Reviewed, UniProtKB/Swiss-Prot P17140 (CO4A2_CAEEL)

Names and origin

Protein names

Recommended name:
    Collagen alpha-2(IV) chain
Alternative name(s):
    Lethal protein 2

Gene names

Name:	let-2
Synonyms:	clb-1
ORF Names:	F01G12.5

Organism

Caenorhabditis elegans [Complete proteome]

Taxonomic identifier

6239 [NCBI]

Taxonomic lineage

Eukaryota › Metazoa › Nematoda › Chromadorea › Rhabditida › Rhabditoidea › Rhabditidae › Peloderinae › Caenorhabditis

Protein attributes

Sequence length	1758 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	Collagen type IV is specific for basement membranes. Vital for embryonic development. Ref.1
Subunit structure	Trimers of two alpha 1(IV) and one alpha 2(IV) chain. Type IV collagen forms a mesh-like network linked through intermolecular interactions between 7S domains and between NC1 domains.
Subcellular location	Secreted › extracellular space › extracellular matrix › basement membrane.
Developmental stage	Isoform I is predominant in embryos and isoform II is predominant in the larvae and adults.
Domain	Alpha chains of type IV collagen have a non-collagenous domain (NC1) at their C-terminus, frequent interruptions of the G-X-Y repeats in the long central triple-helical domain (which may cause flexibility in the triple helix), and a short N-terminal triple-helical 7S domain.
Post-translational modification	Prolines at the third position of the tripeptide repeating unit (G-X-Y) are hydroxylated in some or all of the chains. Type IV collagens contain numerous cysteine residues which are involved in inter- and intramolecular disulfide bonding. 12 of these, located in the NC1 domain, are conserved in all known type IV collagens. The trimeric structure of the NC1 domains is stabilized by covalent bonds between Lys and Met residues By similarity.
Sequence similarities	Belongs to the type IV collagen family. Contains 1 collagen IV NC1 (C-terminal non-collagenous) domain.

Ontologies

Keywords
Cellular component	Basement membrane Extracellular matrix Secreted
Coding sequence diversity	Alternative splicing
Domain	Collagen Repeat Signal
PTM	Disulfide bond Glycoprotein Hydroxylation
Technical term	Complete proteome
Gene Ontology (GO)
Biological process	cellular component organization Ref.1 Non-traceable author statement. Source: UniProtKB embryonic development ending in birth or egg hatching Inferred from mutant phenotype. Source: WormBase growth Inferred from mutant phenotype. Source: WormBase locomotion Inferred from mutant phenotype. Source: WormBase nematode larval development Inferred from mutant phenotype. Source: WormBase positive regulation of multicellular organism growth Inferred from mutant phenotype. Source: WormBase reproduction Inferred from mutant phenotype. Source: WormBase
Cellular component	collagen type IV Ref.1 Inferred from mutant phenotype. Source: UniProtKB
Molecular function	binding Inferred from electronic annotation. Source: InterPro extracellular matrix structural constituent conferring tensile strength Ref.1 Inferred from mutant phenotype. Source: UniProtKB
Complete GO annotation...

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]

Isoform I (identifier: P17140-1)

Also known as: a;

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.

Isoform II (identifier: P17140-2)

Also known as: b;

The sequence of this isoform differs from the canonical sequence as follows:
     229-264: GDLGSVGPPGPPGPREFTGSGSIVGPRGNPGEKGDK → GDIGAMGPAGPPGPIASTMSKGTIIGPKGDLGEKGEK

