SCP2 sterol carrier protein 2 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SCP2provided by HGNC
Official Full Name: sterol carrier protein 2provided by HGNC
Primary source: HGNC:HGNC:10606
See related: Ensembl:ENSG00000116171 MIM:184755; AllianceGenome:HGNC:10606
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: NLTP; SCOX; SCPX; SCP-2; SCP-X; NSL-TP; SCP-CHI
Summary: This gene encodes two proteins: sterol carrier protein X (SCPx) and sterol carrier protein 2 (SCP2), as a result of transcription initiation from 2 independently regulated promoters. The transcript initiated from the proximal promoter encodes the longer SCPx protein, and the transcript initiated from the distal promoter encodes the shorter SCP2 protein, with the 2 proteins sharing a common C-terminus. Evidence suggests that the SCPx protein is a peroxisome-associated thiolase that is involved in the oxidation of branched chain fatty acids, while the SCP2 protein is thought to be an intracellular lipid transfer protein. This gene is highly expressed in organs involved in lipid metabolism, and may play a role in Zellweger syndrome, in which cells are deficient in peroxisomes and have impaired bile acid synthesis. Alternative splicing of this gene produces multiple transcript variants, some encoding different isoforms.[provided by RefSeq, Aug 2010]
Expression: Ubiquitous expression in liver (RPKM 77.0), duodenum (RPKM 30.8) and 24 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 1p32.3

Exon count:: 19

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	1	NC_000001.11 (52927276..53051698)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	1	NC_060925.1 (52808787..52933201)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	1	NC_000001.10 (53392948..53517370)

Chromosome 1 - NC_000001.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

LINC00261 elevation inhibits angiogenesis and cell cycle progression of pancreatic cancer cells by upregulating SCP2 via targeting FOXP3.
Title: LINC00261 elevation inhibits angiogenesis and cell cycle progression of pancreatic cancer cells by upregulating SCP2 via targeting FOXP3.
Methylation dependent microRNA 1285-5p and sterol carrier proteins 2 in type 2 diabetes mellitus
Title: Methylation dependent microRNA 1285-5p and sterol carrier proteins 2 in type 2 diabetes mellitus.
We (1) analyzed the structural basis of the fold and the classification of SCP2 domains; (2) identified structure-determined sequence features; (3) compared the lipid binding cavity of SCP2 and other lipid binding proteins; (4) surveyed proposed mechanisms of SCP2 mediated lipid transfer between membranes; and (5) uncovered a possible new function of the SCP2 domain as a protein-protein recognition device.
Title: A structural appraisal of sterol carrier protein 2.
imported protein sterol carrier protein 2 (SCP2) occupies only a subregion of larger peroxisomes, highlighting the heterogeneous distribution of proteins even within the peroxisome.
Title: Super-resolution Microscopy Reveals Compartmentalization of Peroxisomal Membrane Proteins.
Mice harboring a deletion of the Scp2 locus present a modulated diurnal accumulation of lipids in the liver and a perturbed activation of several signaling pathways including PPARalpha, SREBP, LRH-1, TORC1 and its upstream regulators.
Title: Perturbed rhythmic activation of signaling pathways in mice deficient for Sterol Carrier Protein 2-dependent diurnal lipid transport and metabolism.
We conclude that SCP-2 is a low affinity binding protein for arachidonylethanolamine that can facilitate its cellular uptake but does not contribute significantly to intracellular sequestration of AEA.
Title: Sterol carrier protein-2: binding protein for endocannabinoids.
The Peroxisomal targeting signal 1 in Scp2 is autonomous and is essential for binding to pex5.
Title: The Peroxisomal Targeting Signal 1 in sterol carrier protein 2 is autonomous and essential for receptor recognition.
cellular SCP-2 not only binds and translocates cholesterol but also cholesterol hydroperoxides, thus expanding their redox toxicity and signaling ranges under oxidative stress conditions
Title: Sterol carrier protein-2 (SCP-2) involvement in cholesterol hydroperoxide cytotoxicity as revealed by SCP-2 inhibitor effects.
Statistical analysis indicated that six genes, NFATC2, SCP2, CACNA1C, TCRA, POLE, and FAM3D, were associated with narcolepsy.
Title: An approach based on a genome-wide association study reveals candidate loci for narcolepsy.
Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.

