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HAMAP rule MF_01210

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General rule information [?]

Accession MF_01210
Dates 19-JUL-2002 (Created)
14-MAY-2024 (Last updated, Version 52)
Name CPSase_L_chain
Scope(s) Bacteria
Archaea
Template(s) P00968 (CARB_ECOLI); O50302 (CARB_GEOSE); Q9ZB63 (CARY_GEOSE); O32771 (CARB_LACLM); P77886 (CARB_LACPL); Q9RLS9 (CARY_LACPL); [ Recover all ]
Triggered by
case c? <OC:Bacteria>
HAMAP; MF_01210_B (Get profile general information and statistics)
end case
case c? <OC:Archaea>
HAMAP; MF_01210_A (Get profile general information and statistics)
end case

Propagated annotation [?]

Identifier, protein and gene names [?]

Identifier CARB
Protein name RecName: Full=Carbamoyl phosphate synthase large chain;
                 EC=6.3.4.16;
                 EC=6.3.5.5;
AltName: Full=Carbamoyl phosphate synthetase ammonia chain;
Gene name Name=carB;

Comments [?]

FUNCTIONLarge subunit of the glutamine-dependent carbamoyl phosphate synthetase (CPSase). CPSase catalyzes the formation of carbamoyl phosphate from the ammonia moiety of glutamine, carbonate, and phosphate donated by ATP, constituting the first step of 2 biosynthetic pathways, one leading to arginine and/or urea and the other to pyrimidine nucleotides. The large subunit (synthetase) binds the substrates ammonia (free or transferred from glutamine from the small subunit), hydrogencarbonate and ATP and carries out an ATP-coupled ligase reaction, activating hydrogencarbonate by forming carboxy phosphate which reacts with ammonia to form carbamoyl phosphate.
CATALYTIC ACTIVITY Reaction=2 ATP + H2O + hydrogencarbonate + L-glutamine = 2 ADP + carbamoyl phosphate + 2 H(+) + L-glutamate + phosphate; Xref=Rhea:RHEA:18633, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:17544, ChEBI:CHEBI:29985, ChEBI:CHEBI:30616, ChEBI:CHEBI:43474, ChEBI:CHEBI:58228, ChEBI:CHEBI:58359, ChEBI:CHEBI:456216; EC=6.3.5.5;
CATALYTIC ACTIVITY[Carbamoyl phosphate synthase large chain]: Reaction=2 ATP + hydrogencarbonate + NH4(+) = 2 ADP + carbamoyl phosphate + 2 H(+) + phosphate; Xref=Rhea:RHEA:18029, ChEBI:CHEBI:15378, ChEBI:CHEBI:17544, ChEBI:CHEBI:28938, ChEBI:CHEBI:30616, ChEBI:CHEBI:43474, ChEBI:CHEBI:58228, ChEBI:CHEBI:456216; EC=6.3.4.16;
COFACTOR Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Name=Mn(2+); Xref=ChEBI:CHEBI:29035; Note=Binds 4 Mg(2+) or Mn(2+) ions per subunit.
PATHWAYAmino-acid biosynthesis; L-arginine biosynthesis; carbamoyl phosphate from bicarbonate: step 1/1.
PATHWAYPyrimidine metabolism; UMP biosynthesis via de novo pathway; (S)-dihydroorotate from bicarbonate: step 1/3.
SUBUNITComposed of two chains; the small (or glutamine) chain promotes the hydrolysis of glutamine to ammonia, which is used by the large (or ammonia) chain to synthesize carbamoyl phosphate. Tetramer of heterodimers (alpha,beta)4.
DOMAINThe large subunit is composed of 2 ATP-grasp domains that are involved in binding the 2 ATP molecules needed for carbamoyl phosphate synthesis. The N-terminal ATP-grasp domain (referred to as the carboxyphosphate synthetic component) catalyzes the ATP-dependent phosphorylation of hydrogencarbonate to carboxyphosphate and the subsequent nucleophilic attack by ammonia to form a carbamate intermediate. The C-terminal ATP-grasp domain (referred to as the carbamoyl phosphate synthetic component) then catalyzes the phosphorylation of carbamate with the second ATP to form the end product carbamoyl phosphate. The reactive and unstable enzyme intermediates are sequentially channeled from one active site to the next through the interior of the protein over a distance of at least 96 A.
SIMILARITYBelongs to the CarB family.

Keywords [?]