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Signal peptide	1 – 26	26	Potential
	Chain	27 – 1758	1732	Collagen alpha-2(IV) chain		PRO_0000005829
Regions
	Domain	1531 – 1754	224	Collagen IV NC1
	Region	27 – 42	16	7S domain
	Region	42 – 1527	1486	Triple-helical region
Amino acid modifications
	Glycosylation	248	1	O-linked (Xyl...) (glycosaminoglycan) Potential
	Disulfide bond	1546 ↔ 1635		By similarity
	Disulfide bond	1579 ↔ 1632		By similarity
	Disulfide bond	1591 ↔ 1597		By similarity
	Disulfide bond	1654 ↔ 1750		By similarity
	Disulfide bond	1688 ↔ 1747		By similarity
	Disulfide bond	1700 ↔ 1707		By similarity
Natural variations
	Alternative sequence	229 – 264	36	GDLGS…EKGDK → GDIGAMGPAGPPGPIASTMS KGTIIGPKGDLGEKGEK in isoform II.		VSP_001160
Experimental info
	Mutagenesis	48	1	G → E in MN114; 73% lethal.
	Mutagenesis	366	1	A → T in MN126; 100% lethal.
	Mutagenesis	570	1	G → E in MN109; 37% lethal.
	Mutagenesis	588	1	G → R in MN103 and MN151; 96% lethal.
	Mutagenesis	597	1	G → R in MN152; 50% lethal.
	Mutagenesis	690	1	G → E in MN129; 100% lethal.
	Mutagenesis	690	1	G → R in MN101; 100% lethal.
	Mutagenesis	737	1	G → E in MN143; 100% lethal.
	Mutagenesis	877	1	G → R in G30; 90% lethal.
	Mutagenesis	904	1	G → R in E1470; 94% lethal.
	Mutagenesis	1003	1	G → E in MN139; 20% lethal.
	Mutagenesis	1125	1	G → D in G25; 2% lethal.
	Mutagenesis	1152	1	G → D in MN147; 7% lethal.
	Mutagenesis	1286	1	G → D in G37 and B246; 9% lethal.
	Sequence conflict	1604	1	E → D in AAA96215. Ref.2
	Sequence conflict	1604	1	E → D in AAA96216. Ref.2
	Sequence conflict	1682	1	P → L in AAA96215. Ref.2
	Sequence conflict	1682	1	P → L in AAA96216. Ref.2

