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Reviewed, UniProtKB/Swiss-Prot P31327 (CPSM_HUMAN)

Last modified July 7, 2009. Version 113. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (6) | Third-party data | Customize display text xml rdf/xml gff fasta
Names and origin · Protein attributes · General annotation (Comments) · Ontologies · Binary interactions · Alternative products · Sequence annotation (Features) · Sequences · References · Web resources · Cross-references · Entry information · Relevant documents

Names and origin

Protein namesRecommended name:
    Carbamoyl-phosphate synthase [ammonia], mitochondrial
    EC=6.3.4.16
Alternative name(s):
    Carbamoyl-phosphate synthetase I
      Short name=CPSase I
Gene names
Name: CPS1
OrganismHomo sapiens (Human) [Complete proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length1500 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level.

General annotation (Comments)

Function

Involved in the urea cycle of ureotelic animals where the enzyme plays an important role in removing excess ammonia from the cell.

Catalytic activity

2 ATP + NH3 + CO2 + H2O = 2 ADP + phosphate + carbamoyl phosphate.

Enzyme regulation

Requires N-acetylglutamate as an allosteric activator.

Subcellular location

Mitochondrion.

Tissue specificity

Primarily in the liver and small intestine.

Domain

The type-1 glutamine amidotransferase domain is defective.

Involvement in disease

Defects in CPS1 are the cause of carbamoyl phosphate synthetase 1 deficiency (CPS1D) [MIM:237300]. CPS1D is an autosomal recessive disorder of the urea cycle causing hyperammonemia. Clinical features include protein intolerance, intermittent ataxia, seizures, lethargy, developmental delay and mental retardation. Ref.2 Ref.5 Ref.6 Ref.9 Ref.11 Ref.12

Defects in CPS1 are associated with susceptibility to familial persistent pulmonary hypertension of the newborn [MIM:265380]; also called congenital alveolar capillary dysplasia or CACD. Failure of the transition to a cardiorespiratory circulation at birth results in persistent pulmonary hypertension of the newborn. Characterized by elevated pulmonary vascular resistance with extrapulmonary right-to-left shunting of blood across the patent ductus arteriosus or the foramen ovale, persistent pulmonary hypertension can cause life-threatening hypoxemia in newborn infants. Transitional pulmonary hypertension occurs in 1.9 of every 1000 newborn infants and is associated with a mortality rate of 11 percent.

Sequence similarities

Contains 2 ATP-grasp domains.

Contains 1 glutamine amidotransferase type-1 domain.

Ontologies

Keywords
   Biological processUrea cycle
   Cellular componentMitochondrion
   Coding sequence diversityAlternative splicing
Polymorphism
   DiseaseDisease mutation
   DomainRepeat
Transit peptide
   LigandATP-binding
Nucleotide-binding
   Molecular functionLigase
   PTMAcetylation
Phosphoprotein
   Technical term3D-structure
Allosteric enzyme
Complete proteome
Gene Ontology (GO)
   Biological processcarbamoyl phosphate biosynthetic process

Inferred from mutant phenotype. Source: UniProtKB

citrulline biosynthetic process

Non-traceable author statement. Source: UniProtKB

glutamine metabolic process

Inferred from electronic annotation. Source: InterPro

glycogen catabolic process Ref.2

Inferred from mutant phenotype. Source: UniProtKB

nitric oxide metabolic process

Inferred from mutant phenotype. Source: UniProtKB

positive regulation of vasodilation

Inferred from mutant phenotype. Source: UniProtKB

response to lipopolysaccharide

Inferred from direct assay. Source: UniProtKB

triglyceride catabolic process Ref.2

Inferred from mutant phenotype. Source: UniProtKB

urea cycle Ref.1

Non-traceable author statement. Source: UniProtKB

   Cellular componentmitochondrial nucleoid

Inferred from direct assay. Source: UniProtKB

   Molecular functionATP binding

Inferred from electronic annotation. Source: UniProtKB-KW

carbamoyl-phosphate synthase (ammonia) activity Ref.2

Inferred from mutant phenotype. Source: UniProtKB

protein binding

Inferred from physical interaction. Source: IntAct

Complete GO annotation...