Amino-acid biosynthesis
Arginine biosynthesis
Pyrimidine biosynthesis
Ligase
Repeat
ATP-binding
Nucleotide-binding

Gene Ontology [?]

GO:0005524; Molecular function:ATP binding
GO:0004088; Molecular function:carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity
GO:0006526; Biological process:arginine biosynthetic process
GO:0044205; Biological process:'de novo' UMP biosynthetic process

Cross-references [?]

Pfam PF00289; CPSase_L_chain; 1;
Pfam PF02142; MGS; 1;
Pfam PF02786; CPSase_L_D2; 1;
Pfam PF02787; CPSase_L_D3; 1;
PRINTS PR00098; CPSASE; 1;
PROSITE PS00866; CPSASE_1; 1;
PROSITE PS00867; CPSASE_2; 1;
PROSITE PS50975; ATP_GRASP; 1-2;
PROSITE PS51855; MGS; 1;
NCBIfam TIGR01369; CPSaseII_lrg; 1;

Features [?]

From: CARB_ECOLI (P00968)
Key From To Description Tag Condition FTGroup
case <OC:Bacteria>
REGION Nter 403 /note="Carboxyphosphate synthetic domain"
REGION 404 553 /note="Oligomerization domain"
REGION 554 936 /note="Carbamoyl phosphate synthetic domain"
REGION 937 Cter /note="Allosteric domain"
BINDING 129 129 /ligand="ATP"
/ligand_id="ChEBI:CHEBI:30616"
/ligand_label="1"		 R
BINDING 169 169 /ligand="ATP"
/ligand_id="ChEBI:CHEBI:30616"
/ligand_label="1"		 R
BINDING 175 175 /ligand="ATP"
/ligand_id="ChEBI:CHEBI:30616"
/ligand_label="1"		 G
BINDING 176 176 /ligand="ATP"
/ligand_id="ChEBI:CHEBI:30616"
/ligand_label="1"		 G
BINDING 208 208 /ligand="ATP"
/ligand_id="ChEBI:CHEBI:30616"
/ligand_label="1"		 [EKQR]
BINDING 210 210 /ligand="ATP"
/ligand_id="ChEBI:CHEBI:30616"
/ligand_label="1"		 [LIV]
BINDING 215 215 /ligand="ATP"
/ligand_id="ChEBI:CHEBI:30616"
/ligand_label="1"		 E
BINDING 241 241 /ligand="ATP"
/ligand_id="ChEBI:CHEBI:30616"
/ligand_label="1"		 G
BINDING 242 242 /ligand="ATP"
/ligand_id="ChEBI:CHEBI:30616"
/ligand_label="1"		 [IV]
BINDING 243 243 /ligand="ATP"
/ligand_id="ChEBI:CHEBI:30616"
/ligand_label="1"		 H
BINDING 285 285 /ligand="ATP"
/ligand_id="ChEBI:CHEBI:30616"
/ligand_label="1"		 Q
BINDING 285 285 /ligand="Mg(2+)"
/ligand_id="ChEBI:CHEBI:18420"
/ligand_label="1"		 Q
BINDING 285 285 /ligand="Mn(2+)"
/ligand_id="ChEBI:CHEBI:29035"
/ligand_label="1"		 Q
BINDING 299 299 /ligand="ATP"
/ligand_id="ChEBI:CHEBI:30616"
/ligand_label="1"		 E
BINDING 299 299 /ligand="Mg(2+)"
/ligand_id="ChEBI:CHEBI:18420"
/ligand_label="1"		 E
BINDING 299 299 /ligand="Mg(2+)"
/ligand_id="ChEBI:CHEBI:18420"
/ligand_label="2"		 E
BINDING 299 299 /ligand="Mn(2+)"
/ligand_id="ChEBI:CHEBI:29035"
/ligand_label="1"		 E
BINDING 299 299 /ligand="Mn(2+)"
/ligand_id="ChEBI:CHEBI:29035"
/ligand_label="2"		 E
BINDING 301 301 /ligand="Mg(2+)"
/ligand_id="ChEBI:CHEBI:18420"
/ligand_label="2"		 N
BINDING 301 301 /ligand="Mn(2+)"
/ligand_id="ChEBI:CHEBI:29035"
/ligand_label="2"		 N
BINDING 715 715 /ligand="ATP"
/ligand_id="ChEBI:CHEBI:30616"
