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- PDB-5dou: Crystal Structure of Human Carbamoyl phosphate synthetase I (CPS1... -

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Basic information

Entry
Database: PDB / ID: 5dou
TitleCrystal Structure of Human Carbamoyl phosphate synthetase I (CPS1), ligand-bound form
ComponentsCarbamoyl-phosphate synthase [ammonia], mitochondrial
KeywordsLIGASE / Carbamoyl Phosphate Synthase (ammonia utilizing) / Carbamoyl Phosphate / Ammonia / N-acetyl-L-glutamate / Adenosine Triphosphate / ligand-bound / urea cycle / Multi-domain / Allosteric site / Rare disease / CPS1 deficiency / Hyperammonemia
Function / homology
Function and homology information


carbamoyl phosphate biosynthetic process / cellular response to oleic acid / monoatomic anion homeostasis / modified amino acid binding / carbamoyl-phosphate synthase (ammonia) activity / triglyceride catabolic process / carbamoyl-phosphate synthase (ammonia) / carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity / midgut development / Urea cycle ...carbamoyl phosphate biosynthetic process / cellular response to oleic acid / monoatomic anion homeostasis / modified amino acid binding / carbamoyl-phosphate synthase (ammonia) activity / triglyceride catabolic process / carbamoyl-phosphate synthase (ammonia) / carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity / midgut development / Urea cycle / homocysteine metabolic process / cellular response to ammonium ion / citrulline biosynthetic process / urea cycle / hepatocyte differentiation / glutamine metabolic process / response to growth hormone / glutamate binding / response to food / response to zinc ion / response to starvation / response to dexamethasone / response to amine / small molecule binding / potassium ion binding / mitochondrial nucleoid / response to amino acid / 'de novo' pyrimidine nucleobase biosynthetic process / nitric oxide metabolic process / cellular response to fibroblast growth factor stimulus / cellular response to glucagon stimulus / cellular response to cAMP / phospholipid binding / response to toxic substance / vasodilation / endopeptidase activity / response to lipopolysaccharide / mitochondrial inner membrane / mitochondrial matrix / response to xenobiotic stimulus / calcium ion binding / protein-containing complex binding / nucleolus / protein-containing complex / mitochondrion / ATP binding / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
Carbamoyl Phosphate Synthetase; Chain A, domain 4 / Carbamoyl-phosphate synthetase, large subunit oligomerisation domain / Methylglyoxal synthase-like domain / Carbamoyl-phosphate synthase small subunit, N-terminal domain / Carbamoyl-phosphate synthetase, large subunit oligomerisation domain / Carbamoyl-phosphate synthase large subunit, CPSase domain / Carbamoyl-phosphate synthase, small subunit / Carbamoyl-phosphate synthase, large subunit / Carbamoyl-phosphate synthase small subunit, GATase1 domain / Carbamoyl-phosphate synthase small subunit, N-terminal domain superfamily ...Carbamoyl Phosphate Synthetase; Chain A, domain 4 / Carbamoyl-phosphate synthetase, large subunit oligomerisation domain / Methylglyoxal synthase-like domain / Carbamoyl-phosphate synthase