Binary interactions

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: P31327-1)

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 2 (identifier: P31327-2)

The sequence of this isoform differs from the canonical sequence as follows:
     1-451: Missing.
Note: No experimental confirmation available.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Transit peptide1 – 3838Mitochondrion By similarity
Chain39 – 15001462Carbamoyl-phosphate synthase [ammonia], mitochondrial
PRO_0000029897

Regions

Domain219 – 404186Glutamine amidotransferase type-1
Domain551 – 743193ATP-grasp 1
Domain1093 – 1284192ATP-grasp 2
Region39 – 218180Anthranilate phosphoribosyltransferase homolog

Amino acid modifications

Modified residue551N6-acetyllysine By similarity
Modified residue1191N6-acetyllysine By similarity
Modified residue2871N6-acetyllysine By similarity
Modified residue5271N6-acetyllysine By similarity
Modified residue8411N6-acetyllysine By similarity
Modified residue8921N6-acetyllysine By similarity
Modified residue8981Phosphoserine By similarity
Modified residue12911N6-acetyllysine By similarity

Natural variations

Alternative sequence1 – 451451Missing in isoform 2.
VSP_009332
Natural variant3371H → R in CPS1D. dbSNP rs28940283. Ref.9
VAR_014077
Natural variant3441T → A: dbSNP rs1047883. Ref.2 Ref.3
VAR_006834
Natural variant4571V → G in CPS1D. Ref.5
VAR_017562
Natural variant5441T → M in CPS1D. Ref.2
VAR_006835
Natural variant8101Q → R in CPS1D. Ref.5
VAR_017563
Natural variant8431L → S in CPS1D. Ref.6 Ref.12
VAR_017564
Natural variant8501R → H in CPS1D. Ref.11
VAR_030675
Natural variant8751K → E in CPS1D. Ref.6 Ref.12
VAR_017565
Natural variant9181S → P in CPS1D. Ref.11
VAR_030676
Natural variant12661F → S: dbSNP rs1047886. Ref.1
VAR_017566
Natural variant12831M → L: dbSNP rs1047887. Ref.1
VAR_017567
Natural variant13761G → S Ref.3
VAR_017568
Natural variant14061T → N 30-40% higher activity; risk factor for persistent pulmonary hypertension of the newborn. dbSNP rs1047891. Ref.5 Ref.3 Ref.1 Ref.10
VAR_017569

Experimental info

Sequence conflict1111A → S in BAA14328. Ref.1
Sequence conflict2791R → Q in BAA14328. Ref.1
Sequence conflict3381G → C in BAA14328. Ref.1
Sequence conflict718 – 7225RLSRS → KMSPN in BAA14328. Ref.1
Sequence conflict7291A → T in BAA14328. Ref.1
Sequence conflict7491E → G in BAA14328. Ref.1
Sequence conflict9121F → L in CAE45707. Ref.6
Sequence conflict1161 – 11622EH → AT in BAA14328. Ref.1
Sequence conflict1204 – 12052GD → EN in BAA14328. Ref.1
Sequence conflict12541I → N in BAA14328. Ref.1
Sequence conflict13031A → V in BAA14328. Ref.1

Secondary structure

......................... 1500
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 [UniParc].

Last modified December 15, 1998. Version 2.
Checksum: E53A22D77563961D

FASTA1,500164,939
        10         20         30         40         50         60 
MTRILTAFKV VRTLKTGFGF TNVTAHQKWK FSRPGIRLLS VKAQTAHIVL EDGTKMKGYS 

        70         80         90        100        110        120 
FGHPSSVAGE VVFNTGLGGY PEAITDPAYK GQILTMANPI IGNGGAPDTT ALDELGLSKY 

       130        140        150        160        170        180 
LESNGIKVSG LLVLDYSKDY NHWLATKSLG QWLQEEKVPA IYGVDTRMLT KIIRDKGTML 

       190        200        210        220        230        240 
GKIEFEGQPV DFVDPNKQNL IAEVSTKDVK VYGKGNPTKV VAVDCGIKNN VIRLLVKRGA 

       250        260        270        280        290        300 
EVHLVPWNHD FTKMEYDGIL IAGGPGNPAL AEPLIQNVRK ILESDRKEPL FGISTGNLIT 

       310        320        330        340        350        360 
GLAAGAKTYK MSMANRGQNQ PVLNITNKQA FITAQNHGYA LDNTLPAGWK PLFVNVNDQT 

       370        380        390        400        410        420 
NEGIMHESKP FFAVQFHPEV TPGPIDTEYL FDSFFSLIKK GKATTITSVL PKPALVASRV 

       430        440        450        460        470        480 
EVSKVLILGS GGLSIGQAGE FDYSGSQAVK AMKEENVKTV LMNPNIASVQ TNEVGLKQAD 