/ligand_label="2"		 R
BINDING 754 754 /ligand="ATP"
/ligand_id="ChEBI:CHEBI:30616"
/ligand_label="2"
BINDING 756 756 /ligand="ATP"
/ligand_id="ChEBI:CHEBI:30616"
/ligand_label="2"		 [LIV]
BINDING 761 761 /ligand="ATP"
/ligand_id="ChEBI:CHEBI:30616"
/ligand_label="2"		 E
BINDING 786 786 /ligand="ATP"
/ligand_id="ChEBI:CHEBI:30616"
/ligand_label="2"		 G
BINDING 787 787 /ligand="ATP"
/ligand_id="ChEBI:CHEBI:30616"
/ligand_label="2"		 [IV]
BINDING 788 788 /ligand="ATP"
/ligand_id="ChEBI:CHEBI:30616"
/ligand_label="2"		 H
BINDING 789 789 /ligand="ATP"
/ligand_id="ChEBI:CHEBI:30616"
/ligand_label="2"		 S
BINDING 829 829 /ligand="ATP"
/ligand_id="ChEBI:CHEBI:30616"
/ligand_label="2"		 Q
BINDING 829 829 /ligand="Mg(2+)"
/ligand_id="ChEBI:CHEBI:18420"
/ligand_label="3"		 Q
BINDING 829 829 /ligand="Mn(2+)"
/ligand_id="ChEBI:CHEBI:29035"
/ligand_label="3"		 Q
BINDING 841 841 /ligand="ATP"
/ligand_id="ChEBI:CHEBI:30616"
/ligand_label="2"		 E
BINDING 841 841 /ligand="Mg(2+)"
/ligand_id="ChEBI:CHEBI:18420"
/ligand_label="3"		 E
BINDING 841 841 /ligand="Mg(2+)"
/ligand_id="ChEBI:CHEBI:18420"
/ligand_label="4"		 E
BINDING 841 841 /ligand="Mn(2+)"
/ligand_id="ChEBI:CHEBI:29035"
/ligand_label="3"		 E
BINDING 841 841 /ligand="Mn(2+)"
/ligand_id="ChEBI:CHEBI:29035"
/ligand_label="4"		 E
BINDING 843 843 /ligand="Mg(2+)"
/ligand_id="ChEBI:CHEBI:18420"
/ligand_label="4"		 N
BINDING 843 843 /ligand="Mn(2+)"
/ligand_id="ChEBI:CHEBI:29035"
/ligand_label="4"		 N
end case
From: CARB_SULTO (Q970U7)
Key From To Description Tag Condition FTGroup
case <OC:Archaea>
REGION Nter 399 /note="Carboxyphosphate synthetic domain"
REGION 400 548 /note="Oligomerization domain"
REGION 549 930 /note="Carbamoyl phosphate synthetic domain"
REGION 931 Cter /note="Allosteric domain"
BINDING 127 127 /ligand="ATP"
/ligand_id="ChEBI:CHEBI:30616"
/ligand_label="1"		 R
BINDING 167 167 /ligand="ATP"
/ligand_id="ChEBI:CHEBI:30616"
/ligand_label="1"		 R
BINDING 173 173 /ligand="ATP"
/ligand_id="ChEBI:CHEBI:30616"
/ligand_label="1"		 G
BINDING 174 174 /ligand="ATP"
/ligand_id="ChEBI:CHEBI:30616"
/ligand_label="1"		 G
BINDING 206 206 /ligand="ATP"
/ligand_id="ChEBI:CHEBI:30616"
/ligand_label="1"		 [EKQR]
BINDING 208 208 /ligand="ATP"
/ligand_id="ChEBI:CHEBI:30616"
/ligand_label="1"		 [LIV]
BINDING 213 213 /ligand="ATP"
/ligand_id="ChEBI:CHEBI:30616"
/ligand_label="1"		 E
BINDING 239 239 /ligand="ATP"
/ligand_id="ChEBI:CHEBI:30616"
/ligand_label="1"		 G
BINDING 240 240 /ligand="ATP"
/ligand_id="ChEBI:CHEBI:30616"
/ligand_label="1"		 [IV]
BINDING 241 241 /ligand="ATP"
/ligand_id="ChEBI:CHEBI:30616"
/ligand_label="1"		 H
BINDING 282 282 /ligand="ATP"
/ligand_id="ChEBI:CHEBI:30616"
/ligand_label="1"		 Q
BINDING 282 282 /ligand="Mg(2+)"
/ligand_id="ChEBI:CHEBI:18420"
/ligand_label="1"		 Q
