoxal phosphate binding Inferred from electronic annotation. Source: InterPro selenocysteine lyase activity Traceable author statement. Source: ProtInc transferase activity Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Alternative products

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

Isoform 1 (identifier: Q96I15-1)

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: Q96I15-2)

The sequence of this isoform differs from the canonical sequence as follows:
     308-445: AAELVTQNCE...QAVAQLEDQA → VSPGELEEMS

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 445

445

Selenocysteine lyase

PRO_0000317012

Sites

Active site

388

1

S-selanylcysteine intermediate By similarity

Amino acid modifications

Modified residue

1

1

N-acetylmethionine Ref.6

Modified residue

259

1

N6-(pyridoxal phosphate)lysine

Natural variations

Alternative sequence

308 – 445

138

AAELV…LEDQA → VSPGELEEMS in isoform 2.

VSP_030854

Natural variant

52

1

K → E.
Corresponds to variant rs7597367 [ dbSNP | Ensembl ].

VAR_038464

Natural variant

175

1

A → T. Ref.3
Corresponds to variant rs3210400 [ dbSNP | Ensembl ].

VAR_038465

Natural variant

276

1

F → S.
Corresponds to variant rs35637307 [ dbSNP | Ensembl ].

VAR_038466

Experimental info

Sequence conflict

42

1

L → V in AAF36816. Ref.1

Secondary structure

1

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

445

Helix Strand Turn

Details...

Turn

36 – 38

3

Helix

44 – 56

13

Helix

66 – 86

21

Helix

90 – 92

3

Beta strand

93 – 97

5

Helix

99 – 118

20

Beta strand

137 – 141

5

Helix

146 – 157

12

Beta strand

162 – 166

5

Turn

170 – 172

3

Helix

177 – 182

6

Beta strand

188 – 192

5

Turn

198 – 200

3

Helix

206 – 222

17

Beta strand

229 – 233

5

Turn

235 – 240

6

Helix

245 – 248

4

Beta strand

251 – 256

6

Helix

257 – 259

3

Beta strand

266 – 270

5

Turn

271 – 275

5

Helix

288 – 291

4

Helix

299 – 338

40

Helix

340 – 342

3

Beta strand

343 – 347

5

Beta strand

356 – 363

8

Helix

370 – 376

7

Beta strand

378 – 381

4

Beta strand

383 – 387

5

Helix

398 – 402

5

Helix

407 – 411

5

Beta strand

413 – 417

5

Helix

424 – 443

20

Sequences

	Sequence		Length	Mass (Da)
	Isoform 1 [UniParc]. Last modified February 5, 2008. Version 2. Checksum: D26F3FCFB8B165D2	FASTA	445	48,149
	10 20 30 40 50 60 MEAAVAPGRD APAPAASQPS GCGKHNSPER KVYMDYNATT PLEPEVIQAM TKAMWEAWGN 70 80 90 100 110 120 PSSPYSAGRK AKDIINAARE SLAKMIGGKP QDIIFTSGGT ESNNLVIHSV VKHFHANQTS 130 140 150 160 170 180 KGHTGGHHSP VKGAKPHFIT SSVEHDSIRL PLEHLVEEQV AAVTFVPVSK VSGQAEVDDI 190 200 210 220 230 240 LAAVRPTTRL VTIMLANNET GIVMPVPEIS QRIKALNQER VAAGLPPILV HTDAAQALGK 250 260 270 280 290 300 QRVDVEDLGV DFLTIVGHKF YGPRIGALYI RGLGEFTPLY PMLFGGGQER NFRPGTENTP 310 320 330 340 350 360 MIAGLGKAAE LVTQNCEAYE AHMRDVRDYL EERLEAEFGQ KRIHLNSQFP GTQRLPNTCN 370 380 390 400 410 420 FSIRGPRLQG HVVLAQCRVL MASVGAACHS DHGDQPSPVL LSYGVPFDVA RNALRLSVGR 430 440 STTRAEVDLV VQDLKQAVAQ LEDQA
	Isoform 2 [UniParc]. Checksum: A831471CE76E5B11	FASTA	317	33,957
	10 20 30 40 50 60 MEAAVAPGRD APAPAASQPS GCGKHNSPER KVYMDYNATT PLEPEVIQAM TKAMWEAWGN 70 80 90 100 110 120 PSSPYSAGRK AKDIINAARE SLAKMIGGKP QDIIFTSGGT ESNNLVIHSV VKHFHANQTS 130 140 150 160 170 180 KGHTGGHHSP VKGAKPHFIT SSVEHDSIRL PLEHLVEEQV AAVTFVPVSK VSGQAEVDDI 190 200 210 220 230 240 LAAVRPTTRL VTIMLANNET GIVMPVPEIS QRIKALNQER VAAGLPPILV HTDAAQALGK 250 260 270 280 290 300 QRVDVEDLGV DFLTIVGHKF YGPRIGALYI RGLGEFTPLY PMLFGGGQER NFRPGTENTP 310 MIAGLGKVSP GELEEMS

