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Protein

Probable lysosomal cobalamin transporter

Gene

LMBRD1

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Probable lysosomal cobalamin transporter. Required to export cobalamin from lysosomes allowing its conversion to cofactors. Isoform 3 may play a role in the assembly of hepatitis delta virus (HDV).2 Publications

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Biological processi

Host-virus interaction, Transport

Keywords - Ligandi

Cobalamin, Cobalt

Enzyme and pathway databases

ReactomeiR-HSA-196741. Cobalamin (Cbl, vitamin B12) transport and metabolism.

Protein family/group databases

TCDBi9.A.54.1.1. the lysosomal cobalamin (b12) transporter (l-b12t) family.

Names & Taxonomyi

Protein namesi
Recommended name:
Probable lysosomal cobalamin transporter
Alternative name(s):
HDAg-L-interacting protein NESI
LMBR1 domain-containing protein 1
Nuclear export signal-interacting protein
Gene namesi
Name:LMBRD1
Synonyms:C6orf209, NESI
ORF Names:BM-021, CD001, MSTP044
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 6

Organism-specific databases

HGNCiHGNC:23038. LMBRD1.

Subcellular locationi

Topology

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Topological domaini1 – 10ExtracellularSequence analysis10
Transmembranei11 – 31Helical; Name=1Sequence analysisAdd BLAST21
Topological domaini32 – 50CytoplasmicSequence analysisAdd BLAST19
Transmembranei51 – 71Helical; Name=2Sequence analysisAdd BLAST21
Topological domaini72 – 100ExtracellularSequence analysisAdd BLAST29
Transmembranei101 – 121Helical; Name=3Sequence analysisAdd BLAST21
Topological domaini122 – 144CytoplasmicSequence analysisAdd BLAST23
Transmembranei145 – 165Helical; Name=4Sequence analysisAdd BLAST21
Topological domaini166 – 188ExtracellularSequence analysisAdd BLAST23
Transmembranei189 – 209Helical; Name=5Sequence analysisAdd BLAST21
Topological domaini210 – 305CytoplasmicSequence analysisAdd BLAST96
Transmembranei306 – 326Helical; Name=6Sequence analysisAdd BLAST21
Topological domaini327 – 364ExtracellularSequence analysisAdd BLAST38
Transmembranei365 – 385Helical; Name=7Sequence analysisAdd BLAST21
Topological domaini386 – 408CytoplasmicSequence analysisAdd BLAST23
Transmembranei409 – 429Helical; Name=8Sequence analysisAdd BLAST21
Topological domaini430 – 486ExtracellularSequence analysisAdd BLAST57
Transmembranei487 – 507Helical; Name=9Sequence analysisAdd BLAST21
Topological domaini508 – 540CytoplasmicSequence analysisAdd BLAST33

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Lysosome, Membrane

Pathology & Biotechi

Involvement in diseasei

Methylmalonic aciduria and homocystinuria type cblF (MMAHCF)1 Publication
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionA disorder of cobalamin metabolism characterized by decreased levels of the coenzymes adenosylcobalamin (AdoCbl) and methylcobalamin (MeCbl). It is due to accumulation of free cobalamin in lysosomes, thus hindering its conversion to cofactors. Clinical features include developmental delay, stomatitis, glossitis, seizures and methylmalonic aciduria responsive to vitamin B12.
See also OMIM:277380

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi78N → Q: Does not affect glycosylation status; when associated with Q-88. 1 Publication1
Mutagenesisi88N → Q: Does not affect glycosylation status; when associated with Q-78. 1 Publication1
Mutagenesisi448N → Q: Affects glycosylation status; when associated with Q-457. 1 Publication1
Mutagenesisi457N → Q: Affects glycosylation status. Affects glycosylation status; when associated with Q-448. 1 Publication1

Organism-specific databases

DisGeNETi55788.
MalaCardsiLMBRD1.
MIMi277380. phenotype.
OpenTargetsiENSG00000168216.
Orphaneti79284. Methylmalonic acidemia with homocystinuria type cblF.
PharmGKBiPA134948847.