       490        500        510        520        530        540 
TVYFLPITPQ FVTEVIKAEQ PDGLILGMGG QTALNCGVEL FKRGVLKEYG VKVLGTSVES 

       550        560        570        580        590        600 
IMATEDRQLF SDKLNEINEK IAPSFAVESI EDALKAADTI GYPVMIRSAY ALGGLGSGIC 

       610        620        630        640        650        660 
PNRETLMDLS TKAFAMTNQI LVEKSVTGWK EIEYEVVRDA DDNCVTVCNM ENVDAMGVHT 

       670        680        690        700        710        720 
GDSVVVAPAQ TLSNAEFQML RRTSINVVRH LGIVGECNIQ FALHPTSMEY CIIEVNARLS 

       730        740        750        760        770        780 
RSSALASKAT GYPLAFIAAK IALGIPLPEI KNVVSGKTSA CFEPSLDYMV TKIPRWDLDR 

       790        800        810        820        830        840 
FHGTSSRIGS SMKSVGEVMA IGRTFEESFQ KALRMCHPSI EGFTPRLPMN KEWPSNLDLR 

       850        860        870        880        890        900 
KELSEPSSTR IYAIAKAIDD NMSLDEIEKL TYIDKWFLYK MRDILNMEKT LKGLNSESMT 

       910        920        930        940        950        960 
EETLKRAKEI GFSDKQISKC LGLTEAQTRE LRLKKNIHPW VKQIDTLAAE YPSVTNYLYV 

       970        980        990       1000       1010       1020 
TYNGQEHDVN FDDHGMMVLG CGPYHIGSSV EFDWCAVSSI RTLRQLGKKT VVVNCNPETV 

      1030       1040       1050       1060       1070       1080 
STDFDECDKL YFEELSLERI LDIYHQEACG GCIISVGGQI PNNLAVPLYK NGVKIMGTSP 

      1090       1100       1110       1120       1130       1140 
LQIDRAEDRS IFSAVLDELK VAQAPWKAVN TLNEALEFAK SVDYPCLLRP SYVLSGSAMN 

      1150       1160       1170       1180       1190       1200 
VVFSEDEMKK FLEEATRVSQ EHPVVLTKFV EGAREVEMDA VGKDGRVISH AISEHVEDAG 

      1210       1220       1230       1240       1250       1260 
VHSGDATLML PTQTISQGAI EKVKDATRKI AKAFAISGPF NVQFLVKGND VLVIECNLRA 

      1270       1280       1290       1300       1310       1320 
SRSFPFVSKT LGVDFIDVAT KVMIGENVDE KHLPTLDHPI IPADYVAIKA PMFSWPRLRD 

      1330       1340       1350       1360       1370       1380 
ADPILRCEMA STGEVACFGE GIHTAFLKAM LSTGFKIPQK GILIGIQQSF RPRFLGVAEQ 

      1390       1400       1410       1420       1430       1440 
LHNEGFKLFA TEATSDWLNA NNVPATPVAW PSQEGQNPSL SSIRKLIRDG SIDLVINLPN 

      1450       1460       1470       1480       1490       1500 
NNTKFVHDNY VIRRTAVDSG IPLLTNFQVT KLFAEAVQKS RKVDSKSLFH YRQYSAGKAA 

« Hide

Isoform 2.

Checksum: 74C9ABBFABAD2AD2
Show »

