Structure of PDB 5dou Chain D

Receptor sequence

>5douD (length=1430) Species: 9606 (Homo sapiens)

AQTAHIVLEDGTKMKGYSFGHPSSVAGEVVFNTGLGGYPEAITDPAYKGQ
ILTMANPIIGNGGAPDTTALDELGLSKYLESNGIKVSGLLVLDYSKDYNH
WLATKSLGQWLQEEKVPAIYGVDTRMLTKIIRDKGTMLGKIEFEGQPVDF
VDPNKQNLIAEVSTKDVKVYGKGNPTKVVAVDCGIKNNVIRLLVKRGAEV
HLVPWNHDFTKMEYDGILIAGGPGNPALAEPLIQNVRKILESDRKEPLFG
ISTGNLITGLAAGAKTYKMSMANRGQNQPVLNITNKQAFITAQNHGYALD
NTLPAGWKPLFVNVNDQTNEGIMHESKPFFAVQFHPEVTPGPIDTEYLFD
SFFSLIKKGKATTITSVLPKPALVASRVEVSKVLILGSGGLSIGQAGEFD
YSGSQAVKAMKEENVKTVLMNPNIASVQTNEVGLKQADTVYFLPITPQFV
TEVIKAEQPDGLILGMGGQTALNCGVELFKRGVLKEYGVKVLGTSVESIM
ATEDRQLFSDKLNEINEKIAPSFAVESIEDALKAADTIGYPVMIRSAYAL
GGLGSGICPNRETLMDLSTKAFAMTNQILVEKSVTGWKEIEYEVVRDADD
NCVTVCNMENVDAMGVHTGDSVVVAPAQTLSNAEFQMLRRTSINVVRHLG
IVGECNIQFALHPTSMEYCIIEVNARLSRSSALASKATGYPLAFIAAKIA
LGIPLPEIKNVVSGKTSACFEPSLDYMVTKIPRWDLDRFHGTSSRIGSSM
KSVGEVMAIGRTFEESFQKALRMCHPSIEGFTPRLPMNKEWPSNLDLRKE
LSEPSSTRIYAIAKAIDDNMSLDEIEKLTYIDKWFLYKMRDILNMEKTLK
GLNSESMTEETLKRAKEIGFSDKQISKCLGLTEAQTRELRLKKNIHPWVK
QIDTLAAEYPSVTNYLYVTYNGQEHDVNFDDHGMMVLGCGPYHIGSSVEF
DWCAVSSIRTLRQLGKKTVVVNCNPETVSTDFDECDKLYFEELSLERILD
IYHQEACGGCIISVGGQIPNNLAVPLYKNGVKIMGTSPLQIDRAEDRSIF
SAVLDELKVAQAPWKAVNTLNEALEFAKSVDYPCLLRMNVVFSEDEMKKF
LEHPVVLTKFVEGAREVEMDAVGKDGRVISHAISEHVEDAGVHSGDATLM
LPTQTISQGAIEKVKDATRKIAKAFAISGPFNVQFLVKGNDVLVIECNLR
ASRSFPFVSKTLGVDFIDVATKVMIGENVDEKHLPTLDHPIIPADYVAIK
APMFSWPRLRDADPILRCEMASTGEVACFGEGIHTAFLKAMLSTGFKIPQ
KGILIGIQQSFRPRFLGVAEQLHNEGFKLFATEATSDWLNANNVPATPVA
WPSQEGQNPSLSSIRKLIRDGSIDLVINLPNNNTKFVHDNYVIRRTAVDS
GIPLLTNFQVTKLFAEAVQKDSKSLFHYRQ

3D structure

• PDB: 5dou Structure of human carbamoyl phosphate synthetase: deciphering the on/off switch of human ureagenesis.
• Chain: D
• Resolution: 2.6 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): S294 H377 E379 R547 R587 N618 E631 H659 N698 Q700 E714 N716 R718 S722 G922 A1048 R1129 E1175 K1183 Q1243 E1255 N1257 R1262 R1319
• Catalytic site (residue number reindexed from 1): S252 H335 E337 R505 R545 N576 E589 H617 N656 Q658 E672 N674 R676 S680 G880 A1006 R1087 E1116 K1124 Q1184 E1196 N1198 R1203 R1260
• Enzyme Commision number: 6.3.4.16: carbamoyl-phosphate synthase (ammonia).

