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

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Basic information

Entry
Database: PDB / ID: 5dot
TitleCrystal Structure of Human Carbamoyl phosphate synthetase I (CPS1), apo form
ComponentsCarbamoyl-phosphate synthase [ammonia], mitochondrial
KeywordsLIGASE / Carbamoyl Phosphate Synthase (ammonia utilizing) / Carbamoyl Phosphate / Ammonia / N-acetyl-L-glutamate / Adenosine Triphosphate / apo / 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 / triglyceride catabolic process / carbamoyl-phosphate synthase (ammonia) / carbamoyl-phosphate synthase (ammonia) activity / carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity / homocysteine metabolic process / Urea cycle ...carbamoyl phosphate biosynthetic process / cellular response to oleic acid / monoatomic anion homeostasis / modified amino acid binding / triglyceride catabolic process / carbamoyl-phosphate synthase (ammonia) / carbamoyl-phosphate synthase (ammonia) activity / carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity / homocysteine metabolic process / Urea cycle / cellular response to ammonium ion / citrulline biosynthetic process / urea cycle / hepatocyte differentiation / glutamine metabolic process / response to growth hormone / response to food / midgut development / nitric oxide metabolic process / glutamate binding / response to zinc ion / response to starvation / response to amine / small molecule binding / response to dexamethasone / potassium ion binding / mitochondrial nucleoid / cellular response to fibroblast growth factor stimulus / response to amino acid / 'de novo' pyrimidine nucleobase biosynthetic process / cellular response to cAMP / cellular response to glucagon stimulus / 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 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 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.
Similarity search - Domain/homology
NICKEL (II) ION / Carbamoyl-phosphate synthase [ammonia], mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsPolo, L.M. / de Cima, S. / Fita, I. / Rubio, V.
Funding support Spain, 3items
OrganizationGrant numberCountry
Fundacion Alicia KoplowitzNo grant 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 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / 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 / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)328,92013
Polymers328,1242
Non-polymers79611
Water14,754819
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4710 Å2
ΔGint2 kcal/mol
Surface area96620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.337, 133.482, 142.907
Angle α, β, γ (deg.)90.000, 102.510, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: SER / End label comp-ID: SER / Refine code: _ / Auth seq-ID: 43 - 1495 / Label seq-ID: 32 - 1484

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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


Mass: 164061.797 Da / Num. of mol.: 2 / 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)
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 819 / 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: 2.82 Å3/Da / Density % sol: 56.37 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.2 / Details: 20% PEG3350, 0.2 M tri-sodium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.96112 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 9, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96112 Å / Relative weight: 1
ReflectionResolution: 2.4→139.516 Å / Num. all: 136595 / Num. obs: 136595 / % possible obs: 96.3 % / Redundancy: 3.5 % / Biso Wilson estimate: 28.5 Å2 / Rpim(I) all: 0.071 / Rrim(I) all: 0.135 / Rsym value: 0.114 / Net I/av σ(I): 4.77 / Net I/σ(I): 7.9 / Num. measured all: 475967
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
2.4-2.533.50.342259848172370.2120.3423.783.4
2.53-2.683.60.2682.668507192840.1640.2684.698.3
2.68-2.873.50.2033.463723180230.1260.2035.598.4
2.87-3.13.50.1514.559241168960.0940.151798.5
3.1-3.393.50.1215.353901154640.0750.1218.698.5
3.39-3.793.50.1026.148879141010.0640.10210.498.7
3.79-4.383.50.0926.542958124300.0580.09211.798.9
4.38-5.373.40.0876.936274105470.0550.08712.298.7
5.37-7.593.40.0886.72752281430.0560.08811.298.5
7.59-44.4943.40.0797.41511444700.050.07912.897.1

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Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
PDB_EXTRACT3.14data extraction
REFMAC5.7.0032refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
XSCALEdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JDB, 2YVQ

