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Protein

Collagen alpha-1(II) chain

Gene

Col2a1

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

Functioni

Type II collagen is specific for cartilaginous tissues. It is essential for the normal embryonic development of the skeleton, for linear growth and for the ability of cartilage to resist compressive forces.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sitei113 – 1142Cleavage; by procollagen N-endopeptidaseBy similarity
Sitei1173 – 11742Cleavage; by procollagen C-endopeptidaseBy similarity
Metal bindingi1233 – 12331CalciumBy similarity
Metal bindingi1235 – 12351CalciumBy similarity
Metal bindingi1236 – 12361Calcium; via carbonyl oxygenBy similarity
Metal bindingi1238 – 12381Calcium; via carbonyl oxygenBy similarity
Metal bindingi1241 – 12411CalciumBy similarity

GO - Molecular functioni

  • extracellular matrix structural constituent Source: RGD
  • metal ion binding Source: UniProtKB-KW

GO - Biological processi

  • cartilage development Source: RGD
  • cartilage development involved in endochondral bone morphogenesis Source: RGD
  • cellular response to mechanical stimulus Source: RGD
  • cellular response to nicotine Source: RGD
  • cellular response to parathyroid hormone stimulus Source: RGD
  • cellular response to peptide hormone stimulus Source: RGD
  • cellular response to retinoic acid Source: RGD
  • cellular response to tumor necrosis factor Source: RGD
  • cellular response to vitamin E Source: RGD
  • chondrocyte differentiation Source: RGD
  • growth plate cartilage development Source: RGD
  • response to fibroblast growth factor Source: RGD
  • response to mechanical stimulus Source: RGD
  • response to X-ray Source: RGD
Complete GO annotation...

Keywords - Ligandi

Calcium, Metal-binding

Names & Taxonomyi

Protein namesi
Recommended name:
Collagen alpha-1(II) chain
Alternative name(s):
Alpha-1 type II collagen
Cleaved into the following 2 chains:
Gene namesi
Name:Col2a1
OrganismiRattus norvegicus (Rat)
Taxonomic identifieri10116 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus
ProteomesiUP000002494 Componenti: Unplaced

Organism-specific databases

RGDi2375. Col2a1.

Subcellular locationi

GO - Cellular componenti

  • collagen type II trimer Source: RGD
  • cytoplasm Source: RGD
Complete GO annotation...

Keywords - Cellular componenti

Extracellular matrix, Secreted

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 2525Sequence AnalysisAdd
BLAST
Propeptidei26 – 11388N-terminal propeptideBy similarityPRO_0000005735Add
BLAST
Chaini114 – 11731060Collagen alpha-1(II) chainPRO_0000005736Add
BLAST
Chaini1174 – 1419246ChondrocalcinBy similarityPRO_0000043407Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei122 – 12215-hydroxylysineBy similarity
Glycosylationi122 – 1221O-linked (Gal...)By similarity
Modified residuei219 – 21915-hydroxylysineBy similarity
Glycosylationi219 – 2191O-linked (Gal...)By similarity
Modified residuei231 – 23115-hydroxylysineBy similarity
Glycosylationi231 – 2311O-linked (Gal...)By similarity
Modified residuei240 – 24015-hydroxylysineBy similarity
Glycosylationi240 – 2401O-linked (Gal...)By similarity
Modified residuei306 – 30615-hydroxylysineBy similarity
Glycosylationi306 – 3061O-linked (Gal...)By similarity
Modified residuei540 – 54015-hydroxylysineBy similarity
Glycosylationi540 – 5401O-linked (Gal...)By similarity
Modified residuei552 – 55215-hydroxylysineBy similarity
Glycosylationi552 – 5521O-linked (Gal...)By similarity
Modified residuei602 – 60213-hydroxyproline; partial1 Publication
Modified residuei839 – 83913-hydroxyproline; partial1 Publication
Modified residuei1076 – 107613-hydroxyproline; partial1 Publication
Modified residuei1118 – 111813-hydroxyproline1 Publication
Modified residuei1133 – 113313-hydroxyproline; partial1 Publication
Modified residuei1139 – 113913-hydroxyproline; partial1 Publication
Modified residuei1145 – 114513-hydroxyproline; partial1 Publication
Disulfide bondi1215 ↔ 1247PROSITE-ProRule annotation
Disulfide bondi1221 – 1221Interchain (with C-1238)PROSITE-ProRule annotation
Disulfide bondi1238 – 1238Interchain (with C-1221)PROSITE-ProRule annotation
Disulfide bondi1255 ↔ 1417PROSITE-ProRule annotation
Glycosylationi1320 – 13201N-linked (GlcNAc...)Sequence Analysis
Disulfide bondi1325 ↔ 1370PROSITE-ProRule annotation

Post-translational modificationi

Prolines at the third position of the tripeptide repeating unit (G-X-P) are hydroxylated in some or all of the chains. Probably 3-hydroxylated on Pro-602, Pro-839, Pro-1076, Pro-1133, Pro-1139 and Pro-1145 by LEPREL1.1 Publication

Keywords - PTMi

Disulfide bond, Glycoprotein, Hydroxylation

Proteomic databases

PaxDbiP05539.
PRIDEiP05539.