Submit: New GeneRIF Correction See all GeneRIFs (19)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Sterol carrier protein 2 deficiency MedGen: C3150990 OMIM: 613724 GeneReviews: Not available	Compare labs

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

G17313 (e-PCR)
- UniSTS:60989

RH79910 (e-PCR)
- UniSTS:89168

RH40056 (e-PCR)
- UniSTS:85592

SCP2 (e-PCR)
- UniSTS:105162

S52450 (e-PCR)
- UniSTS:52476

SHGC-74838 (e-PCR)
- UniSTS:44542

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables acetyl-CoA C-acyltransferase activity	ISS Inferred from Sequence or Structural Similarity more info
enables acetyl-CoA C-myristoyltransferase activity	ISS Inferred from Sequence or Structural Similarity more info
enables cholesterol binding	IDA Inferred from Direct Assay more info	PubMed
enables cholesterol transfer activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables cholesterol transfer activity	ISS Inferred from Sequence or Structural Similarity more info
enables fatty-acyl-CoA binding	IDA Inferred from Direct Assay more info	PubMed
enables long-chain fatty acyl-CoA binding	IDA Inferred from Direct Assay more info	PubMed
enables oleic acid binding	IDA Inferred from Direct Assay more info	PubMed
enables phosphatidylcholine transfer activity	ISS Inferred from Sequence or Structural Similarity more info
enables phosphatidylinositol transfer activity	IDA Inferred from Direct Assay more info	PubMed
enables propanoyl-CoA C-acyltransferase activity	IEA Inferred from Electronic Annotation more info
enables propionyl-CoA C2-trimethyltridecanoyltransferase activity	EXP Inferred from Experiment more info	PubMed
enables propionyl-CoA C2-trimethyltridecanoyltransferase activity	ISS Inferred from Sequence or Structural Similarity more info
enables propionyl-CoA C2-trimethyltridecanoyltransferase activity	TAS Traceable Author Statement more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables signaling receptor binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in alpha-linolenic acid metabolic process	TAS Traceable Author Statement more info
involved_in bile acid biosynthetic process	TAS Traceable Author Statement more info
involved_in bile acid metabolic process	ISS Inferred from Sequence or Structural Similarity more info
involved_in fatty acid beta-oxidation	ISS Inferred from Sequence or Structural Similarity more info
involved_in fatty acid beta-oxidation using acyl-CoA oxidase	TAS Traceable Author Statement more info
involved_in inositol trisphosphate biosynthetic process	IDA Inferred from Direct Assay more info	PubMed
involved_in intermembrane lipid transfer	IEA Inferred from Electronic Annotation more info
involved_in intracellular cholesterol transport	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in lipid hydroperoxide transport	IDA Inferred from Direct Assay more info	PubMed
involved_in phospholipid transport	IDA Inferred from Direct Assay more info	PubMed
involved_in phospholipid transport	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of intracellular cholesterol transport	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of intracellular cholesterol transport	NAS Non-traceable Author Statement more info	PubMed
involved_in positive regulation of steroid metabolic process	IDA Inferred from Direct Assay more info	PubMed
involved_in progesterone biosynthetic process	IDA Inferred from Direct Assay more info	PubMed
involved_in protein localization to plasma membrane	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of phospholipid biosynthetic process	ISS Inferred from Sequence or Structural Similarity more info
involved_in steroid biosynthetic process	IDA Inferred from Direct Assay more info	PubMed
involved_in sterol transport	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in cytoplasm	ISS Inferred from Sequence or Structural Similarity more info
located_in cytosol	TAS Traceable Author Statement more info
located_in endoplasmic reticulum	IEA Inferred from Electronic Annotation more info
located_in endoplasmic reticulum	ISS Inferred from Sequence or Structural Similarity more info
located_in membrane	HDA more info	PubMed
located_in mitochondrion	IEA Inferred from Electronic Annotation more info
located_in mitochondrion	ISS Inferred from Sequence or Structural Similarity more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info
located_in peroxisomal matrix	ISS Inferred from Sequence or Structural Similarity more info
located_in peroxisomal matrix	TAS Traceable Author Statement more info
is_active_in peroxisome	IBA Inferred from Biological aspect of Ancestor more info
located_in peroxisome	IDA Inferred from Direct Assay more info	PubMed
located_in peroxisome	ISS Inferred from Sequence or Structural Similarity more info
part_of protein-containing complex	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: sterol carrier protein 2

