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Basic information

Entry
Database: PDB / ID: 7vva
TitlePseudouridine bound structure of Pseudouridine kinase (PUKI) from Escherichia coli strain B
ComponentsPseudouridine kinase
KeywordsTRANSFERASE / pseudouridine kinase / pseudourdine / pfkb family
Function / homology
Function and homology information


pseudouridine kinase activity / pseudouridine kinase
Similarity search - Function
pfkB family of carbohydrate kinases signature 1. / pfkB family of carbohydrate kinases signature 2. / Carbohydrate/purine kinase, PfkB, conserved site / Carbohydrate kinase PfkB / pfkB family carbohydrate kinase / Ribokinase-like
Similarity search - Domain/homology
Chem-FJF / Pseudouridine kinase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75029193467 Å
AuthorsKim, S.H. / Rhee, S.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2021R1A2C2092118 Korea, Republic Of
CitationJournal: J.Biol.Chem. / Year: 2022
Title: Substrate-binding loop interactions with pseudouridine trigger conformational changes that promote catalytic efficiency of pseudouridine kinase PUKI.
Authors: Kim, S.H. / Kim, M. / Park, D. / Byun, S. / Rhee, S.
History
DepositionNov 5, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 6, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 13, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation_author.name
Revision 1.2May 11, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_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: Pseudouridine kinase
B: Pseudouridine kinase
C: Pseudouridine kinase
D: Pseudouridine kinase
E: Pseudouridine kinase
F: Pseudouridine kinase
G: Pseudouridine kinase
H: Pseudouridine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)271,22612
Polymers270,2498
Non-polymers9774
Water61334
1
A: Pseudouridine kinase
B: Pseudouridine kinase
C: Pseudouridine kinase
D: Pseudouridine kinase
E: Pseudouridine kinase
F: Pseudouridine kinase
G: Pseudouridine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)237,44411
Polymers236,4687
Non-polymers9774
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2700 Å2
ΔGint-23 kcal/mol
Surface area19530 Å2
MethodPISA
2
A: Pseudouridine kinase
B: Pseudouridine kinase
C: Pseudouridine kinase
D: Pseudouridine kinase
E: Pseudouridine kinase
F: Pseudouridine kinase
G: Pseudouridine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)237,44411
Polymers236,4687
Non-polymers9774
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2740 Å2
ΔGint-22 kcal/mol
Surface area23470 Å2
MethodPISA
3
A: Pseudouridine kinase
B: Pseudouridine kinase
C: Pseudouridine kinase
E: Pseudouridine kinase
H: Pseudouridine kinase
hetero molecules

A: Pseudouridine kinase
D: Pseudouridine kinase
F: Pseudouridine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)271,47013
Polymers270,2498
Non-polymers1,2215
Water1267
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area2660 Å2
ΔGint-17 kcal/mol
Surface area24740 Å2
MethodPISA
4
A: Pseudouridine kinase
B: Pseudouridine kinase
C: Pseudouridine kinase
D: Pseudouridine kinase
E: Pseudouridine kinase
F: Pseudouridine kinase
H: Pseudouridine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)237,44411
Polymers236,4687
Non-polymers9774
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2520 Å2
ΔGint-20 kcal/mol
Surface area25600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.954, 271.889, 101.202
Angle α, β, γ (deg.)90.0, 110.909, 90.0
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUASPASPchain 'A'AA3 - 53 - 5
12VALVALSERSERchain 'A'AA7 - 217 - 21
13SERSERLEULEUchain 'A'AA30 - 5030 - 50
14GLYGLYLEULEUchain 'A'AA54 - 6054 - 60
15VALVALLEULEUchain 'A'AA63 - 10063 - 100
16VALVALPHEPHEchain 'A'AA109 - 162109 - 162
17LYSLYSTHRTHRchain 'A'AA170 - 183170 - 183
18ALAALAILEILEchain 'A'AA198 - 249198 - 249
19ALAALAVALVALchain 'A'AA254 - 306254 - 306
21GLUGLUASPASPchain 'B'BB3 - 53 - 5
22VALVALSERSERchain 'B'BB7 - 217 - 21
23SERSERLEULEUchain 'B'BB30 - 5030 - 50
24GLYGLYLEULEUchain 'B'BB54 - 6054 - 60
25VALVALLEULEUchain 'B'BB63 - 10063 - 100
26VALVALPHEPHEchain 'B'BB109 - 162109 - 162
27LYSLYSTHRTHRchain 'B'BB170 - 183170 - 183
28ALAALAILEILEchain 'B'BB198 - 249198 - 249
29ALAALAVALVALchain 'B'BB254 - 306254 - 306
31GLUGLUASPASPchain 'C'CC3 - 53 - 5
32VALVALSERSERchain 'C'CC7 - 217 - 21
33SERSERLEULEUchain 'C'CC30 - 5030 - 50
34GLYGLYLEULEUchain 'C'CC54 - 6054 - 60
35VALVALLEULEUchain 'C'CC63 - 10063 - 100
36VALVALPHEPHEchain 'C'CC109 - 162109 - 162
37LYSLYSTHRTHRchain 'C'CC170 - 183170 - 183
38ALAALAILEILEchain 'C'CC198 - 249198 - 249
39ALAALAVALVALchain 'C'CC254 - 306254 - 306
41GLUGLUASPASPchain 'D'DD3 - 53 - 5
42VALVALSERSERchain 'D'DD7 - 217 - 21
43SERSERLEULEUchain 'D'DD30 - 5030 - 50
44GLYGLYLEULEUchain 'D'DD54 - 6054 - 60
45VALVALLEULEUchain 'D'DD63 - 10063 - 100
46VALVALPHEPHEchain 'D'DD109 - 162109 - 162
47LYSLYSTHRTHRchain 'D'DD170 - 183170 - 183
48ALAALAILEILEchain 'D'DD198 - 249198 - 249
49ALAALAVALVALchain 'D'DD254 - 306254 - 306
51GLUGLUASPASPchain 'E'EE3 - 53 - 5
52VALVALSERSERchain 'E'EE7 - 217 - 21
53SERSERLEULEUchain 'E'EE30 - 5030 - 50
54GLYGLYLEULEUchain 'E'EE54 - 6054 - 60
55VALVALLEULEUchain 'E'EE63 - 10063 - 100
56VALVALPHEPHEchain 'E'EE109 - 162109 - 162
57LYSLYSTHRTHRchain 'E'EE170 - 183170 - 183
58ALAALAILEILEchain 'E'EE198 - 249198 - 249
59ALAALAVALVALchain 'E'EE254 - 306254 - 306
61GLUGLUASPASPchain 'F'FF3 - 53 - 5
62VALVALSERSERchain 'F'FF7 - 217 - 21
63SERSERLEULEUchain 'F'FF30 - 5030 - 50
64GLYGLYLEULEUchain 'F'FF54 - 6054 - 60
65VALVALLEULEUchain 'F'FF63 - 10063 - 100
66VALVALPHEPHEchain 'F'FF109 - 162109 - 162
67LYSLYSTHRTHRchain 'F'FF170 - 183170 - 183
68ALAALAILEILEchain 'F'FF198 - 249198 - 249
69ALAALAVALVALchain 'F'FF254 - 306254 - 306