Expressioni

Tissue specificityi

Expressed in chondrocytes.1 Publication

Gene expression databases

GenevestigatoriP05539.

Interactioni

Subunit structurei

Homotrimers of alpha 1(II) chains.

Protein-protein interaction databases

IntActiP05539. 1 interaction.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini1185 – 1419235Fibrillar collagen NC1PROSITE-ProRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni133 – 11461014Triple-helical regionAdd
BLAST
Regioni1147 – 117327Nonhelical region (C-terminal)Add
BLAST

Domaini

The C-terminal propeptide, also known as COLFI domain, have crucial roles in tissue growth and repair by controlling both the intracellular assembly of procollagen molecules and the extracellular assembly of collagen fibrils. It binds a calcium ion which is essential for its function (By similarity).By similarity

Sequence similaritiesi

Belongs to the fibrillar collagen family.PROSITE-ProRule annotation
Contains 1 fibrillar collagen NC1 domain.PROSITE-ProRule annotation

Keywords - Domaini

Collagen, Repeat, Signal

Phylogenomic databases

eggNOGiNOG12793.
HOGENOMiHOG000085654.
HOVERGENiHBG004933.
InParanoidiP05539.
KOiK06236.
PhylomeDBiP05539.

Family and domain databases

InterProiIPR008160. Collagen.
IPR000885. Fib_collagen_C.
[Graphical view]
PfamiPF01410. COLFI. 1 hit.
PF01391. Collagen. 4 hits.
[Graphical view]
ProDomiPD002078. Fib_collagen_C. 1 hit.
[Graphical view] [Entries sharing at least one domain]
SMARTiSM00038. COLFI. 1 hit.
[Graphical view]
PROSITEiPS51461. NC1_FIB. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

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

P05539-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MIRLGAPQSL VLLTLLIATV LQCQGQDARK LGPKGQKGEP GDIKDIIGPK
60 70 80 90 100
GPPGPQGPAG EQGPRGDRGD KGERGAPGPR GRDGEPGTPG NPGPPGPPGP
110 120 130 140 150
PGPPGLGGGN FAAQMAGGFD EKAGGAQMGV MQGPMGPMGP RGPPGPAGAP
160 170 180 190 200
GPQGFQGNPG EPGEPGVSGP IGPRGPPGPA GKPGDDGEAG KPGKAGERGL
210 220 230 240 250
PGPQGARGFP GTPGLPGVKG HRGYPGLDGA KGEAGAPGVK GESGSPGENG
260 270 280 290 300
SPGPMGPRGL PGERGRTGPA GAAGARGNDG QPGPAGPPGP VGPAGGPGFL
310 320 330 340 350
GAPGAKGEAG PTGARGPEGA QGSRGEPGNP GSPGPAGASG NPGTDGIPGA
360 370 380 390 400
KGSAGAPGIA GAPGFPGPRG PPGPQGATGP LGPKGQTGEP GIAGFKGEQG
410 420 430 440 450
PKGETGPAGP QGAPGPAGEE GKRGARGEPG GAGPIGPPGE RGAPGNRGFP
460 470 480 490 500
GQDGLAGPKG APGERGPSGL AGPKGANGDP GRPGEPGLPG ARGLTGRPGD
510 520 530 540 550
AGPQGKVGPS GAPGEDGRPG PPGPQGARGQ PGVMGFPGPK GANGEPGKAG
560 570 580 590 600
EKGLAGAPGL RGLPGKDGET GAAGPPGPSG PAGERGEQGA PGPSGFQGLP
610 620 630 640 650
GPPGPPGEGG KQGDQGIPGE AGAPGLVGPR GERGFPGERG SPGAQGLQGP
660 670 680 690 700
RGLPGTPGTD GPKGAAGPDG PPGAQGPPGL QGMPGERGAA GIAGPKGDRG
710 720 730 740 750
DVGEKGPEGA PGKDGGRGLT GPIGPPGPAG ANGEKGEVGP PGPSGSTGAR
760 770 780 790 800
GAPGERGETG PPGPAGFAGP PGADGQPGAK GDQGEAGQKG DAGAPGPQGP
810 820 830 840 850
SGAPGPQGPT GVTGPKGARG AQGPPGATGF PGAAGRVGPP GSNGNPGPAG
860 870 880 890 900
PPGPAGKDGP KGARGDTGAP GRAGDPGLQG PAGAPGEKGE PGDDGPSGSD
910 920 930 940 950
GPPGPQGLAG QRGIVGLPGQ RGERGFPGLP GPSGEPGKQG APGASGDRGP
960 970 980 990 1000
PGPVGPPGLT GPAGEPGREG SPGADGPPGR DGAAGVKGDR GETGALGAPG
1010 1020 1030 1040 1050
APGPPGSPGP AGPTGKQGDR GEAGAQGPMG PSGPAGARGI AGPQGPRGDK
1060 1070 1080 1090 1100
GEAGEPGERG LKGHRGFTGL QGLPGPPGPS GDQGTSGPAG PSGPRGPPGP
1110 1120 1130 1140 1150
VGPSGKDGSN GIPGPIGPPG PRGRSGETGP AGPPGNPGPP GPPGPPGPGI
1160 1170 1180 1190 1200
DMSAFAGLGQ REKGPDPLQY MRADEADSTL RQHDVEVDAT LKSLNNQIES
1210 1220 1230 1240 1250
IRSPDGSRKN PARTCQDLKL CHPEWKSGDY WIDPNQGCTL DAMKVFCNME
1260 1270 1280 1290 1300
TGESCVYPNP ATVPRKNWWS SKSKEKKHIW FGETMNGGFH FSYGDGNLAP
1310 1320 1330 1340 1350
NTANVQMTFL RLLSTEGSQN ITYHCKNSIA YLDEAAGNLK KALLIQGSND
1360 1370 1380 1390 1400
VEMRAEGNSR FTYTALKDGC TKHTGKWGKT IIEYRSQKTS RLPIVDIAPM
1410
DIGGPDQEFG VDIGPVCFL
Length:1,419
Mass (Da):134,570
Last modified:December 6, 2005 - v2
Checksum:iB7C63B77819CE50B
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti121 – 1211E → Q in AAA40919 (PubMed:6094525).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L48440 mRNA. Translation: AAA79780.1.
K02804 mRNA. Translation: AAA40919.1.
M10613 Genomic DNA. Translation: AAA40920.1.
X79816 mRNA. Translation: CAA56213.1.
PIRiA05152.
I60384.
RefSeqiNP_037061.1. NM_012929.1.
UniGeneiRn.10124.