Names: SCP-2/3-oxoacyl-CoA thiolase; SCP-2/thiolase; acetyl-CoA C-myristoyltransferase; epididymis secretory sperm binding protein; non-specific lipid-transfer protein; propanoyl-CoA C-acyltransferase; sterol carrier protein X; straight-chain acyl-CoA oxidase

NP_001007099.1

EC 2.3.1.155

EC 2.3.1.16

EC 2.3.1.176

NP_001007100.1

EC 2.3.1.155

EC 2.3.1.16

EC 2.3.1.176

NP_001007101.1

EC 2.3.1.155

EC 2.3.1.16

EC 2.3.1.176

NP_001007251.1

EC 2.3.1.155

EC 2.3.1.16

EC 2.3.1.176

NP_001180528.1

EC 2.3.1.155

EC 2.3.1.16

EC 2.3.1.176

NP_001180529.1

EC 2.3.1.155

EC 2.3.1.16

EC 2.3.1.176

NP_001180546.1

EC 2.3.1.155

EC 2.3.1.16

EC 2.3.1.176

NP_001317516.1

EC 2.3.1.155

EC 2.3.1.16

EC 2.3.1.176

NP_002970.2

EC 2.3.1.155

EC 2.3.1.16

EC 2.3.1.176

XP_005271160.1

EC 2.3.1.155

EC 2.3.1.16

EC 2.3.1.176

XP_011540237.1

EC 2.3.1.155

EC 2.3.1.16

EC 2.3.1.176

XP_047283460.1

EC 2.3.1.155

EC 2.3.1.16

EC 2.3.1.176

XP_047283462.1

EC 2.3.1.155

EC 2.3.1.16

EC 2.3.1.176

XP_047283463.1

EC 2.3.1.155

EC 2.3.1.16

EC 2.3.1.176

XP_047283464.1

EC 2.3.1.155

EC 2.3.1.16

EC 2.3.1.176

XP_054194110.1

EC 2.3.1.155

EC 2.3.1.16

EC 2.3.1.176

XP_054194111.1

EC 2.3.1.155

EC 2.3.1.16

EC 2.3.1.176

XP_054194112.1

EC 2.3.1.155

EC 2.3.1.16

EC 2.3.1.176

XP_054194113.1

EC 2.3.1.155

EC 2.3.1.16

EC 2.3.1.176

XP_054194114.1

EC 2.3.1.155

EC 2.3.1.16

EC 2.3.1.176

XP_054194115.1

EC 2.3.1.155

EC 2.3.1.16

EC 2.3.1.176

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_012211.1 RefSeqGene

Range

5001..129423

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001007098.3 → NP_001007099.1 sterol carrier protein 2 isoform 2

See identical proteins and their annotated locations for NP_001007099.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) has multiple differences in the coding region, compared to variant 1, one of which results in a translational frameshift. The resulting isoform (2) is shorter and has a distinct C-terminus, compared to isoform 1. It is unknown whether this isoform (2) is proteolytically processed like isoforms 1 and 5.

Source sequence(s)

AL445183, BC067108, DC330171

Consensus CDS

CCDS41338.1

UniProtKB/Swiss-Prot

P22307

Related

ENSP00000360568.5, ENST00000371513.9

Conserved Domains (1) summary

cl27752
Location:12 → 317

PRK06064; acetyl-CoA acetyltransferase; Provisional
NM_001007099.3 → NP_001007100.1 sterol carrier protein 2 isoform 5 precursor

See identical proteins and their annotated locations for NP_001007100.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) results from transcription initiation from a downstream promoter. This variant (3) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (5, also known as SCP2) has a distinct N-terminus and is shorter than isoform 1.