small subunit, N-terminal domain / Carbamoyl-phosphate synthetase, large subunit oligomerisation domain / Carbamoyl-phosphate synthase large subunit, CPSase domain / Carbamoyl-phosphate synthase, small subunit / Carbamoyl-phosphate synthase, large subunit / Carbamoyl-phosphate synthase small subunit, GATase1 domain / Carbamoyl-phosphate synthase small subunit, N-terminal domain superfamily / Carbamoyl-phosphate synthetase, large subunit oligomerisation domain superfamily / Carbamoyl-phosphate synthase small chain, CPSase domain / Carbamoyl-phosphate synthetase large chain, oligomerisation domain / Carbamoyl-phosphate synthetase large chain, oligomerisation domain / Carbamoyl-phosphate synthase small chain, CPSase domain / Methylglyoxal synthase-like domain / Methylglyoxal synthase-like domain superfamily / MGS-like domain / MGS-like domain profile. / MGS-like domain / Glutamine amidotransferase / Glutamine amidotransferase class-I / Glutamine amidotransferase type 1 domain profile. / Carbamoyl-phosphate synthase subdomain signature 1. / Carbamoyl-phosphate synthetase large subunit-like, ATP-binding domain / Carbamoyl-phosphate synthase L chain, ATP binding domain / ATP-grasp fold, subdomain 1 / Pre-ATP-grasp domain superfamily / ATP-grasp fold / ATP-grasp fold profile. / Class I glutamine amidotransferase-like / Carbamoyl-phosphate synthase subdomain signature 2. / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / : / NICKEL (II) ION / N-ACETYL-L-GLUTAMATE / PHOSPHATE ION / Carbamoyl-phosphate synthase [ammonia], mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
Authorsde Cima, S. / Polo, L.M. / Fita, I. / Rubio, V.
Funding support Spain, 3items
OrganizationGrant numberCountry
Fundacion Alicia KoplowitzNo number Spain
Valencian GovernmentPrometeo 2009/051 Spain
Spanish GovernmentBFU2011-30407 Spain
CitationJournal: Sci Rep / Year: 2015
Title: Structure of human carbamoyl phosphate synthetase: deciphering the on/off switch of human ureagenesis.
Authors: de Cima, S. / Polo, L.M. / Diez-Fernandez, C. / Martinez, A.I. / Cervera, J. / Fita, I. / Rubio, V.
History
DepositionSep 11, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 9, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carbamoyl-phosphate synthase [ammonia], mitochondrial
B: Carbamoyl-phosphate synthase [ammonia], mitochondrial
C: Carbamoyl-phosphate synthase [ammonia], mitochondrial
D: Carbamoyl-phosphate synthase [ammonia], mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)662,38460
Polymers656,2474
Non-polymers6,13756
Water11,530640
1
A: Carbamoyl-phosphate synthase [ammonia], mitochondrial
B: Carbamoyl-phosphate synthase [ammonia], mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)331,24131
Polymers328,1242
Non-polymers3,11729
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Carbamoyl-phosphate synthase [ammonia], mitochondrial
D: Carbamoyl-phosphate synthase [ammonia], mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)331,14329
Polymers328,1242
Non-polymers3,02027
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.919, 98.558, 214.890
Angle α, β, γ (deg.)90.660, 98.650, 90.080
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: _ / Auth seq-ID: 43 - 1493 / Label seq-ID: 32 - 1482

