Structure of PDB 1jdb Chain B

Receptor sequence

>1jdbB (length=1057) Species: 562 (Escherichia coli)

MPKRTDIKSILILGAGPIVIGQACEFDYSGAQACKALREEGYRVILVNSN
PATIMTDPEMADATYIEPIHWEVVRKIIEKERPDAVLPTMGGQTALNCAL
ELERQGVLEEFGVTMIGATADAIDKAEDRRRFDVAMKKIGLETARSGIAH
TMEEALAVAADVGFPCIIRPSFTMGGSGGGIAYNREEFEEICARGLDLSP
TKELLIDESLIGWKEYEMEVVRDKNDNCIIVCSIENFDAMGIHTGDSITV
APAQTLTDKEYQIMRNASMAVLREIGVETGGSNVQFAVNPKNGRLIVIEM
NPRVSRSSALASKATGFPIAKVAAKLAVGYTLDELMNDITGGRTPASFEP
SIDYVVTKIPRFNFEKFAGANDRLTTQMKSVGEVMAIGRTQQESLQKALR
GLEVGATGFDPKVSLDDPEALTKIRRELKDAGADRIWYIADAFRAGLSVD
GVFNLTNIDRWFLVQIEELVRLEEKVAEVGITGLNADFLRQLKRKGFADA
RLAKLAGVREAEIRKLRDQYDLHPVYKRVDTCAAEFATDTAYMYSTYEEE
CEANPSTDREKIMVLGGGPNRIGQGIEFDYCCVHASLALREDGYETIMVN
CNPETVSTDYDTSDRLYFEPVTLEDVLEIVRIEKPKGVIVQYGGQTPLKL
ARALEAAGVPVIGTSPDAIDRAEDRERFQHAVERLKLKQPANATVTAIEM
AVEKAKEIGYPLVVRAMEIVYDEADLRRYFQTAVLLDHFLDDAVEVDVDA
ICDGEMVLIGGIMEHIEQAGVHSGDSACSLPAYTLSQEIQDVMRQQVQKL
AFELQVRGLMNVQFAVKNNEVYLIEVNPRAARTVPFVSKATGVPLAKVAA
RVMAGKSLAEQGVTKEVIPPYYSVKEVVLPFNKFPGVDPLLGPEMRSTGE
VMGVGRTFAEAFAKAQLGSNSTMKKHGRALLSVREGDKERVVDLAAKLLK
QGFELDATHGTAIVLGEAGINPRLVNKVHEGRPHIQDRIKNGEYTYIINT
TSGRRAIEDSRVIRRSALQYKVHYDTTLNGGFATAMALNADATEKVISVQ
EMHAQIK

3D structure

• PDB: 1jdb The structure of carbamoyl phosphate synthetase determined to 2.1 A resolution.
• Chain: B
• Resolution: 2.1 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): R128 R168 G174 S176 K201 E214 H242 N282 Q284 F285 E298 M299 N300 P301 R302 S307 D337 G506 K633 R714 E760 D768 Q828 E840 N842 R847 P900
• Catalytic site (residue number reindexed from 1): R129 R169 G175 S177 K202 E215 H243 N283 Q285 F286 E299 M300 N301 P302 R303 S308 D338 G507 K634 R715 E745 D753 Q813 E825 N827 R832 P885
• Enzyme Commision number: 6.3.4.16: carbamoyl-phosphate synthase (ammonia).
  6.3.5.5: carbamoyl-phosphate synthase (glutamine-hydrolyzing).

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	MN	B	E298 N300	E299 N301
BS02	MN	B	Q284 E298	Q285 E299
BS03	PO4	B	M173 G174 H242 E298 N300 R302 R305	M174 G175 H243 E299 N301 R303 R306
BS04	MN	B	Q828 E840	Q813 E825
BS05	MN	B	E840 N842	E825 N827
BS06	PO4	B	K953 T973 G975 T976 K992	K938 T958 G960 T961 K977
BS07	GLN	B	R527 A536 T537 E551 N553	R528 A537 T538 E552 N554
BS08	ADP	B	R128 I166 R168 M173 G174 G175 E207 L209 I210 E214 M239 G240 I241 H242 T243 Q284 I297 E298 T375	R129 I167 R169 M174 G175 G176 E208 L210 I211 E215 M240 G241 I242 H243 T244 Q285 I298 E299 T376
BS09	ADP	B	P689 V712 R714 F754 L755 E760 A784 G785 V786 H787 E840	P690 V713 R715 F739 L740 E745 A769 G770 V771 H772 E825
BS10	ORN	B	E782 D790 E891 V892 L906 Y1039 D1040 T1041	E767 D775 E876 V877 L891 Y1024 D1025 T1026

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding
• GO:0004087 carbamoyl-phosphate synthase (ammonia) activity
• GO:0004088 carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity
• GO:0005515 protein binding
• GO:0005524 ATP binding
• GO:0016597 amino acid binding
• GO:0016874 ligase activity
• GO:0046872 metal ion binding

Biological Process

• GO:0006221 pyrimidine nucleotide biosynthetic process
• GO:0006526 L-arginine biosynthetic process
• GO:0006541 glutamine metabolic process
• GO:0008652 amino acid biosynthetic process
• GO:0019856 pyrimidine nucleobase biosynthetic process
• GO:0044205 'de novo' UMP biosynthetic process

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005951 carbamoyl-phosphate synthase complex

External links

• PDB: RCSB:1jdb, PDBe:1jdb, PDBj:1jdb
• PDBsum: 1jdb
• PubMed: 10089390
• UniProt: P00968|CARB_ECOLI Carbamoyl phosphate synthase large chain (Gene Name=carB)