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40  structures 7559  species 5  interactions 8742  sequences 76  architectures

Family: CPSase_L_D3 (PF02787)

Summary: Carbamoyl-phosphate synthetase large chain, oligomerisation domain

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This is the Wikipedia entry entitled "Carbamoyl phosphate synthetase". More...

Carbamoyl phosphate synthetase Edit Wikipedia article

CPSase large subunit ATP-binding domain
PDB 1dv2 EBI.jpg
the structure of biotin carboxylase, mutant e288k, complexed with atp
Identifiers
Symbol CPSase_L_D2
Pfam PF02786
Pfam clan CL0179
InterPro IPR005479
PROSITE PDOC00676
SCOP 1bnc
SUPERFAMILY 1bnc
CPSase large subunit oligomerisation domain
PDB 1bxr EBI.jpg
structure of carbamoyl phosphate synthetase complexed with the atp analog amppnp
Identifiers
Symbol CPSase_L_D3
Pfam PF02787
InterPro IPR005480
PROSITE PDOC00676
SCOP 1bnc
SUPERFAMILY 1bnc
CPSase large subunit N-terminal domain
PDB 1ulz EBI.jpg
crystal structure of the biotin carboxylase subunit of pyruvate carboxylase
Identifiers
Symbol CPSase_L_chain
Pfam PF00289
InterPro IPR005481
PROSITE PDOC00676
SCOP 1bnc
SUPERFAMILY 1bnc
CPSase small subunit N-terminal domain
PDB 1kee EBI.jpg
inactivation of the amidotransferase activity of carbamoyl phosphate synthetase by the antibiotic acivicin
Identifiers
Symbol CPSase_sm_chain
Pfam PF00988
InterPro IPR002474
PROSITE PDOC00676
SCOP 1jdb
SUPERFAMILY 1jdb

Carbamoyl phosphate synthetase catalyzes the ATP-dependent synthesis of carbamoyl phosphate from glutamine (EC 6.3.5.5) or ammonia (EC 6.3.4.16) and bicarbonate.[1] This enzyme catalyzes the reaction of ATP and bicarbonate to produce carbamoyl phosphate and ADP. Carbomoyl phosphate reacts with ammonia to give carbamate. In turn, carbamate reacts with a second ATP to give carbamoyl phosphate plus ADP.

It represents the first committed step in pyrimidine and arginine biosynthesis in prokaryotes and eukaryotes, and in the urea cycle in most terrestrial vertebrates.[2] Most prokaryotes carry one form of CPSase that participates in both arginine and pyrimidine biosynthesis, however certain bacteria can have separate forms.

There are three different forms that serve very different functions:

Mechanism[edit]

Carbamoyl phosphate synthase has three main steps in its mechanism and is, in essence, irreversible.[4]

  1. Bicarbonate ion is phosphorylated with ATP to create carboxylphosphate.
  2. The carboxylphosphate then reacts with ammonia to form carbamic acid, releasing inorganic phosphate.
  3. A second molecule of ATP then phosphorylates carbamic acid, creating carbamoyl phosphate.

The activity of the enzyme is known to be inhibited by both Tris and HEPES buffers.[5]

Structure[edit]

Carbamoyl phosphate synthase (CPSase) is a heterodimeric enzyme composed of a small and a large subunit (with the exception of CPSase III, which is composed of a single polypeptide that may have arisen from gene fusion of the glutaminase and synthetase domains).[2][3][6] CPSase has three active sites, one in the small subunit and two in the large subunit. The small subunit contains the glutamine binding site and catalyses the hydrolysis of glutamine to glutamate and ammonia, which in turn used by the large chain to synthesize carbamoyl phosphate. The small subunit has a 3-layer beta/beta/alpha structure, and is thought to be mobile in most proteins that carry it. The C-terminal domain of the small subunit of CPSase has glutamine amidotransferase activity. The large subunit has two homologous carboxy phosphate domains, both of which have ATP-binding sites; however, the N-terminal carboxy phosphate domain catalyses the phosphorylation of biocarbonate, while the C-terminal domain catalyses the phosphorylation of the carbamate intermediate.[7] The carboxy phosphate domain found duplicated in the large subunit of CPSase is also present as a single copy in the biotin-dependent enzymes acetyl-CoA carboxylase (ACC), propionyl-CoA carboxylase (PCCase), pyruvate carboxylase (PC) and urea carboxylase.

The large subunit in bacterial CPSase has four structural domains: the carboxy phosphate domain 1, the oligomerisation domain, the carbamoyl phosphate domain 2 and the allosteric domain.[8] CPSase heterodimers from Escherichia coli contain two molecular tunnels: an ammonia tunnel and a carbamate tunnel. These inter-domain tunnels connect the three distinct active sites, and function as conduits for the transport of unstable reaction intermediates (ammonia and carbamate) between successive active sites.[9] The catalytic mechanism of CPSase involves the diffusion of carbamate through the interior of the enzyme from the site of synthesis within the N-terminal domain of the large subunit to the site of phosphorylation within the C-terminal domain.