1jdb

2yvq


Resolution: 2.4→43.95 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.937 / WRfactor Rfree: 0.2068 / WRfactor Rwork: 0.1733 / FOM work R set: 0.899 / SU B: 10.173 / SU ML: 0.124 / SU R Cruickshank DPI: 0.293 / SU Rfree: 0.1995 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.293 / ESU R Free: 0.199 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1964 6849 5 %RANDOM
Rwork0.1646 129708 --
obs0.1662 136557 96.13 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso max: 188.88 Å2 / Biso mean: 40.365 Å2 / Biso min: 13.89 Å2
Baniso -1Baniso -2Baniso -3
1--0.21 Å2-0 Å2-0.27 Å2
2--1.19 Å2-0 Å2
3----0.84 Å2
Refinement stepCycle: final / Resolution: 2.4→43.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20944 0 46 819 21809
Biso mean--54.34 35.45 -
Num. residues----2703
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01921450
X-RAY DIFFRACTIONr_bond_other_d0.0030.0220823
X-RAY DIFFRACTIONr_angle_refined_deg1.2931.96829046
X-RAY DIFFRACTIONr_angle_other_deg0.835348056
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.70852706
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.13325.022916
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.463153787
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8231599
X-RAY DIFFRACTIONr_chiral_restr0.0720.23320
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02124120
X-RAY DIFFRACTIONr_gen_planes_other0.0030.024627
X-RAY DIFFRACTIONr_mcbond_it2.9292.07910815
X-RAY DIFFRACTIONr_mcbond_other2.9292.07910814
X-RAY DIFFRACTIONr_mcangle_it4.5573.10313497
Refine LS restraints NCS