FASTA1,049116,038

References

« Hide 'large scale' references
[1]"Cloning and sequence of a cDNA encoding human carbamyl phosphate synthetase I: molecular analysis of hyperammonemia."
Haraguchi Y., Uchino T., Takiguchi M., Endo F., Mori M., Matsuda I.
Gene 107:335-340(1991) [PubMed: 1840546] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), VARIANTS SER-1266; LEU-1283 AND ASN-1406.
Tissue: Liver.
[2]"Prenatal diagnosis of carbamoyl phosphate synthetase I deficiency by identification of a missense mutation in CPS1."
Finckh U., Kohlschuetter A., Schaefer H., Sperhake K., Colombo J.-P., Gal A.
Hum. Mutat. 12:206-211(1998) [PubMed: 9711878] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), VARIANT CPS1D MET-544, VARIANT ALA-344.
Tissue: Liver.
[3]"Characterization of genomic structure and polymorphisms in the human carbamyl phosphate synthetase I gene."
Summar M.L., Hall L.D., Eeds A.M., Hutcheson H.B., Kuo A.N., Willis A.S., Rubio V., Arvin M.K., Schofield J.P., Dawson E.P.
Gene 311:51-57(2003) [PubMed: 12853138] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), VARIANTS ALA-344; SER-1376 AND ASN-1406.
[4]"Cloning of an isoform of CPS1 gene related to spermatogenesis."
Huo R., Zhu H., Huang X.Y., Xu Z.Y., Lu L., Xu M., Yin L.L., Li J.M., Zhou Z.M., Sha J.H.
Submitted (JUN-2003) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2).
Tissue: Testis.
[5]"Structural organization of the human carbamyl phosphate synthetase I gene (CPS1) and identification of two novel genetic lesions."
Funghini S., Donati M.A., Pasquini E., Zammarchi E., Morrone A.
Hum. Mutat. 22:340-341(2003) [PubMed: 12955727] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] (ISOFORM 1), VARIANTS CPS1D GLY-457 AND ARG-810, VARIANT ASN-1406.
[6]"Gene structure of human carbamylphosphate synthetase 1 and novel mutations in patients with neonatal onset."
Haeberle J., Schmidt E., Pauli S., Rapp B., Christensen E., Wermuth B., Koch H.G.
Hum. Mutat. 21:444-444(2003) [PubMed: 12655559] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] (ISOFORM 1), VARIANTS CPS1D SER-843 AND GLU-875.
[7]"The full-ORF clone resource of the German cDNA consortium."
Bechtel S., Rosenfelder H., Duda A., Schmidt C.P., Ernst U., Wellenreuther R., Mehrle A., Schuster C., Bahr A., Blocker H., Heubner D., Hoerlein A., Michel G., Wedler H., Kohrer K., Ottenwalder B., Poustka A., Wiemann S., Schupp I.
BMC Genomics 8:399-399(2007) [PubMed: 17974005] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 795-1500.
Tissue: Small intestine.
[8]Colinge J., Superti-Furga G., Bennett K.L.
Submitted (OCT-2008) to UniProtKB
Cited for: IDENTIFICATION [LARGE SCALE ANALYSIS], MASS SPECTROMETRY.
[9]"Novel mutations (H337R and 238-362del) in the CPS1 gene cause carbamoyl phosphate synthetase I deficiency."
Aoshima T., Kajita M., Sekido Y., Kikuchi S., Yasuda I., Saheki T., Watanabe K., Shimokata K., Niwa T.
Hum. Hered. 52:99-101(2001) [PubMed: 11474210] [Abstract]
Cited for: VARIANT CPS1D ARG-337.
[10]"Neonatal pulmonary hypertension -- urea-cycle intermediates, nitric oxide production, and carbamoyl-phosphate synthetase function."
Pearson D.L., Dawling S., Walsh W.F., Haines J.L., Christman B.W., Bazyk A., Scott N., Summar M.L.
N. Engl. J. Med. 344:1832-1838(2001) [PubMed: 11407344] [Abstract]
Cited for: VARIANT ASN-1406.
[11]"Mutational analysis of carbamoylphosphate synthetase I deficiency in three Japanese patients."
Wakutani Y., Nakayasu H., Takeshima T., Adachi M., Kawataki M., Kihira K., Sawada H., Bonno M., Yamamoto H., Nakashima K.
J. Inherit. Metab. Dis. 27:787-788(2004) [PubMed: 15617192] [Abstract]
Cited for: VARIANTS CPS1D HIS-850 AND PRO-918.
[12]"Genetic approach to prenatal diagnosis in urea cycle defects."
Haeberle J., Koch H.G.
Prenat. Diagn. 24:378-383(2004) [PubMed: 15164414] [Abstract]
Cited for: VARIANTS CPS1D SER-843 AND GLU-875.
+Additional computationally mapped references.

Web resources

Cross-references

Sequence databases

D90282 mRNA. Translation: BAA14328.1.
Y15793 mRNA. Translation: CAA75785.1.
AF154830 mRNA. Translation: AAD38072.1.
AY317138 mRNA. Translation: AAP84318.1.
AY167007 expand/collapse EMBL AC list , AY166970, AY166971, AY166972, AY166973, AY166974, AY166975, AY166976, AY166977, AY166978, AY166979, AY166980, AY166981, AY166982, AY166983, AY166984, AY166985, AY166986, AY166987, AY166988, AY166989, AY166990, AY166991, AY166992, AY166993, AY166994, AY166995, AY166996, AY166997, AY166998, AY166999, AY167000, AY167001, AY167002, AY167003, AY167004, AY167005, AY167006 Genomic DNA. Translation: AAO31763.1.
AF536523 Genomic DNA. Translation: AAN77181.1.
BX640601 mRNA. Translation: CAE45707.1.
IPIIPI00011062.
IPI00397498.
PIRJQ1348.
RefSeqNP_001116105.1.
NP_001116106.1.
NP_001866.2.
UniGeneHs.149252

3D structure databases

EntryMethodResolution (Å)ChainPositionsPDBsum
2YVQX-ray1.98A1343-1478[»]
ModBaseSearch...