Polymorphism and mutation databases

BioMutaiLMBRD1.
DMDMi74752981.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002605151 – 540Probable lysosomal cobalamin transporterAdd BLAST540

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Glycosylationi78N-linked (GlcNAc...)Sequence analysis1
Glycosylationi88N-linked (GlcNAc...)Sequence analysis1
Glycosylationi170N-linked (GlcNAc...)Sequence analysis1
Modified residuei238PhosphothreonineBy similarity1
Glycosylationi347N-linked (GlcNAc...)Sequence analysis1
Glycosylationi448N-linked (GlcNAc...)Sequence analysis1
Glycosylationi457N-linked (GlcNAc...)1 Publication1
Modified residuei528PhosphoserineCombined sources1
Modified residuei531PhosphoserineCombined sources1

Post-translational modificationi

N-glycosylated.1 Publication

Keywords - PTMi

Glycoprotein, Phosphoprotein

Proteomic databases

EPDiQ9NUN5.
MaxQBiQ9NUN5.
PaxDbiQ9NUN5.
PeptideAtlasiQ9NUN5.
PRIDEiQ9NUN5.

PTM databases

iPTMnetiQ9NUN5.
PhosphoSitePlusiQ9NUN5.
SwissPalmiQ9NUN5.

Expressioni

Tissue specificityi

Isoform 3 is expressed in liver.1 Publication

Gene expression databases

BgeeiENSG00000168216.
CleanExiHS_LMBRD1.
GenevisibleiQ9NUN5. HS.

Organism-specific databases

HPAiHPA019547.

Interactioni

Subunit structurei

Isoform 3 interacts with Hepatitis delta virus NES(HDAg-L).1 Publication

Protein-protein interaction databases

BioGridi120902. 3 interactors.
IntActiQ9NUN5. 1 interactor.
STRINGi9606.ENSP00000359609.

Structurei

3D structure databases

ProteinModelPortaliQ9NUN5.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the LIMR family. LMBRD1 subfamily.Curated

Keywords - Domaini

Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiENOG410IFHV. Eukaryota.
ENOG410XPKG. LUCA.
GeneTreeiENSGT00390000002581.
HOVERGENiHBG059142.
InParanoidiQ9NUN5.
KOiK14617.
OMAiCTQIKTA.
OrthoDBiEOG091G0BP6.
PhylomeDBiQ9NUN5.
TreeFamiTF329170.

Family and domain databases

InterProiIPR006876. LMBR1-like_membr_prot.
[Graphical view]
PfamiPF04791. LMBR1. 1 hit.
[Graphical view]

Sequences (4)i

Sequence statusi: Complete.

This entry describes 4 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q9NUN5-1) [UniParc]FASTAAdd to basket

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.

« Hide

        10         20         30         40         50
MATSGAASAE LVIGWCIFGL LLLAILAFCW IYVRKYQSRR ESEVVSTITA
60 70 80 90 100
IFSLAIALIT SALLPVDIFL VSYMKNQNGT FKDWANANVS RQIEDTVLYG
110 120 130 140 150
YYTLYSVILF CVFFWIPFVY FYYEEKDDDD TSKCTQIKTA LKYTLGFVVI
160 170 180 190 200
CALLLLVGAF VPLNVPNNKN STEWEKVKSL FEELGSSHGL AALSFSISSL
210 220 230 240 250
TLIGMLAAIT YTAYGMSALP LNLIKGTRSA AYERLENTED IEEVEQHIQT
260 270 280 290 300
IKSKSKDGRP LPARDKRALK QFEERLRTLK KRERHLEFIE NSWWTKFCGA
310 320 330 340 350
LRPLKIVWGI FFILVALLFV ISLFLSNLDK ALHSAGIDSG FIIFGANLSN
360 370 380 390 400
PLNMLLPLLQ TVFPLDYILI TIIIMYFIFT SMAGIRNIGI WFFWIRLYKI
410 420 430 440 450
RRGRTRPQAL LFLCMILLLI VLHTSYMIYS LAPQYVMYGS QNYLIETNIT
460 470 480 490 500
SDNHKGNSTL SVPKRCDADA PEDQCTVTRT YLFLHKFWFF SAAYYFGNWA
510 520 530 540
FLGVFLIGLI VSCCKGKKSV IEGVDEDSDI SDDEPSVYSA
Length:540
Mass (Da):61,389
Last modified:October 1, 2000 - v1
Checksum:iCC7578B0F5FD7BA6
GO
Isoform 2 (identifier: Q9NUN5-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     362-392: VFPLDYILITIIIMYFIFTSMAGIRNIGIWF → EFEILAYGSFGLDYIKSEEVEPGPKHSFFSA
     393-540: Missing.

