Seroatlas · Human Serome Atlas

PLOD3

Multifunctional procollagen lysine hydroxylase and glycosyltransferase LH3

Also known as: LH3, PLOD3_HUMAN

Cross-references: UniProt · Ensembl · Human Protein Atlas · GeneCards · NCBI Gene

Protein identityUniProt · HPA

UniProt accession: O60568
Gene: PLOD3
Ensembl: ENSG00000106397
Chromosome: 7
Canonical length: 738 aa
Protein class: Disease related genes, Enzymes, Human disease related genes, Metabolic proteins, Potential drug targets, Predicted intracellular proteins, Predicted secreted proteins
Secretome location: Secreted to extracellular matrix
Quaternary structure: Homodimer

OverviewNCBI Gene

The protein encoded by this gene is a membrane-bound homodimeric enzyme that is localized to the cisternae of the rough endoplasmic reticulum. The enzyme (cofactors iron and ascorbate) catalyzes the hydroxylation of lysyl residues in collagen-like peptides. The resultant hydroxylysyl groups are attachment sites for carbohydrates in collagen and thus are critical for the stability of intermolecular crosslinks. Some patients with Ehlers-Danlos syndrome type VIB have deficiencies in lysyl hydroxylase activity. [provided by RefSeq, Jul 2008]

Canonical amino-acid sequenceUniProt

738 residues, UniProt reviewed canonical sequence.

>O60568|PLOD3
     1  MTSSGPGPRF LLLLPLLLPP AASASDRPRG RDPVNPEKLL VITVATAETE GYLRFLRSAE
    61  FFNYTVRTLG LGEEWRGGDV ARTVGGGQKV RWLKKEMEKY ADREDMIIMF VDSYDVILAG
   121  SPTELLKKFV QSGSRLLFSA ESFCWPEWGL AEQYPEVGTG KRFLNSGGFI GFATTIHQIV
   181  RQWKYKDDDD DQLFYTRLYL DPGLREKLSL NLDHKSRIFQ NLNGALDEVV LKFDRNRVRI
   241  RNVAYDTLPI VVHGNGPTKL QLNYLGNYVP NGWTPEGGCG FCNQDRRTLP GGQPPPRVFL
   301  AVFVEQPTPF LPRFLQRLLL LDYPPDRVTL FLHNNEVFHE PHIADSWPQL QDHFSAVKLV
   361  GPEEALSPGE ARDMAMDLCR QDPECEFYFS LDADAVLTNL QTLRILIEEN RKVIAPMLSR
   421  HGKLWSNFWG ALSPDEYYAR SEDYVELVQR KRVGVWNVPY ISQAYVIRGD TLRMELPQRD
   481  VFSGSDTDPD MAFCKSFRDK GIFLHLSNQH EFGRLLATSR YDTEHLHPDL WQIFDNPVDW
   541  KEQYIHENYS RALEGEGIVE QPCPDVYWFP LLSEQMCDEL VAEMEHYGQW SGGRHEDSRL
   601  AGGYENVPTV DIHMKQVGYE DQWLQLLRTY VGPMTESLFP GYHTKARAVM NFVVRYRPDE
   661  QPSLRPHHDS STFTLNVALN HKGLDYEGGG CRFLRYDCVI SSPRKGWALL HPGRLTHYHE
   721  GLPTTWGTRY IMVSFVDP

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against PLOD3 can act on the native protein depends on physical access: surface and secreted proteins are reachable by circulating antibodies, intracellular proteins usually are not.

Antibody reachability: Secreted
Secreted: Yes
Transmembrane segments: 0
Mean surface accessibility (rSASA): 0.24
Highest tissue expression: 52 nTPM

Expression across tissuesHPA

Tissue

liver: 52 nTPM
spinal cord: 51 nTPM
adipose tissue: 41 nTPM
heart muscle: 41 nTPM
pancreas: 41 nTPM
choroid plexus: 39 nTPM

Single-cell type

extravillous trophoblasts: 115 nCPM
melanocytes: 110 nCPM
schwann cells: 81 nCPM
decidual stromal cells: 75 nCPM
hofbauer cells: 59 nCPM
enterocytes: 54 nCPM

Immune cell

non-classical monocyte: 23 nTPM
intermediate monocyte: 22 nTPM
plasmacytoid DC: 20 nTPM
classical monocyte: 18 nTPM
myeloid DC: 17 nTPM
gdT-cell: 13 nTPM

Brain region

white matter: 82 nTPM
medulla oblongata: 64 nTPM
cerebellum: 51 nTPM
pons: 49 nTPM
basal ganglia: 46 nTPM
midbrain: 46 nTPM

DiseaseUniProt · ClinVar · IEDB · PubMed

Four sources answering four different questions about PLOD3.

Disease | AllUniProt

Conditions PLOD3 is implicated in, by any mechanism.

BCARD syndrome (BCARD) MIM:612394

Disease | GeneticClinVar

37 pathogenic / likely-pathogenic of 778 ClinVar records.

Conditions with pathogenic or likely-pathogenic variants.

Bone fragility with contractures, arterial rupture, and deafness
Neurodevelopmental delay
PLOD3-related disorder
Gastric cancer

Genetic constraint and essentialitygnomAD · DepMap

Does the body need this protein intact? Low LOEUF or a strong DepMap dependency means loss or blockade of the protein is likely to be felt.

gnomAD LOEUF (loss-of-function intolerance): 0.82
gnomAD pLI: 0
gnomAD missense Z: 0.16
DepMap mean gene effect: 0.09
DepMap dependency class: selective

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 10% of surveyed tumor types (aggregate summary; per-cohort expression, alteration, and survival load in the interactive view).

OntologyGO

Biological processes

basement membrane assembly
collagen biosynthetic process
collagen fibril organization
endothelial cell morphogenesis
epidermis morphogenesis
hydroxylysine biosynthetic process
in utero embryonic development
intracellular protein localization
lung morphogenesis
neural tube development
vasodilation
protein O-linked glycosylation via galactose

Molecular functions

iron ion binding
L-ascorbic acid binding
metal ion binding
procollagen galactosyltransferase activity
procollagen-lysine 5-dioxygenase activity
small molecule binding
procollagen glucosyltransferase activity

Cellular components

Protein domainsUniProt · Pfam · InterPro

KeywordsUniProt

InteractionsUniProt · HPA

Protein binding partners of PLOD3 in the human serome: UniProt-annotated complex subunits plus reported interactors. Each links to its own Seroatlas record.

Antibody and autoantibody relevanceSeroatlas analysis

Seroatlas reads PLOD3 as an antibody target. Whether an autoantibody or antibody against PLOD3 could matter depends on whether native PLOD3 is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

PLOD3 is annotated as secreted, so native PLOD3 circulates and is directly accessible to antibodies. Secreted and cell-surface proteins are the autoantibody targets most likely to act like drugs, blocking or depleting the native protein.

Annotation status

The present source text does not explicitly label PLOD3 as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

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