Source sequence(s)

AA664009, AB208789, AL445183, BC005911, M55421

Consensus CDS

CCDS44149.1

UniProtKB/Swiss-Prot

P22307

UniProtKB/TrEMBL

Q59HG9

Related

ENSP00000396413.2, ENST00000435345.6

Conserved Domains (1) summary

pfam02036
Location:48 → 134

SCP2; SCP-2 sterol transfer family
NM_001007100.3 → NP_001007101.1 sterol carrier protein 2 isoform 4

See identical proteins and their annotated locations for NP_001007101.1

Status: REVIEWED

Description

Transcript Variant: This variant (4) results from transcription initiation from a downstream promoter. This variant (4) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (4) has a distinct N-terminus and is shorter than isoform 1. It is unknown whether this isoform (4) is proteolytically processed like isoforms 1 and 5.

Source sequence(s)

AA664009, AB208789, AL445183, DB459183, M55421

Consensus CDS

CCDS44150.1

UniProtKB/Swiss-Prot

P22307

UniProtKB/TrEMBL

Q59HG9

Related

ENSP00000406636.2, ENST00000430330.6

Conserved Domains (1) summary

pfam02036
Location:45 → 131

SCP2; SCP-2 sterol transfer family
NM_001007250.3 → NP_001007251.1 sterol carrier protein 2 isoform 3

See identical proteins and their annotated locations for NP_001007251.1

Status: REVIEWED

Description

Transcript Variant: This variant (5) results from transcription initiation from a downstream promoter. This variant (5) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (3) has a distinct N-terminus and is shorter than isoform 1. It is unknown whether this isoform (3) is proteolytically processed like isoforms 1 and 5.

Source sequence(s)

AA664009, AB208789, AL445183, CA867670, M55421

Consensus CDS

CCDS30719.1

UniProtKB/Swiss-Prot

P22307

UniProtKB/TrEMBL

Q59HG9

Related

ENSP00000386214.3, ENST00000408941.7
NM_001193599.2 → NP_001180528.1 sterol carrier protein 2 isoform 7

Status: REVIEWED

Description

Transcript Variant: This variant (7) lacks an in-frame exon in the coding region, compared to variant 1. The encoded isoform (7) is shorter than isoform 1. It is unknown whether this isoform (7) is proteolytically processed like isoforms 1 and 5.

Source sequence(s)

AA664009, AB208789, AK294631, AL445183, DC330171

Consensus CDS

CCDS53318.1

UniProtKB/TrEMBL

B2R761

Related

ENSP00000384569.2, ENST00000407246.6

Conserved Domains (3) summary

PRK08256
Location:12 → 380

PRK08256; lipid-transfer protein; Provisional

cd00826
Location:17 → 379

nondecarbox_cond_enzymes; nondecarboxylating condensing enzymes; In general, thiolases catalyze the reversible thiolytic cleavage of 3-ketoacyl-CoA into acyl-CoA and acetyl-CoA, a 2-step reaction involving a covalent intermediate formed with a catalytic cysteine. There are 2 ...

pfam02036
Location:428 → 514

SCP2; SCP-2 sterol transfer family
NM_001193600.2 → NP_001180529.1 sterol carrier protein 2 isoform 6

Status: REVIEWED

Description

Transcript Variant: This variant (6) lacks an in-frame exon in the coding region, compared to variant 1. The encoded isoform (6) is shorter than isoform 1. It is unknown whether this isoform (6) is proteolytically processed like isoforms 1 and 5.

Source sequence(s)

AA664009, AB208789, AC099677, AK308105, AL445183, DC330171

Consensus CDS

CCDS53317.1

UniProtKB/TrEMBL

B2R761

Related

ENSP00000360564.4, ENST00000371509.8

Conserved Domains (3) summary

PRK08256
Location:12 → 360

PRK08256; lipid-transfer protein; Provisional

pfam02036
Location:408 → 494

SCP2; SCP-2 sterol transfer family

cl09938
Location:17 → 359

cond_enzymes; Condensing enzymes; Family of enzymes that catalyze a (decarboxylating or non-decarboxylating) Claisen-like condensation reaction. Members are share strong structural similarity, and are involved in the synthesis and degradation of fatty acids, and the ...
NM_001193617.2 → NP_001180546.1 sterol carrier protein 2 isoform 8

See identical proteins and their annotated locations for NP_001180546.1

Status: REVIEWED

Description

Transcript Variant: This variant (8) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (8) has a shorter N-terminus, compared to isoform 1. It is unknown whether this isoform (8) is proteolytically processed like isoforms 1 and 5.