Sequences

	Sequence		Length	Mass (Da)
	Isoform I (a) [UniParc]. Last modified October 1, 1994. Version 2. Checksum: 97EE3F3DBB2D2AC5	FASTA	1,758	167,751
	10 20 30 40 50 60 MKQRAALGPV LRLAILALLA VSYVQSQATC RDCSNRGCFC VGEKGSMGAP GPQGPPGTQG 70 80 90 100 110 120 IRGFPGPEGL AGPKGLKGAQ GPPGPVGIKG DRGAVGVPGF PGNDGGNGRP GEPGPPGAPG 130 140 150 160 170 180 WDGCNGTDGA PGIPGRPGPP GMPGFPGPPG MDGLKGEPAI GYAGAPGEKG DGGMPGMPGL 190 200 210 220 230 240 PGPSGRDGYP GEKGDRGDTG NAGPRGPPGE AGSPGNPGIG SIGPKGDPGD LGSVGPPGPP 250 260 270 280 290 300 GPREFTGSGS IVGPRGNPGE KGDKGEPGEG GQRGYPGNGG LSGQPGLPGM KGEKGLSGPA 310 320 330 340 350 360 GPRGKEGRPG NAGPPGFKGD RGLDGLGGIP GLPGQKGEAG YPGRDGPKGN SGPPGPPGGG 370 380 390 400 410 420 TFNDGAPGPP GLPGRPGNPG PPGTDGYPGA PGPAGPIGNT GGPGLPGYPG NEGLPGPKGD 430 440 450 460 470 480 KGDGGIPGAP GVSGPSGIPG LPGPKGEPGY RGTPGQSIPG LPGKDGKPGL DGAPGRKGEN 490 500 510 520 530 540 GLPGVRGPPG DSLNGLPGAP GQRGAPGPNG YDGRDGVNGL PGAPGTKGDR GGTCSACAPG 550 560 570 580 590 600 TKGEKGLPGY SGQPGPQGDR GLPGMPGPVG DAGDDGLPGP AGRPGSPGPP GQDGFPGLPG 610 620 630 640 650 660 QKGEPTQLTL RPGPPGYPGL KGENGFPGQP GVDGLPGPSG PVGPPGAPGY PGEKGDAGLP 670 680 690 700 710 720 GLSGKPGQDG LPGLPGNKGE AGYGQPGQPG FPGAKGDGGL PGLPGTPGLQ GMPGEPAPEN 730 740 750 760 770 780 QVNPAPPGQP GLPGLPGTKG EGGYPGRPGE VGQPGFPGLP GMKGDSGLPG PPGLPGHPGV 790 800 810 820 830 840 PGDKGFGGVP GLPGIPGPKG DVGNPGLPGL NGQKGEPGVG VPGQPGSPGF PGLKGDAGLP 850 860 870 880 890 900 GLPGTPGLEG QRGFPGAPGL KGGDGLPGLS GQPGYPGEKG DAGLPGVPGR EGSPGFPGQD 910 920 930 940 950 960 GLPGVPGMKG EDGLPGLPGV TGLKGDLGAP GQSGAPGLPG APGYPGMKGN AGIPGVPGFK 970 980 990 1000 1010 1020 GDGGLPGLPG LNGPKGEPGV PGMPGTPGMK GNGGLPGLPG RDGLSGVPGM KGDRGFNGLP 1030 1040 1050 1060 1070 1080 GEKGEAGPAA RDGQKGDAGL PGQPGLRGPQ GPSGLPGVPG FKGETGLPGY GQPGQPGEKG 1090 1100 1110 1120 1130 1140 LPGIPGKAGR QGAPGSPGQD GLPGFPGMKG ESGYPGQDGL PGRDGLPGVP GQKGDLGQSG 1150 1160 1170 1180 1190 1200 QPGLSGAPGL DGQPGVPGIR GDKGQGGLPG IPGDRGMDGY PGQKGENGYP GQPGLPGLGG 1210 1220 1230 1240 1250 1260 EKGFAGTPGF PGLKGSPGYP GQDGLPGIPG LKGDSGFPGQ PGQEGLPGLS GEKGMGGLPG 1270 1280 1290 1300 1310 1320 MPGQPGQSIA GPVGPPGAPG LQGKDGFPGL PGQKGESGLS GLPGAPGLKG ESGMPGFPGA 1330 1340 1350 1360 1370 1380 KGDLGANGIP GKRGEDGLPG VPGRDGQPGI PGLKGEVGGA GLPGQPGFPG IPGLKGEGGL 1390 1400 1410 1420 1430 1440 PGFPGAKGEA GFPGTPGVPG YAGEKGDGGL PGLPGRDGLP GADGPVGPPG PSGPQNLVEP 1450 1460 1470 1480 1490 1500 GEKGLPGLPG APGLRGEKGM PGLDGPPGND GPPGLPGQRG NDGYPGAPGL SGEKGMGGLP 1510 1520 1530 1540 1550 1560 GFPGLDGQPG GPGAPGLPGA PGAAGPAYRD GFVLVKHSQT TEVPRCPEGQ TKLWDGYSLL 1570 1580 1590 1600 1610 1620 YIEGNEKSHN QDLGHAGSCL QRFSTMPFLF CDFNNVCNYA SRNEKSYWLS TSEAIPMMPV 1630 1640 1650 1660 1670 1680 NEREIEPYIS RCAVCEAPAN TIAVHSQTIQ IPNCPAGWSS LWIGYSFAMH TGAGAEGGGQ 1690 1700 1710 1720 1730 1740 SPSSPGSCLE DFRATPFIEC NGARGSCHYF ANKFSFWLTT IDNDSEFKVP ESQTLKSGNL 1750 RTRVSRCQVC VKSTDGRH
