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Protein

Neutrophil gelatinase-associated lipocalin

Gene

Lcn2

Organism
Rattus norvegicus (Rat)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Iron-trafficking protein involved in multiple processes such as apoptosis, innate immunity and renal development. Binds iron through association with 2,5-dihydroxybenzoic acid (2,5-DHBA), a siderophore that shares structural similarities with bacterial enterobactin, and delivers or removes iron from the cell, depending on the context. Iron-bound form (holo-24p3) is internalized following binding to the SLC22A17 (24p3R) receptor, leading to release of iron and subsequent increase of intracellular iron concentration. In contrast, association of the iron-free form (apo-24p3) with the SLC22A17 (24p3R) receptor is followed by association with an intracellular siderophore, iron chelation and iron transfer to the extracellular medium, thereby reducing intracellular iron concentration. Involved in apoptosis due to interleukin-3 (IL3) deprivation: iron-loaded form increases intracellular iron concentration without promoting apoptosis, while iron-free form decreases intracellular iron levels, inducing expression of the proapoptotic protein BCL2L11/BIM, resulting in apoptosis. Involved in innate immunity, possibly by sequestrating iron, leading to limit bacterial growth (By similarity).By similarity

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei126 – 1261Catecholate-type ferric siderophoreBy similarity
Binding sitei145 – 1451Catecholate-type ferric siderophoreBy similarity
Binding sitei154 – 1541Catecholate-type ferric siderophoreBy similarity

GO - Molecular functioni

  • iron ion binding Source: UniProtKB
  • protease binding Source: RGD
  • protein homodimerization activity Source: RGD
  • small molecule binding Source: InterPro
  • transporter activity Source: InterPro

GO - Biological processi

  • cellular response to hydrogen peroxide Source: RGD
  • cellular response to interleukin-1 Source: RGD
  • cellular response to lipopolysaccharide Source: RGD
  • cellular response to nutrient levels Source: RGD
  • cellular response to tumor necrosis factor Source: RGD
  • extrinsic apoptotic signaling pathway in absence of ligand Source: Ensembl
  • innate immune response Source: UniProtKB
  • ion transport Source: UniProtKB-KW
  • iron ion homeostasis Source: UniProtKB-KW
  • positive regulation of cell projection organization Source: RGD
  • positive regulation of gene expression Source: RGD
  • protein homotrimerization Source: RGD
  • response to bacterium Source: RGD
  • response to drug Source: RGD
  • response to herbicide Source: RGD
  • response to mycotoxin Source: RGD
  • response to nutrient levels Source: RGD
  • response to oxidative stress Source: RGD
  • response to virus Source: Ensembl
  • siderophore transport Source: UniProtKB
Complete GO annotation...

Keywords - Biological processi

Apoptosis, Immunity, Innate immunity, Ion transport, Iron transport, Transport

Keywords - Ligandi

Iron

Enzyme and pathway databases

ReactomeiR-RNO-917937. Iron uptake and transport.

Names & Taxonomyi

Protein namesi
Recommended name:
Neutrophil gelatinase-associated lipocalin
Short name:
NGAL
Alternative name(s):
Alpha-2-microglobulin-related protein
Alpha-2U globulin-related protein
Lipocalin-2
Siderocalin LCN2
p25
Gene namesi
Name:Lcn2
OrganismiRattus norvegicus (Rat)
Taxonomic identifieri10116 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus
Proteomesi
  • UP000002494 Componenti: Chromosome 3

Organism-specific databases

RGDi69408. Lcn2.

Subcellular locationi

  • Secreted By similarity

  • Note: Upon binding to the SLC22A17 (24p3R) receptor, it is internalized.By similarity

GO - Cellular componenti

  • cytosol Source: RGD
  • extracellular region Source: UniProtKB
  • extracellular space Source: RGD
Complete GO annotation...

Keywords - Cellular componenti

Secreted

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 2020By similarityAdd
BLAST
Chaini21 – 198178Neutrophil gelatinase-associated lipocalinPRO_0000017935Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei21 – 211Pyrrolidone carboxylic acidBy similarity
Glycosylationi85 – 851N-linked (GlcNAc...)Sequence analysis
Disulfide bondi96 ↔ 1951 Publication

Keywords - PTMi

Disulfide bond, Glycoprotein, Pyrrolidone carboxylic acid

Proteomic databases

PaxDbiP30152.

PTM databases

iPTMnetiP30152.

Expressioni

Gene expression databases

GenevisibleiP30152. RN.

Interactioni

Subunit structurei

Homodimer; disulfide-linked. Heterodimer; disulfide-linked with MMP9 (By similarity).By similarity

GO - Molecular functioni

  • protease binding Source: RGD
  • protein homodimerization activity Source: RGD

Protein-protein interaction databases

STRINGi10116.ENSRNOP00000018776.

Structurei

Secondary structure

1
198
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi33 – 353Combined sources
Helixi44 – 474Combined sources
Beta strandi49 – 5810Combined sources
Beta strandi64 – 663Combined sources
Beta strandi73 – 786Combined sources
Beta strandi84 – 907Combined sources
Beta strandi97 – 1059Combined sources
Beta strandi111 – 1144Combined sources
Helixi117 – 1193Combined sources
Beta strandi121 – 13212Combined sources
Beta strandi135 – 1373Combined sources
Beta strandi139 – 1479Combined sources
Beta strandi150 – 16213Combined sources
Helixi166 – 17813Combined sources
Helixi183 – 1853Combined sources
Beta strandi193 – 1953Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2K23NMR-A21-198[»]
ProteinModelPortaliP30152.
SMRiP30152. Positions 21-197.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP30152.