Protein-protein interaction databases

IntActP31327. 2 interactions.

Protein family/group databases

MEROPSC26.951.

PTM databases

PhosphoSiteP31327.

Proteomic databases

PRIDEP31327.

Genome annotation databases

EnsemblENSG00000021826. Homo sapiens. [Contig view]
GeneID1373.
KEGGhsa:1373.
UCSCuc002vee.2. human.
uc010fus.1. human.

Organism-specific databases

GeneCardsGC02P211050.
HGNCHGNC:2323. CPS1.
HPACAB003781.
MIM237300. phenotype.
265380. phenotype.
608307. gene.
Orphanet147. Carbamoylphosphate synthetase deficiency.
PharmGKBPA26840.
GenAtlasSearch...

Phylogenomic databases

HOVERGENP31327.
OMAP31327. MDLSTKA.

Enzyme and pathway databases

BioCycMetaCyc:MON-11364.
BRENDA6.3.4.16. 247.
ReactomeREACT_13. Metabolism of amino acids.

Gene expression databases

ArrayExpressP31327.
BgeeP31327.
CleanExHS_CPS1.
GermOnlineENSG00000021826. Homo sapiens.

Family and domain databases

InterProIPR011761. ATP-grasp.
IPR013816. ATP_grasp_subdomain_2.
IPR001317. CarbamoylP_synth_GATase.
IPR005483. CarbamoylP_synth_lsu.
IPR005479. CarbamoylP_synth_lsu_ATP-bd.
IPR006275. CarbamoylP_synth_lsu_Gln-dep.
IPR005481. CarbamoylP_synth_lsu_N.
IPR005480. CarbamoylP_synth_lsu_oligo.
IPR006274. CarbamoylP_synth_ssu.
IPR002474. CarbamoylP_synth_ssu_N.
IPR017926. GATASE_1.
IPR000991. GATase_class1_C.
IPR011607. MGS.
IPR013817. Pre-ATP_grasp.
[Graphical view]
Gene3DG3DSA:3.30.470.20. ATP_grasp_subdomain_2. 2 hits.
G3DSA:3.40.50.20. Pre-ATP_grasp. 1 hit.
PfamPF00289. CPSase_L_chain. 2 hits.
PF02786. CPSase_L_D2. 2 hits.
PF02787. CPSase_L_D3. 1 hit.
PF00988. CPSase_sm_chain. 1 hit.
PF00117. GATase. 1 hit.
PF02142. MGS. 1 hit.
[Graphical view]
PRINTSPR00098. CPSASE.
PR00099. CPSGATASE.
TIGRFAMsTIGR01369. CPSaseII_lrg. 1 hit.
TIGR01368. CPSaseIIsmall. 1 hit.
PROSITEPS50975. ATP_GRASP. 2 hits.
PS00866. CPSASE_1. 2 hits.
PS00867. CPSASE_2. 2 hits.
PS51273. GATASE_TYPE_1. 1 hit.
[Graphical view]
ProtoNetSearch...

Other Resources

NextBio5565.
SOURCESearch...

Entry information

Entry nameCPSM_HUMAN
AccessionPrimary (citable) accession number: P31327
Secondary accession number(s): O43774, Q7Z5I5
Entry history
Integrated into UniProtKB/Swiss-Prot: July 1, 1993
Last sequence update: December 15, 1998
Last modified: July 7, 2009
This is version 113 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation projectHPI (Human Proteome Initiative)

Relevant documents

Human chromosome 2

Human chromosome 2: entries, gene names and cross-references to MIM

Human entries with polymorphisms or disease mutations

List of human entries with polymorphisms or disease mutations

Human polymorphisms and disease mutations

Index of human polymorphisms and disease mutations

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Names and origin · Protein attributes · General annotation (Comments) · Ontologies · Binary interactions · Alternative products · Sequence annotation (Features) · Sequences · References · Web resources · Cross-references · Entry information · Relevant documents