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"cDNA cloning, purification, and characterization of mouse liver selenocysteine lyase. Candidate for selenium delivery protein in selenoprotein synthesis." Mihara H., Kurihara T., Watanabe T., Yoshimura T., Esaki N. J. Biol. Chem. 275:6195-6200(2000) [PubMed: 10692412] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2). Tissue: Brain.
[2]	"Generation and annotation of the DNA sequences of human chromosomes 2 and 4." Hillier L.W., Graves T.A., Fulton R.S., Fulton L.A., Pepin K.H., Minx P., Wagner-McPherson C., Layman D., Wylie K., Sekhon M., Becker M.C., Fewell G.A., Delehaunty K.D., Miner T.L., Nash W.E., Kremitzki C., Oddy L., Du H. , Sun H., Bradshaw-Cordum H., Ali J., Carter J., Cordes M., Harris A., Isak A., van Brunt A., Nguyen C., Du F., Courtney L., Kalicki J., Ozersky P., Abbott S., Armstrong J., Belter E.A., Caruso L., Cedroni M., Cotton M., Davidson T., Desai A., Elliott G., Erb T., Fronick C., Gaige T., Haakenson W., Haglund K., Holmes A., Harkins R., Kim K., Kruchowski S.S., Strong C.M., Grewal N., Goyea E., Hou S., Levy A., Martinka S., Mead K., McLellan M.D., Meyer R., Randall-Maher J., Tomlinson C., Dauphin-Kohlberg S., Kozlowicz-Reilly A., Shah N., Swearengen-Shahid S., Snider J., Strong J.T., Thompson J., Yoakum M., Leonard S., Pearman C., Trani L., Radionenko M., Waligorski J.E., Wang C., Rock S.M., Tin-Wollam A.-M., Maupin R., Latreille P., Wendl M.C., Yang S.-P., Pohl C., Wallis J.W., Spieth J., Bieri T.A., Berkowicz N., Nelson J.O., Osborne J., Ding L., Meyer R., Sabo A., Shotland Y., Sinha P., Wohldmann P.E., Cook L.L., Hickenbotham M.T., Eldred J., Williams D., Jones T.A., She X., Ciccarelli F.D., Izaurralde E., Taylor J., Schmutz J., Myers R.M., Cox D.R., Huang X., McPherson J.D., Mardis E.R., Clifton S.W., Warren W.C., Chinwalla A.T., Eddy S.R., Marra M.A., Ovcharenko I., Furey T.S., Miller W., Eichler E.E., Bork P., Suyama M., Torrents D., Waterston R.H., Wilson R.K. Nature 434:724-731(2005) [PubMed: 15815621] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[3]	"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)." The MGC Project Team Genome Res. 14:2121-2127(2004) [PubMed: 15489334] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1), VARIANT THR-175. Tissue: Brain.
[4]	"Complete sequencing and characterization of 21,243 full-length human cDNAs." Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S. , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S. Nat. Genet. 36:40-45(2004) [PubMed: 14702039] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 189-445. Tissue: Teratocarcinoma.
[5]	"Enhanced expression of selenocysteine lyase in acute glomerulonephritis and its regulation by AP-1." Jafari C., Panzer U., Steinmetz O.M., Zahner G., Stahl R.A., Harendza S. Cell. Mol. Biol. Lett. 11:424-437(2006) [PubMed: 16874457] [Abstract] Cited for: INDUCTION BY JUN.
[6]	"Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach." Gauci S., Helbig A.O., Slijper M., Krijgsveld J., Heck A.J., Mohammed S. Anal. Chem. 81:4493-4501(2009) [PubMed: 19413330] [Abstract] Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT MET-1, MASS SPECTROMETRY. Tissue: Embryonic kidney.
[7]	"Initial characterization of the human central proteome." Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T., Bennett K.L., Superti-Furga G., Colinge J. BMC Syst. Biol. 5:17-17(2011) [PubMed: 21269460] [Abstract] Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[8]	"Structure of human selenocysteine lyase." Structural genomics consortium (SGC) Submitted (JUL-2006) to the PDB data bank Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF 8-445 IN COMPLEX WITH PYRIDOXAL PHOSPHATE.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