	Isoform II (b). Checksum: 816D72C403FB81CB	FASTA	1,759	167,813
	10 20 30 40 50 60 MKQRAALGPV LRLAILALLA VSYVQSQATC RDCSNRGCFC VGEKGSMGAP GPQGPPGTQG 70 80 90 100 110 120 IRGFPGPEGL AGPKGLKGAQ GPPGPVGIKG DRGAVGVPGF PGNDGGNGRP GEPGPPGAPG 130 140 150 160 170 180 WDGCNGTDGA PGIPGRPGPP GMPGFPGPPG MDGLKGEPAI GYAGAPGEKG DGGMPGMPGL 190 200 210 220 230 240 PGPSGRDGYP GEKGDRGDTG NAGPRGPPGE AGSPGNPGIG SIGPKGDPGD IGAMGPAGPP 250 260 270 280 290 300 GPIASTMSKG TIIGPKGDLG EKGEKGEPGE GGQRGYPGNG GLSGQPGLPG MKGEKGLSGP 310 320 330 340 350 360 AGPRGKEGRP GNAGPPGFKG DRGLDGLGGI PGLPGQKGEA GYPGRDGPKG NSGPPGPPGG 370 380 390 400 410 420 GTFNDGAPGP PGLPGRPGNP GPPGTDGYPG APGPAGPIGN TGGPGLPGYP GNEGLPGPKG 430 440 450 460 470 480 DKGDGGIPGA PGVSGPSGIP GLPGPKGEPG YRGTPGQSIP GLPGKDGKPG LDGAPGRKGE 490 500 510 520 530 540 NGLPGVRGPP GDSLNGLPGA PGQRGAPGPN GYDGRDGVNG LPGAPGTKGD RGGTCSACAP 550 560 570 580 590 600 GTKGEKGLPG YSGQPGPQGD RGLPGMPGPV GDAGDDGLPG PAGRPGSPGP PGQDGFPGLP 610 620 630 640 650 660 GQKGEPTQLT LRPGPPGYPG LKGENGFPGQ PGVDGLPGPS GPVGPPGAPG YPGEKGDAGL 670 680 690 700 710 720 PGLSGKPGQD GLPGLPGNKG EAGYGQPGQP GFPGAKGDGG LPGLPGTPGL QGMPGEPAPE 730 740 750 760 770 780 NQVNPAPPGQ PGLPGLPGTK GEGGYPGRPG EVGQPGFPGL PGMKGDSGLP GPPGLPGHPG 790 800 810 820 830 840 VPGDKGFGGV PGLPGIPGPK GDVGNPGLPG LNGQKGEPGV GVPGQPGSPG FPGLKGDAGL 850 860 870 880 890 900 PGLPGTPGLE GQRGFPGAPG LKGGDGLPGL SGQPGYPGEK GDAGLPGVPG REGSPGFPGQ 910 920 930 940 950 960 DGLPGVPGMK GEDGLPGLPG VTGLKGDLGA PGQSGAPGLP GAPGYPGMKG NAGIPGVPGF 970 980 990 1000 1010 1020 KGDGGLPGLP GLNGPKGEPG VPGMPGTPGM KGNGGLPGLP GRDGLSGVPG MKGDRGFNGL 1030 1040 1050 1060 1070 1080 PGEKGEAGPA ARDGQKGDAG LPGQPGLRGP QGPSGLPGVP GFKGETGLPG YGQPGQPGEK 1090 1100 1110 1120 1130 1140 GLPGIPGKAG RQGAPGSPGQ DGLPGFPGMK GESGYPGQDG LPGRDGLPGV PGQKGDLGQS 1150 1160 1170 1180 1190 1200 GQPGLSGAPG LDGQPGVPGI RGDKGQGGLP GIPGDRGMDG YPGQKGENGY PGQPGLPGLG 1210 1220 1230 1240 1250 1260 GEKGFAGTPG FPGLKGSPGY PGQDGLPGIP GLKGDSGFPG QPGQEGLPGL SGEKGMGGLP 1270 1280 1290 1300 1310 1320 GMPGQPGQSI AGPVGPPGAP GLQGKDGFPG LPGQKGESGL SGLPGAPGLK GESGMPGFPG 1330 1340 1350 1360 1370 1380 AKGDLGANGI PGKRGEDGLP GVPGRDGQPG IPGLKGEVGG AGLPGQPGFP GIPGLKGEGG 1390 1400 1410 1420 1430 1440 LPGFPGAKGE AGFPGTPGVP GYAGEKGDGG LPGLPGRDGL PGADGPVGPP GPSGPQNLVE 1450 1460 1470 1480 1490 1500 PGEKGLPGLP GAPGLRGEKG MPGLDGPPGN DGPPGLPGQR GNDGYPGAPG LSGEKGMGGL 1510 1520 1530 1540 1550 1560 PGFPGLDGQP GGPGAPGLPG APGAAGPAYR DGFVLVKHSQ TTEVPRCPEG QTKLWDGYSL 1570 1580 1590 1600 1610 1620 LYIEGNEKSH NQDLGHAGSC LQRFSTMPFL FCDFNNVCNY ASRNEKSYWL STSEAIPMMP 1630 1640 1650 1660 1670 1680 VNEREIEPYI SRCAVCEAPA NTIAVHSQTI QIPNCPAGWS SLWIGYSFAM HTGAGAEGGG 1690 1700 1710 1720 1730 1740 QSPSSPGSCL EDFRATPFIE CNGARGSCHY FANKFSFWLT TIDNDSEFKV PESQTLKSGN 1750 LRTRVSRCQV CVKSTDGRH