Note: No experimental confirmation available.
Show »
Length:392
Mass (Da):44,211
Checksum:i6DE93B0127AC0BE5
GO
Isoform 3 (identifier: Q9NUN5-3) [UniParc]FASTAAdd to basket
Also known as: NESI

The sequence of this isoform differs from the canonical sequence as follows:
     1-73: Missing.

Show »
Length:467
Mass (Da):53,435
Checksum:i51C91051CD071AC5
GO
Isoform 4 (identifier: Q9NUN5-4) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-204: Missing.
     362-392: VFPLDYILITIIIMYFIFTSMAGIRNIGIWF → EFEILAYGSFGLDYIKSEEVEPGPKHSFFSA
     393-540: Missing.

Note: No experimental confirmation available.
Show »
Length:188
Mass (Da):21,394
Checksum:i028B19ED4912A09C
GO

Sequence cautioni

The sequence AAK26247 differs from that shown. Reason: Frameshift at position 137.Curated

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_029047144T → A.Corresponds to variant rs12214456dbSNPEnsembl.1
Natural variantiVAR_029048395I → V.1 PublicationCorresponds to variant rs17854411dbSNPEnsembl.1
Natural variantiVAR_029049469D → E.Corresponds to variant rs9354880dbSNPEnsembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0365391 – 204Missing in isoform 4. 1 PublicationAdd BLAST204
Alternative sequenceiVSP_0216291 – 73Missing in isoform 3. 4 PublicationsAdd BLAST73
Alternative sequenceiVSP_021630362 – 392VFPLD…IGIWF → EFEILAYGSFGLDYIKSEEV EPGPKHSFFSA in isoform 2 and isoform 4. 1 PublicationAdd BLAST31
Alternative sequenceiVSP_036540393 – 540Missing in isoform 2 and isoform 4. 1 PublicationAdd BLAST148

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY136817 mRNA. Translation: AAN11301.1.
AF113224 mRNA. Translation: AAG39295.1.
AF208863 mRNA. Translation: AAF64277.1.
AK002102 mRNA. Translation: BAA92087.1.
AK290069 mRNA. Translation: BAF82758.1.
AL583831, AL358133, AL590702 Genomic DNA. Translation: CAH74081.1.
AL583831, AL358133, AL590702 Genomic DNA. Translation: CAH74083.1.
AL358133, AL583831, AL590702 Genomic DNA. Translation: CAI16835.1.
AL358133, AL583831, AL590702 Genomic DNA. Translation: CAI16836.1.
AL590702, AL358133, AL583831 Genomic DNA. Translation: CAI17314.1.
AL590702, AL358133, AL583831 Genomic DNA. Translation: CAI17316.1.
CH471051 Genomic DNA. Translation: EAW48832.1.
CH471051 Genomic DNA. Translation: EAW48833.1.
CH471051 Genomic DNA. Translation: EAW48835.1.
BC010360 mRNA. Translation: AAH10360.1.
BC047073 mRNA. Translation: AAH47073.1.
AF211480 mRNA. Translation: AAK26247.1. Frameshift.
CCDSiCCDS4969.1. [Q9NUN5-1]
RefSeqiNP_060838.3. NM_018368.3. [Q9NUN5-1]
XP_011534243.1. XM_011535941.1. [Q9NUN5-3]
UniGeneiHs.271643.
Hs.736005.