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6
DetailsThe biological unit is a dimer. There are 2 biological units in the asymmetric unit (chains A & B and chains C & D)

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Carbamoyl-phosphate synthase [ammonia], mitochondrial / Carbamoyl-phosphate synthetase I / CPSase I


Mass: 164061.797 Da / Num. of mol.: 4 / Fragment: mature enzyme
Source method: isolated from a genetically manipulated source
Details: Mature CPS1 with N-terminal His-tag for purification purposes
Source: (gene. exp.) Homo sapiens (human) / Gene: CPS1 / Organ: LIVER / Plasmid: pFastBac-bMON14272 / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P31327, carbamoyl-phosphate synthase (ammonia)

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Non-polymers , 10 types, 696 molecules

#2: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ni
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: K
#5: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#6: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#7: Chemical
ChemComp-NLG / N-ACETYL-L-GLUTAMATE


Mass: 189.166 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H11NO5
#8: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#9: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#10: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C2H6O2
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 640 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.15 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.2 / Details: 0.4 M MgCl2, 0.2 M ammonium tartrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97947 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 21, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97947 Å / Relative weight: 1
ReflectionResolution: 2.6→40 Å / Num. all: 178654 / Num. obs: 178654 / % possible obs: 90.7 % / Redundancy: 1.8 % / Rpim(I) all: 0.076 / Rrim(I) all: 0.111 / Rsym value: 0.081 / Net I/av σ(I): 7.98 / Net I/σ(I): 7.9 / Num. measured all: 329157
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.6-2.741.70.3212.140514245420.3180.321384.9
2.74-2.911.70.2452.741046239340.240.2453.888
2.91-3.111.80.1733.941639231130.1650.1734.990.5
3.11-3.361.80.1235.639652219040.1150.1236.492.1
3.36-3.681.90.0877.938693203510.080.0878.692.9
3.68-4.1120.06610.136988184880.0590.06611.193.2
4.11-4.751.90.05511.431645163010.0490.05512.993.5
4.75-5.8120.05212.127466138290.0470.05212.793.6
5.81-8.221.90.04813.320396105410.0430.04812.292.8
8.22-39.98220.03616.11111856510.0330.03615.790.7

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
SCALA3.3.21data scaling
PDB_EXTRACT3.14data extraction
XDSdata reduction
PHASERphasing
XSCALEdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DOT

5dot


Resolution: 2.6→40 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.899 / WRfactor Rfree: 0.2244 / WRfactor Rwork: 0.1917 / FOM work R set: 0.8393 / SU B: 22.763 / SU ML: 0.232 / SU R Cruickshank DPI: 0.2867 / SU Rfree: 0.3226 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.323 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2292 8988 5 %RANDOM
Rwork0.1949 169655 --
obs0.1967 169655 90.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso max: 186.26 Å2 / Biso mean: 45.659 Å2 / Biso min: 2.58 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å2-0.29 Å20.32 Å2
2---2.92 Å2-0.17 Å2
3---2.54 Å2
Refinement stepCycle: final / Resolution: 2.6→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms44008 0 341 640 44989
Biso mean--26.65 23.43 -
Num. residues----5699
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01945207
X-RAY DIFFRACTIONr_bond_other_d0.0050.0243636
X-RAY DIFFRACTIONr_angle_refined_deg1.4041.97261268
X-RAY DIFFRACTIONr_angle_other_deg0.9483100695
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.90355689
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.25624.9681900
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.187157897
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.73915208
X-RAY DIFFRACTIONr_chiral_restr0.0720.26999
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02150735
X-RAY DIFFRACTIONr_gen_planes_other0.0040.029753
X-RAY DIFFRACTIONr_mcbond_it1.7592.94322794
X-RAY DIFFRACTIONr_mcbond_other1.7592.94322793
X-RAY DIFFRACTIONr_mcangle_it2.8834.40928457
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A924720.05
12B924720.05
21A932250.04
22C932250.04
31A938180.03
32D938180.03
41B928970.05
42C928970.05
51B934030.04
52D934030.04
61C932610.04
62D932610.04
LS refinement shellResolution: 2.6→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 625 -
Rwork0.273 11722 -
all-12347 -
obs--84.5 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)DetailsOrigin x (Å)Origin y (Å)Origin z (Å)
10.21030.07090.0790.13280.04160.1267-0.02440.00010.0165-0.06190.0287-0.00010.01230.017-0.00430.0824-0.01070.01140.01980.00050.0076chain A-8.2163-1.655577.04
20.32390.12280.07610.06850.07940.4345-0.00440.1799-0.0761-0.04170.0448-0.00630.0904-0.0649-0.04040.298-0.0469-0.1010.154-0.04320.0606chain B-51.4958-64.470326.1763
31.27010.0653-0.18510.08710.04790.45430.0577-0.5407-0.3650.1563-0.0284-0.08160.18730.1274-0.02930.40160.005-0.16790.23860.1450.1631chain C19.7954-113.05186.0575
40.1622-0.04910.0780.1238-0.0250.1102-0.0248-0.00520.0140.05920.0243-0.00070.0069-0.01470.00050.0833-0.01990.01420.0313-0.01020.0076chain D-23.6885-50.8967134.588
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A43 - 1493
2X-RAY DIFFRACTION2B43 - 1493
3X-RAY DIFFRACTION3C43 - 1493
4X-RAY DIFFRACTION4D43 - 1493

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