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Genetic identification, sequence, and alternative splicing of the Caenorhabditis elegans alpha 2(IV) collagen gene." Sibley M.H., Johnson J.J., Mello C.C., Kramer J.M. J. Cell Biol. 123:255-264(1993) [PubMed: 7691828] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], ALTERNATIVE SPLICING, FUNCTION. Strain: Bristol N2.
[2]	"Genome sequence of the nematode C. elegans: a platform for investigating biology." The C. elegans sequencing consortium Science 282:2012-2018(1998) [PubMed: 9851916] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA], ALTERNATIVE SPLICING. Strain: Bristol N2.
[3]	"The two Caenorhabditis elegans basement membrane (type IV) collagen genes are located on separate chromosomes." Guo X., Kramer J.M. J. Biol. Chem. 264:17574-17582(1989) [PubMed: 2793871] [Abstract] Cited for: PRELIMINARY NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1495-1758. Strain: Bristol N2.
[4]	"Mutations in the alpha 2(IV) basement membrane collagen gene of Caenorhabditis elegans produce phenotypes of differing severities." Sibley M.H., Graham P.L., von Mende N., Kramer J.M. EMBO J. 13:3278-3285(1994) [PubMed: 8045258] [Abstract] Cited for: MUTAGENESIS.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBLGenBankDDBJ	Z22964 Genomic DNA. Translation: CAA80536.1. Z22964 Genomic DNA. Translation: CAA80537.1. U22327 Genomic DNA. Translation: AAA64312.1. Sequence problems. U53342 Genomic DNA. Translation: AAA96215.1. U53342 Genomic DNA. Translation: AAA96216.1. J05066 Genomic DNA. Translation: AAA27989.1.
PIR	A34476. T29350. T29351.
RefSeq	NP_510663.1. NP_510664.1.
UniGene	Cel.17195
3D structure databases
HSSP	HSSP built from PDB template 1LI1 based on UniProtKB P08572.
SMR	P17140. Positions 1531-1753.
ModBase	Search...
Protein-protein interaction databases
STRING	P17140.
Proteomic databases
PRIDE	P17140.
Genome annotation databases
Ensembl	F01G12.5a; F01G12.5a; F01G12.5; Caenorhabditis elegans. [Genome view] F01G12.5b.1; F01G12.5b.1; F01G12.5; Caenorhabditis elegans. [Genome view] F01G12.5b.2; F01G12.5b.2; F01G12.5; Caenorhabditis elegans. [Genome view]
GeneID	181708.
KEGG	cel:F01G12.5.
UCSC	F01G12.5b.1. c. elegans.
Organism-specific databases
WormBase	WBGene00002280. let-2.
WormPep	F01G12.5a. CE04334. [WorfDB] F01G12.5b. CE04335. [WorfDB]
Gene expression databases
ArrayExpress	P17140.
Family and domain databases
InterPro	IPR008160. Collagen. IPR001442. Procollagn4_C. [Graphical view]
Gene3D	G3DSA:2.170.240.10. Procollagn4_C. 1 hit.
Pfam	PF01413. C4. 2 hits. PF01391. Collagen. 22 hits. [Graphical view]
ProDom	PD000007. Clg_helix. 14 hits. PD003923. Procollagn4_C. 2 hits. PD003992. XGLTT_domain. 2 hits. [Graphical view] [Entries sharing at least one domain]
SMART	SM00111. C4. 2 hits. [Graphical view]
PROSITE	PS51403. NC1_IV. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

CO4A2_CAEEL

Accession

Primary (citable) accession number: P17140
Secondary accession number(s): Q19098, Q19099

Entry history

Integrated into UniProtKB/Swiss-Prot:	August 1, 1990
Last sequence update:	October 1, 1994
Last modified:	November 3, 2009
This is version 100 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

Caenorhabditis annotation project