BINDING 282 282 /ligand="Mn(2+)"
/ligand_id="ChEBI:CHEBI:29035"
/ligand_label="1"		 Q
BINDING 296 296 /ligand="ATP"
/ligand_id="ChEBI:CHEBI:30616"
/ligand_label="1"		 E
BINDING 296 296 /ligand="Mg(2+)"
/ligand_id="ChEBI:CHEBI:18420"
/ligand_label="1"		 E
BINDING 296 296 /ligand="Mg(2+)"
/ligand_id="ChEBI:CHEBI:18420"
/ligand_label="2"		 E
BINDING 296 296 /ligand="Mn(2+)"
/ligand_id="ChEBI:CHEBI:29035"
/ligand_label="1"		 E
BINDING 296 296 /ligand="Mn(2+)"
/ligand_id="ChEBI:CHEBI:29035"
/ligand_label="2"		 E
BINDING 298 298 /ligand="Mg(2+)"
/ligand_id="ChEBI:CHEBI:18420"
/ligand_label="2"		 N
BINDING 298 298 /ligand="Mn(2+)"
/ligand_id="ChEBI:CHEBI:29035"
/ligand_label="2"		 N
BINDING 710 710 /ligand="ATP"
/ligand_id="ChEBI:CHEBI:30616"
/ligand_label="2"		 R
BINDING 749 749 /ligand="ATP"
/ligand_id="ChEBI:CHEBI:30616"
/ligand_label="2"
BINDING 751 751 /ligand="ATP"
/ligand_id="ChEBI:CHEBI:30616"
/ligand_label="2"		 [LIV]
BINDING 756 756 /ligand="ATP"
/ligand_id="ChEBI:CHEBI:30616"
/ligand_label="2"		 E
BINDING 780 780 /ligand="ATP"
/ligand_id="ChEBI:CHEBI:30616"
/ligand_label="2"		 G
BINDING 781 781 /ligand="ATP"
/ligand_id="ChEBI:CHEBI:30616"
/ligand_label="2"		 [IV]
BINDING 782 782 /ligand="ATP"
/ligand_id="ChEBI:CHEBI:30616"
/ligand_label="2"		 H
BINDING 783 783 /ligand="ATP"
/ligand_id="ChEBI:CHEBI:30616"
/ligand_label="2"		 S
BINDING 823 823 /ligand="ATP"
/ligand_id="ChEBI:CHEBI:30616"
/ligand_label="2"		 Q
BINDING 823 823 /ligand="Mg(2+)"
/ligand_id="ChEBI:CHEBI:18420"
/ligand_label="3"		 Q
BINDING 823 823 /ligand="Mn(2+)"
/ligand_id="ChEBI:CHEBI:29035"
/ligand_label="3"		 Q
BINDING 835 835 /ligand="ATP"
/ligand_id="ChEBI:CHEBI:30616"
/ligand_label="2"		 E
BINDING 835 835 /ligand="Mg(2+)"
/ligand_id="ChEBI:CHEBI:18420"
/ligand_label="3"		 E
BINDING 835 835 /ligand="Mg(2+)"
/ligand_id="ChEBI:CHEBI:18420"
/ligand_label="4"		 E
BINDING 835 835 /ligand="Mn(2+)"
/ligand_id="ChEBI:CHEBI:29035"
/ligand_label="3"		 E
BINDING 835 835 /ligand="Mn(2+)"
/ligand_id="ChEBI:CHEBI:29035"
/ligand_label="4"		 E
BINDING 837 837 /ligand="Mg(2+)"
/ligand_id="ChEBI:CHEBI:18420"
/ligand_label="4"		 N
BINDING 837 837 /ligand="Mn(2+)"
/ligand_id="ChEBI:CHEBI:29035"
/ligand_label="4"		 N
end case

Additional information [?]

Size range 1024-1076 amino acids
Related rules None
Fusion Nter: None Cter: None
Comments Bacillaceae, Geobacillus and lactobacillaceae seem to posess two members of this family: one specific for arginine biosynthesis (called CARY_ in ID, and CARB in GN) and the other specific for pyrimidine synthesis (called CARB_ in ID, and PYRAB in GN). Sequence of carB is split into two genes in AQUAE, METJA and METKA. Weird insertion in NOSS1, THEMA and ZYMMO (sequences not shown in alignment).



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