Genome annotation databases

EnsembliENST00000370570; ENSP00000359602; ENSG00000168216. [Q9NUN5-3]
ENST00000370577; ENSP00000359609; ENSG00000168216. [Q9NUN5-1]
ENST00000472827; ENSP00000433385; ENSG00000168216. [Q9NUN5-2]
GeneIDi55788.
KEGGihsa:55788.
UCSCiuc003pez.4. human. [Q9NUN5-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY136817 mRNA. Translation: AAN11301.1.
AF113224 mRNA. Translation: AAG39295.1.
AF208863 mRNA. Translation: AAF64277.1.
AK002102 mRNA. Translation: BAA92087.1.
AK290069 mRNA. Translation: BAF82758.1.
AL583831, AL358133, AL590702 Genomic DNA. Translation: CAH74081.1.
AL583831, AL358133, AL590702 Genomic DNA. Translation: CAH74083.1.
AL358133, AL583831, AL590702 Genomic DNA. Translation: CAI16835.1.
AL358133, AL583831, AL590702 Genomic DNA. Translation: CAI16836.1.
AL590702, AL358133, AL583831 Genomic DNA. Translation: CAI17314.1.
AL590702, AL358133, AL583831 Genomic DNA. Translation: CAI17316.1.
CH471051 Genomic DNA. Translation: EAW48832.1.
CH471051 Genomic DNA. Translation: EAW48833.1.
CH471051 Genomic DNA. Translation: EAW48835.1.
BC010360 mRNA. Translation: AAH10360.1.
BC047073 mRNA. Translation: AAH47073.1.
AF211480 mRNA. Translation: AAK26247.1. Frameshift.
CCDSiCCDS4969.1. [Q9NUN5-1]
RefSeqiNP_060838.3. NM_018368.3. [Q9NUN5-1]
XP_011534243.1. XM_011535941.1. [Q9NUN5-3]
UniGeneiHs.271643.
Hs.736005.

3D structure databases

ProteinModelPortaliQ9NUN5.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi120902. 3 interactors.
IntActiQ9NUN5. 1 interactor.
STRINGi9606.ENSP00000359609.

Protein family/group databases

TCDBi9.A.54.1.1. the lysosomal cobalamin (b12) transporter (l-b12t) family.

PTM databases

iPTMnetiQ9NUN5.
PhosphoSitePlusiQ9NUN5.
SwissPalmiQ9NUN5.

Polymorphism and mutation databases

BioMutaiLMBRD1.
DMDMi74752981.

Proteomic databases

EPDiQ9NUN5.
MaxQBiQ9NUN5.
PaxDbiQ9NUN5.
PeptideAtlasiQ9NUN5.
PRIDEiQ9NUN5.

Protocols and materials databases

DNASUi55788.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000370570; ENSP00000359602; ENSG00000168216. [Q9NUN5-3]
ENST00000370577; ENSP00000359609; ENSG00000168216. [Q9NUN5-1]
ENST00000472827; ENSP00000433385; ENSG00000168216. [Q9NUN5-2]
GeneIDi55788.
KEGGihsa:55788.
UCSCiuc003pez.4. human. [Q9NUN5-1]

Organism-specific databases

CTDi55788.
DisGeNETi55788.
GeneCardsiLMBRD1.
GeneReviewsiLMBRD1.
HGNCiHGNC:23038. LMBRD1.
HPAiHPA019547.
MalaCardsiLMBRD1.
MIMi277380. phenotype.
612625. gene.
neXtProtiNX_Q9NUN5.
OpenTargetsiENSG00000168216.
Orphaneti79284. Methylmalonic acidemia with homocystinuria type cblF.
PharmGKBiPA134948847.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiENOG410IFHV. Eukaryota.
ENOG410XPKG. LUCA.
GeneTreeiENSGT00390000002581.
HOVERGENiHBG059142.
InParanoidiQ9NUN5.
KOiK14617.
OMAiCTQIKTA.
OrthoDBiEOG091G0BP6.
PhylomeDBiQ9NUN5.
TreeFamiTF329170.

Enzyme and pathway databases

ReactomeiR-HSA-196741. Cobalamin (Cbl, vitamin B12) transport and metabolism.

Miscellaneous databases

ChiTaRSiLMBRD1. human.
GeneWikiiLMBRD1.
GenomeRNAii55788.
PROiQ9NUN5.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000168216.
CleanExiHS_LMBRD1.
GenevisibleiQ9NUN5. HS.

Family and domain databases

InterProiIPR006876. LMBR1-like_membr_prot.
[Graphical view]
PfamiPF04791. LMBR1. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiLMBD1_HUMAN
AccessioniPrimary (citable) accession number: Q9NUN5
Secondary accession number(s): A8K204
, E1P531, Q5VUN6, Q86Y70, Q96FW4, Q9BY56, Q9NZD6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 28, 2006
Last sequence update: October 1, 2000
Last modified: November 30, 2016
This is version 127 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny 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.

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Human chromosome 6
    Human chromosome 6: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.