Family & Domainsi

Sequence similaritiesi

Belongs to the calycin superfamily. Lipocalin family.Curated

Keywords - Domaini

Signal

Phylogenomic databases

eggNOGiENOG410JAXJ. Eukaryota.
ENOG4111A75. LUCA.
GeneTreeiENSGT00530000063610.
HOGENOMiHOG000231660.
HOVERGENiHBG106490.
InParanoidiP30152.
OMAiVPIDQCI.
OrthoDBiEOG78M03G.
PhylomeDBiP30152.
TreeFamiTF336103.

Family and domain databases

Gene3Di2.40.128.20. 1 hit.
InterProiIPR012674. Calycin.
IPR011038. Calycin-like.
IPR003087. LCN2/LCN12.
IPR002345. Lipocalin.
IPR000566. Lipocln_cytosolic_FA-bd_dom.
[Graphical view]
PfamiPF00061. Lipocalin. 1 hit.
[Graphical view]
PRINTSiPR00179. LIPOCALIN.
PR01275. NGELATINASE.
SUPFAMiSSF50814. SSF50814. 1 hit.

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P30152-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MGLGVLCLAL VLLGVLQSQA QDSTQNLIPA PPLISVPLQP GFWTERFQGR
60 70 80 90 100
WFVVGLAGNA VQKERQSRFT MYSTIYELQE DNSYNVTSIL VRGQGCRYWI
110 120 130 140 150
RTFVPSSRPG QFTLGNIHSY PQIQSYDVQV ADTDYDQFAM VFFQKTSENK
160 170 180 190
QYFKVTLYGR TKGLSDELKE RFVSFAKSLG LKDNNIVFSV PTDQCIDN
Length:198
Mass (Da):22,476
Last modified:October 5, 2010 - v2
Checksum:i7673F036DCA5654E
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti18 – 181S → R in CAA31657 (PubMed:2462726).Curated
Sequence conflicti58 – 581G → A in CAA31657 (PubMed:2462726).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X13295 mRNA. Translation: CAA31657.1.
BC089053 mRNA. Translation: AAH89053.1.
PIRiS01989.
RefSeqiNP_570097.1. NM_130741.1.
UniGeneiRn.11303.

Genome annotation databases

EnsembliENSRNOT00000018776; ENSRNOP00000018776; ENSRNOG00000013973.
GeneIDi170496.
KEGGirno:170496.
UCSCiRGD:69408. rat.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X13295 mRNA. Translation: CAA31657.1.
BC089053 mRNA. Translation: AAH89053.1.
PIRiS01989.
RefSeqiNP_570097.1. NM_130741.1.
UniGeneiRn.11303.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2K23NMR-A21-198[»]
ProteinModelPortaliP30152.
SMRiP30152. Positions 21-197.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi10116.ENSRNOP00000018776.

PTM databases

iPTMnetiP30152.

Proteomic databases

PaxDbiP30152.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSRNOT00000018776; ENSRNOP00000018776; ENSRNOG00000013973.
GeneIDi170496.
KEGGirno:170496.
UCSCiRGD:69408. rat.

Organism-specific databases

CTDi3934.
RGDi69408. Lcn2.

Phylogenomic databases

eggNOGiENOG410JAXJ. Eukaryota.
ENOG4111A75. LUCA.
GeneTreeiENSGT00530000063610.
HOGENOMiHOG000231660.
HOVERGENiHBG106490.
InParanoidiP30152.
OMAiVPIDQCI.
OrthoDBiEOG78M03G.
PhylomeDBiP30152.
TreeFamiTF336103.

Enzyme and pathway databases

ReactomeiR-RNO-917937. Iron uptake and transport.

Miscellaneous databases

EvolutionaryTraceiP30152.
NextBioi620993.
PROiP30152.

Gene expression databases

GenevisibleiP30152. RN.

Family and domain databases

Gene3Di2.40.128.20. 1 hit.
InterProiIPR012674. Calycin.
IPR011038. Calycin-like.
IPR003087. LCN2/LCN12.
IPR002345. Lipocalin.
IPR000566. Lipocln_cytosolic_FA-bd_dom.
[Graphical view]
PfamiPF00061. Lipocalin. 1 hit.
[Graphical view]
PRINTSiPR00179. LIPOCALIN.
PR01275. NGELATINASE.
SUPFAMiSSF50814. SSF50814. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "The primary structure of rat alpha 2 mu globulin-related protein."
    Chan Y.-L., Paz V., Wool I.G.
    Nucleic Acids Res. 16:11368-11368(1988) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
  2. "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] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Tissue: Ovary.
  3. "Solution structure of the protein lipocalin 12 from rat epididymis."
    Peng Y., Zhang X., Liu J., Liu Q., Guo C., Zhang Y., Lin D.
    Proteins 79:2316-2320(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: STRUCTURE BY NMR OF 21-198, DISULFIDE BOND.

Entry informationi

Entry nameiNGAL_RAT
AccessioniPrimary (citable) accession number: P30152
Secondary accession number(s): Q5HZF1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 1, 1993
Last sequence update: October 5, 2010
Last modified: May 11, 2016
This is version 115 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. 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.