Source sequence(s)

AA664009, AB208789, AK295214, AL445183, DC330171

Consensus CDS

CCDS53319.1

UniProtKB/TrEMBL

B2R761

Related

ENSP00000434132.1, ENST00000528311.5

Conserved Domains (2) summary

pfam02036
Location:371 → 457

SCP2; SCP-2 sterol transfer family

cl09938
Location:1 → 322

cond_enzymes; Condensing enzymes; Family of enzymes that catalyze a (decarboxylating or non-decarboxylating) Claisen-like condensation reaction. Members are share strong structural similarity, and are involved in the synthesis and degradation of fatty acids, and the ...
NM_001330587.2 → NP_001317516.1 sterol carrier protein 2 isoform 9

Status: REVIEWED

Description

Transcript Variant: This variant (9) differs in the 3' UTR and coding sequence compared to variant 1. The resulting isoform (9) has a shorter and distinct C-terminus compared to isoform 1.

Source sequence(s)

AC099677, AL445183

Consensus CDS

CCDS81325.1

UniProtKB/TrEMBL

E9PLD1, Q59HG9

Related

ENSP00000435194.1, ENST00000478631.6

Conserved Domains (1) summary

PRK08256
Location:12 → 361

PRK08256; lipid-transfer protein; Provisional
NM_002979.5 → NP_002970.2 sterol carrier protein 2 isoform 1 precursor

See identical proteins and their annotated locations for NP_002970.2

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1, also known as SCPx).

Source sequence(s)

AA664009, AB208789, AK312856, AL445183, DC330171

Consensus CDS

CCDS572.1

UniProtKB/Swiss-Prot

A6NM69, B4DGJ9, B4DHP6, C9JC79, D3DQ37, E1B6W5, F2Z3J1, P22307, Q15432, Q16622, Q5VVZ1, Q6NXF4, Q99430

UniProtKB/TrEMBL

A0A384NY87, B2R761

Related

ENSP00000360569.3, ENST00000371514.8

Conserved Domains (2) summary

PRK08256
Location:12 → 404

PRK08256; lipid-transfer protein; Provisional

pfam02036
Location:452 → 538

SCP2; SCP-2 sterol transfer family

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000001.11 Reference GRCh38.p14 Primary Assembly

Range

52927276..53051698

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_005271103.5 → XP_005271160.1 sterol carrier protein 2 isoform X1

See identical proteins and their annotated locations for XP_005271160.1

UniProtKB/TrEMBL

B2R761

Conserved Domains (2) summary

PRK08256
Location:12 → 404

PRK08256; lipid-transfer protein; Provisional

cd00826
Location:17 → 403

nondecarbox_cond_enzymes; nondecarboxylating condensing enzymes; In general, thiolases catalyze the reversible thiolytic cleavage of 3-ketoacyl-CoA into acyl-CoA and acetyl-CoA, a 2-step reaction involving a covalent intermediate formed with a catalytic cysteine. There are 2 ...
XM_047427504.1 → XP_047283460.1 sterol carrier protein 2 isoform X1
XM_047427507.1 → XP_047283463.1 sterol carrier protein 2 isoform X2
XM_011541935.3 → XP_011540237.1 sterol carrier protein 2 isoform X2

UniProtKB/TrEMBL

Q59HG9

Conserved Domains (2) summary

COG0183
Location:12 → 374

PaaJ; Acetyl-CoA acetyltransferase [Lipid transport and metabolism]

cd00826
Location:17 → 380

nondecarbox_cond_enzymes; nondecarboxylating condensing enzymes; In general, thiolases catalyze the reversible thiolytic cleavage of 3-ketoacyl-CoA into acyl-CoA and acetyl-CoA, a 2-step reaction involving a covalent intermediate formed with a catalytic cysteine. There are 2 ...
XM_047427506.1 → XP_047283462.1 sterol carrier protein 2 isoform X2
XM_047427508.1 → XP_047283464.1 sterol carrier protein 2 isoform X3