Ens-ID: 1 / Number: 86500 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.06 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 385 -
Rwork0.219 7356 -
all-7741 -
obs--74.03 %
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)
11.01590.0769-0.21891.47540.0471.7516-0.0195-0.053-0.0527-0.0020.02380.04710.0268-0.1559-0.00430.04270.00610.03910.1977-0.01770.0447Chain A, ISD-98.661-2.46967.436
20.68230.1492-0.03661.32280.35631.47310.01910.0196-0.0079-0.03420.0128-0.143-0.0180.1504-0.03190.03820.00260.05130.1494-0.00020.0771Chain B, ISD19.40314.911-27.113
31.5224-0.0761-0.31591.9813-0.62181.8302-0.0405-0.3108-0.06120.2796-0.0868-0.25950.02190.24840.12730.10180.0341-0.01840.31930.03540.0674Chain A, GSD-85.597-6.32290.836
41.18660.058-0.24461.13340.05271.40430.08130.20290.0428-0.2097-0.0540.0184-0.1616-0.1996-0.02730.12460.04290.03640.1990.00480.0315Chain B, GSD6.07818.861-50.431
52.30320.0836-1.12421.1105-1.00392.3859-0.1357-0.3159-0.1997-0.0041-0.0395-0.22660.12850.50120.17520.0910.0821-0.00610.35060.03830.0876Chain A, BPSD-A-51.018-10.97758.777
61.87870.1388-1.16141.40780.72962.4624-0.00390.2333-0.06090.01120.05190.02740.0784-0.3154-0.0480.0143-0.0374-0.010.28440.02390.0211Chain B, BPSD-A-27.8442.446-21.891
71.2052-0.1125-0.16160.4925-0.20521.1729-0.0976-0.0688-0.07030.06680.0273-0.00990.07830.17370.07030.10080.03370.03740.1979-0.02070.0873Chain A, BPSD-C-73.949-10.45758.142
81.11480.1614-0.19210.30370.10310.8324-0.02210.0289-0.1-0.04790.0485-0.00150.058-0.1608-0.02640.0699-0.00920.03250.18370.01620.1062Chain B, BPSD-C-4.9093.476-21.266
90.76360.40470.00611.3365-0.35731.3141-0.02240.1185-0.0382-0.13870.07280.02640.1229-0.0685-0.05040.06270.00390.04360.2245-0.03940.078Chain A, UFSD-89.92-5.43942.567
101.0151-0.17620.02191.09580.12541.73020.0135-0.1047-0.15220.02650.0329-0.01250.2190.1423-0.04640.05190.01230.02910.1580.04940.0973Chain B, UFSD11.0753.053-4.798
111.9115-0.2719-0.69870.5047-0.45471.120.0149-0.01640.05260.0432-0.0056-0.039-0.05860.0243-0.00940.0431-0.01660.03740.1592-0.02850.0944Chain A, CPSD-A-70.3688.36240.097
121.66630.3219-0.4380.58670.2081.24720.036-0.0080.04750.0187-0.02090.0773-0.0201-0.0539-0.01510.040.0060.04420.17580.01440.0908Chain B, CPSD-A-8.79614.7722.25
134.0721-2.92720.80292.37640.31263.20860.32820.2387-1.3686-0.0987-0.26031.02820.3936-0.288-0.06790.1487-0.0498-0.04840.3241-0.03560.6832Chain A, CPSD-B-65.597-5.4112.243
143.93752.03632.78033.4072-0.3873.42880.44180.2245-1.18810.02320.0538-0.93410.41490.2558-0.49560.15630.0597-0.03360.4001-0.05740.6444Chain B, CPSD-B-14.193-7.54524.11
151.0918-0.5423-0.09891.5249-0.36721.0693-0.0110.0174-0.0190.04930.00660.1051-0.00020.05790.00450.0095-0.00990.02530.20210.01060.0761Chain A, CPSD-C-52.5370.42727.444
161.28860.75270.03541.38280.14841.3703-0.0037-0.01150.0102-0.07460.0304-0.0293-0.03960.0406-0.02670.0180.0280.02920.22540.02370.0733Chain B, CPSD-C-27.3393.91211.642
172.0616-0.6183-0.40322.5380.6322.2478-0.1049-0.0487-0.31220.26350.0320.39720.3459-0.0850.07290.07530.02540.06820.15830.06710.2217Chain A, ASD-48.215-31.09128.203
182.39480.6919-0.31243.7267-1.4412.0848-0.24480.1852-0.4018-0.82050.1423-0.38640.5120.10840.10250.2798-0.00140.12620.2313-0.07240.191Chain B, ASD-30.984-26.5970.475
195.33632.54912.997510.12967.6958.08110.0844-0.2605-0.2410.2270.1787-0.45780.27420.711-0.26310.02820.022-0.00160.40190.10360.0965Chain A, C-terminal-36.715-11.06536.018
205.4792-3.23620.5219.8815-4.23985.06710.02310.3933-0.2011-0.35770.46930.53360.1898-0.7042-0.49230.0501-0.0476-0.0390.44280.05370.0795Chain B, C-terminal-42.801-5.594-0.927
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A43 - 196
2X-RAY DIFFRACTION2B43 - 196
3X-RAY DIFFRACTION3A197 - 411
4X-RAY DIFFRACTION4B197 - 411
5X-RAY DIFFRACTION5A418 - 560
6X-RAY DIFFRACTION6B418 - 560
7X-RAY DIFFRACTION7A650 - 821
8X-RAY DIFFRACTION8B650 - 821
9X-RAY DIFFRACTION9A822 - 973
10X-RAY DIFFRACTION10B822 - 973
11X-RAY DIFFRACTION11A974 - 1080
12X-RAY DIFFRACTION12B974 - 1080
13X-RAY DIFFRACTION13A1081 - 1179
14X-RAY DIFFRACTION14B1081 - 1179
15X-RAY DIFFRACTION15A1180 - 1354
16X-RAY DIFFRACTION16B1180 - 1354
17X-RAY DIFFRACTION17A1355 - 1469
18X-RAY DIFFRACTION18B1355 - 1469
19X-RAY DIFFRACTION19A1470 - 1496
20X-RAY DIFFRACTION20B1470 - 1495

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