AF175767 mRNA. Translation: AAF36816.1.
AC016757 Genomic DNA. Translation: AAY24333.1.
AC016776 Genomic DNA. Translation: AAY24221.1.
BC000586 mRNA. Translation: AAH00586.2.
BC007891 mRNA. Translation: AAH07891.1.
AK001377 mRNA. Translation: BAA91659.1. Different initiation.

IPI

IPI00101652.
IPI00884890.

RefSeq

NP_057594.4. NM_016510.5.

UniGene

Hs.709612.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
3GZC	X-ray	2.10	A/B	8-445	[»]
3GZD	X-ray	1.80	A/B/C/D	8-445	[»]

ProteinModelPortal

Q96I15.

SMR

Q96I15. Positions 29-444.

ModBase

Search...

Protein-protein interaction databases

IntAct

Q96I15. 1 interaction.

STRING

Q96I15.

PTM databases

PhosphoSite

Q96I15.

Polymorphism databases

DMDM

167016561.

Proteomic databases

PRIDE

Q96I15.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

Ensembl

ENST00000254663; ENSP00000254663; ENSG00000132330.

GeneID

51540.

KEGG

hsa:51540.

UCSC

uc002vxm.2. human.
uc002vxn.2. human.

Organism-specific databases

CTD

51540.

GeneCards

GC02P238985.

H-InvDB

HIX0114427.
HIX0200260.

HGNC

HGNC:18161. SCLY.

MIM

611056. gene.

neXtProt

NX_Q96I15.

PharmGKB

PA134979359.

GenAtlas

Search...

Phylogenomic databases

GeneTree

ENSGT00530000063513.

HOGENOM

HBG635316.

HOVERGEN

HBG003708.

InParanoid

Q96I15.

OMA

LEPEVIQ.

OrthoDB

EOG4XH004.

PhylomeDB

Q96I15.

Gene expression databases

ArrayExpress

Q96I15.

Bgee

Q96I15.

CleanEx

HS_SCLY.

Genevestigator

Q96I15.

Family and domain databases

InterPro

IPR000192. Aminotrans_V/Cys_dSase.
IPR016454. Cysteine_dSase_NifS.
IPR015424. PyrdxlP-dep_Trfase_major_dom.
IPR015421. PyrdxlP-dep_Trfase_major_sub1.
IPR015422. PyrdxlP-dep_Trfase_major_sub2.
[Graphical view]

Gene3D

G3DSA:3.40.640.10. PyrdxlP-dep_Trfase_major_sub1. 1 hit.
G3DSA:3.90.1150.10. PyrdxlP-dep_Trfase_major_sub2. 1 hit.

KO

K01763.

Pfam

PF00266. Aminotran_5. 1 hit.
[Graphical view]

PIRSF

PIRSF005572. NifS. 1 hit.

SUPFAM

SSF53383. PyrdxlP-dep_Trfase_major. 1 hit.

PROSITE

PS00595. AA_TRANSFER_CLASS_5. False negative.
[Graphical view]

ProtoNet

Search...

Other

NextBio

55309.

SOURCE

Search...

Entry information

Entry name

SCLY_HUMAN

Accession

Primary (citable) accession number: Q96I15
Secondary accession number(s): B9A068 , Q53SN1, Q53SN8, Q7L670, Q9NVT7, Q9NZR7

Entry history

Integrated into UniProtKB/Swiss-Prot:	February 5, 2008
Last sequence update:	February 5, 2008
Last modified:	January 25, 2012
This is version 86 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program

Disclaimer

Any medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.