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	MG	D	E714 N716	E672 N674
BS02	MG	D	Q700 E714	Q658 E672
BS03	PO4	D	L592 G593 H659 E714 N716 R718 R721	L550 G551 H617 E672 N674 R676 R679
BS04	ADP	D	R547 M585 R587 L592 G593 G594 E623 S625 V626 T627 E631 M656 G657 V658 H659 Q700 I713 E714	R505 M543 R545 L550 G551 G552 E581 S583 V584 T585 E589 M614 G615 V616 H617 Q658 I671 E672
BS05	ADP	D	L1127 F1169 V1170 E1175 A1199 V1201 H1202 S1203 Q1243 L1245 I1254 E1255	L1085 F1110 V1111 E1116 A1140 V1142 H1143 S1144 Q1184 L1186 I1195 E1196
BS06	NLG	D	I1366 Q1367 T1391 A1393 T1394 W1410 L1438 T1443 K1444 F1445 N1449	I1307 Q1308 T1332 A1334 T1335 W1351 L1379 T1384 K1385 F1386 N1390

Gene Ontology

Molecular Function

• GO:0004087 carbamoyl-phosphate synthase (ammonia) activity
• GO:0004088 carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity
• GO:0004175 endopeptidase activity
• GO:0005509 calcium ion binding
• GO:0005515 protein binding
• GO:0005524 ATP binding
• GO:0005543 phospholipid binding
• GO:0016595 glutamate binding
• GO:0016874 ligase activity
• GO:0030955 potassium ion binding
• GO:0036094 small molecule binding
• GO:0044877 protein-containing complex binding
• GO:0046872 metal ion binding
• GO:0072341 modified amino acid binding

Biological Process

• GO:0000050 urea cycle
• GO:0001889 liver development
• GO:0006207 'de novo' pyrimidine nucleobase biosynthetic process
• GO:0006541 glutamine metabolic process
• GO:0007494 midgut development
• GO:0009410 response to xenobiotic stimulus
• GO:0009636 response to toxic substance
• GO:0010043 response to zinc ion
• GO:0014075 response to amine
• GO:0019240 citrulline biosynthetic process
• GO:0019433 triglyceride catabolic process
• GO:0019637 organophosphate metabolic process
• GO:0032094 response to food
• GO:0032496 response to lipopolysaccharide
• GO:0033762 response to glucagon
• GO:0034201 response to oleic acid
• GO:0042311 vasodilation
• GO:0042594 response to starvation
• GO:0043200 response to amino acid
• GO:0044344 cellular response to fibroblast growth factor stimulus
• GO:0046209 nitric oxide metabolic process
• GO:0048545 response to steroid hormone
• GO:0050667 homocysteine metabolic process
• GO:0051384 response to glucocorticoid
• GO:0051591 response to cAMP
• GO:0055081 monoatomic anion homeostasis
• GO:0060416 response to growth hormone
• GO:0070365 hepatocyte differentiation
• GO:0070409 carbamoyl phosphate biosynthetic process
• GO:0071242 cellular response to ammonium ion
• GO:0071320 cellular response to cAMP
• GO:0071377 cellular response to glucagon stimulus
• GO:0071400 cellular response to oleic acid
• GO:0071548 response to dexamethasone

Cellular Component

• GO:0005634 nucleus
• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005739 mitochondrion
• GO:0005743 mitochondrial inner membrane
• GO:0005759 mitochondrial matrix
• GO:0005886 plasma membrane
• GO:0032991 protein-containing complex
• GO:0042645 mitochondrial nucleoid

External links

• PDB: RCSB:5dou, PDBe:5dou, PDBj:5dou
• PDBsum: 5dou
• PubMed: 26592762
• UniProt: P31327|CPSM_HUMAN Carbamoyl-phosphate synthase [ammonia], mitochondrial (Gene Name=CPS1)