Genome annotation databases

GeneIDi25412.
KEGGirno:25412.
UCSCiRGD:2375. rat.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L48440 mRNA. Translation: AAA79780.1.
K02804 mRNA. Translation: AAA40919.1.
M10613 Genomic DNA. Translation: AAA40920.1.
X79816 mRNA. Translation: CAA56213.1.
PIRiA05152.
I60384.
RefSeqiNP_037061.1. NM_012929.1.
UniGeneiRn.10124.

3D structure databases

ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

IntActiP05539. 1 interaction.

Proteomic databases

PaxDbiP05539.
PRIDEiP05539.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi25412.
KEGGirno:25412.
UCSCiRGD:2375. rat.

Organism-specific databases

CTDi1280.
RGDi2375. Col2a1.

Phylogenomic databases

eggNOGiNOG12793.
HOGENOMiHOG000085654.
HOVERGENiHBG004933.
InParanoidiP05539.
KOiK06236.
PhylomeDBiP05539.

Miscellaneous databases

NextBioi606543.
PROiP05539.

Gene expression databases

GenevestigatoriP05539.

Family and domain databases

InterProiIPR008160. Collagen.
IPR000885. Fib_collagen_C.
[Graphical view]
PfamiPF01410. COLFI. 1 hit.
PF01391. Collagen. 4 hits.
[Graphical view]
ProDomiPD002078. Fib_collagen_C. 1 hit.
[Graphical view] [Entries sharing at least one domain]
SMARTiSM00038. COLFI. 1 hit.
[Graphical view]
PROSITEiPS51461. NC1_FIB. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. "Complete rat type II collagen cDNA sequence."
    Urabe K., Sarkar G., Bolander M.E.
    Submitted (OCT-1995) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
    Tissue: Bone.
  2. "Isolation and characterization of a cDNA clone for the amino-terminal portion of the pro-alpha 1(II) chain of cartilage collagen."
    Kohno K., Martin G.R., Yamada Y.
    J. Biol. Chem. 259:13668-13673(1984) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 1-122.
  3. "Structure of the promoter of the rat type II procollagen gene."
    Kohno K., Sullivan M., Yamada Y.
    J. Biol. Chem. 260:4441-4447(1985) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-29.
  4. Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 370-422.
    Strain: DA.
    Tissue: Cartilage.
  5. "A role for prolyl 3-hydroxylase 2 in post-translational modification of fibril-forming collagens."
    Fernandes R.J., Farnand A.W., Traeger G.R., Weis M.A., Eyre D.R.
    J. Biol. Chem. 286:30662-30669(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: HYDROXYLATION AT PRO-602; PRO-839; PRO-1076; PRO-1118; PRO-1133; PRO-1139 AND PRO-1145, TISSUE SPECIFICITY, IDENTIFICATION BY MASS SPECTROMETRY.

Entry informationi

Entry nameiCO2A1_RAT
AccessioniPrimary (citable) accession number: P05539
Secondary accession number(s): Q63123, Q63565, Q78DY3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1988
Last sequence update: December 6, 2005
Last modified: January 7, 2015
This is version 113 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

Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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 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.