References[edit]

  1. ^ Simmer JP, Kelly RE, Scully JL, Evans DR, Rinker Jr AG (1990). "Mammalian carbamyl phosphate synthetase (CPS). DNA sequence and evolution of the CPS domain of the Syrian hamster multifunctional protein CAD". J. Biol. Chem. 265 (18): 10395–10402. PMID 1972379. 
  2. ^ a b Holden HM, Thoden JB, Raushel FM (October 1999). "Carbamoyl phosphate synthetase: an amazing biochemical odyssey from substrate to product". Cell. Mol. Life Sci. 56 (5–6): 507–22. doi:10.1007/s000180050448. PMID 11212301. 
  3. ^ a b Saha N, Datta S, Kharbuli ZY, Biswas K, Bhattacharjee A (July 2007). "Air-breathing catfish, Clarias batrachus upregulates glutamine synthetase and carbamyl phosphate synthetase III during exposure to high external ammonia". Comp. Biochem. Physiol. B, Biochem. Mol. Biol. 147 (3): 520–30. doi:10.1016/j.cbpb.2007.03.007. PMID 17451989. 
  4. ^ Biochemistry, 3rd edition, J.M. Berg, J.L. Tymoczko, L. Stryer
  5. ^ Lund, P.; Wiggins, D. (1987). "Inhibition of carbamoyl-phosphate synthase (ammonia) by Tris and Hepes. Effect on Ka for N-acetylglutamate". Biochem. J. 243 (1): 273–276. PMC 1147843. PMID 3606575. 
  6. ^ Raushel FM, Thoden JB, Holden HM (June 1999). "The amidotransferase family of enzymes: molecular machines for the production and delivery of ammonia". Biochemistry 38 (25): 7891–9. doi:10.1021/bi990871p. PMID 10387030. 
  7. ^ Stapleton MA, Javid-Majd F, Harmon MF, Hanks BA, Grahmann JL, Mullins LS, Raushel FM (November 1996). "Role of conserved residues within the carboxy phosphate domain of carbamoyl phosphate synthetase". Biochemistry 35 (45): 14352–61. doi:10.1021/bi961183y. PMID 8916922. 
  8. ^ Thoden JB, Raushel FM, Benning MM, Rayment I, Holden HM (January 1999). "The structure of carbamoyl phosphate synthetase determined to 2.1 A resolution". Acta Crystallogr. D Biol. Crystallogr. 55 (Pt 1): 8–24. doi:10.1107/S0907444998006234. PMID 10089390. 
  9. ^ Kim J, Howell S, Huang X, Raushel FM (October 2002). "Structural defects within the carbamate tunnel of carbamoyl phosphate synthetase". Biochemistry 41 (42): 12575–81. doi:10.1021/bi020421o. PMID 12379099. 

External links[edit]

This article incorporates text from the public domain Pfam and InterPro IPR005479

This article incorporates text from the public domain Pfam and InterPro IPR005480

This article incorporates text from the public domain Pfam and InterPro IPR005481

This article incorporates text from the public domain Pfam and InterPro IPR002474

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

Carbamoyl-phosphate synthetase large chain, oligomerisation domain Provide feedback

Carbamoyl-phosphate synthase catalyses the ATP-dependent synthesis of carbamyl-phosphate from glutamine or ammonia and bicarbonate. The carbamoyl-phosphate synthase (CPS) enzyme in prokaryotes is a heterodimer of a small and large chain.

Literature references

  1. Thoden JB, Raushel FM, Benning MM, Rayment I, Holden HM; , Acta Crystallogr D Biol Crystallogr 1999;55:8-24.: The structure of carbamoyl phosphate synthetase determined to 2.1 A resolution. PUBMED:10089390 EPMC:10089390


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR005480

This entry represents the oligomerisation domain found in the large subunit of carbamoyl phosphate synthases as well as in certain other carboxy phsophate domain-containing enzymes. This domain forms a primarily alpha-helical fold [PUBMED:10089390].

Domain organisation

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(2587)
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(910)
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(95)
Full
(8742)
Representative proteomes NCBI
(7541)
Meta
(2587)
RP15
(471)
RP35
(910)
RP55
(1212)
RP75
(1436)
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  Seed
(95)
Full
(8742)
Representative proteomes NCBI
(7541)
Meta
(2587)
RP15
(471)
RP35
(910)
RP55
(1212)
RP75
(1436)
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Curation and family details

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Seed source: ref [1]
Previous IDs: none
Type: Domain
Author: Griffiths-Jones SR
Number in seed: 95
Number in full: 8742
Average length of the domain: 120.70 aa
Average identity of full alignment: 43 %
Average coverage of the sequence by the domain: 14.93 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 25.3 25.3
Trusted cut-off 25.3 25.8
Noise cut-off 25.1 25.2
Model length: 123
Family (HMM) version: 14
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Interactions

There are 5 interactions for this family. More...

CPSase_L_D2 CPSase_sm_chain GATase CPSase_L_D3 CPSase_L_chain

Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the CPSase_L_D3 domain has been found. There are 40 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.

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