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Components

#1: Protein
Pseudouridine kinase / Putative pyrimidine kinase


Mass: 33781.094 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: psuK, psuK_1, psuK_2, A8C65_16945, BMT91_00230, BON75_04205, BvCmsHHP019_05067, BvCmsSINP011_02211, D9H68_16155, D9J11_19520, E2127_01880, E2128_04080, E2134_03530, FORC82_1677, G9P50_07470, ...Gene: psuK, psuK_1, psuK_2, A8C65_16945, BMT91_00230, BON75_04205, BvCmsHHP019_05067, BvCmsSINP011_02211, D9H68_16155, D9J11_19520, E2127_01880, E2128_04080, E2134_03530, FORC82_1677, G9P50_07470, GQE64_02140, GQM28_02110, HVV70_14180, HVX33_21995, HVZ33_08660, NCTC11022_02147, NCTC13216_04879, NCTC9706_04998, SAMEA3752557_00486, WP4S18E08_16210
Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A1V3W5E1, pseudouridine kinase
#2: Chemical
ChemComp-FJF / 5-[(2~{S},3~{R},4~{S},5~{R})-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl]-1~{H}-pyrimidine-2,4-dione


Mass: 244.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H12N2O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.42 Å3/Da / Density % sol: 64.05 %
Crystal growTemperature: 295 K / Method: vapor diffusion
Details: 0.1M lithium chloride, 0.1M MES (pH6.0), 18% PEG 6,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97932 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97932 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. obs: 92181 / % possible obs: 99.7 % / Redundancy: 3.5 % / Biso Wilson estimate: 52.7690986986 Å2 / CC1/2: 0.954 / Net I/σ(I): 7.75
Reflection shellResolution: 2.75→2.85 Å / Num. unique obs: 9234 / CC1/2: 0.342

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KZH

3kzh


Resolution: 2.75029193467→33.6410688561 Å / SU ML: 0.494678176716 / Cross valid method: FREE R-VALUE / σ(F): 1.33632185377 / Phase error: 35.8888278332
RfactorNum. reflection% reflection
Rfree0.324860804975 1993 2.16505708668 %
Rwork0.296140865622 90060 -
obs0.29677572334 92053 98.1856774111 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 69.0481354329 Å2
Refinement stepCycle: LAST / Resolution: 2.75029193467→33.6410688561 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15659 0 68 34 15761
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034837552439615988
X-RAY DIFFRACTIONf_angle_d0.80196130258521764
X-RAY DIFFRACTIONf_chiral_restr0.03260377267082534
X-RAY DIFFRACTIONf_plane_restr0.00335213814912805
X-RAY DIFFRACTIONf_dihedral_angle_d16.16571573945588
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7503-2.8190.3340974647891100.3265895732615130X-RAY DIFFRACTION78.1389800179
2.819-2.89520.4338383085891470.3521101030496514X-RAY DIFFRACTION99.5814023023
2.8952-2.98040.4003147861981440.3361963672486526X-RAY DIFFRACTION99.8951624981
2.9804-3.07650.3611308688451440.3314220676046476X-RAY DIFFRACTION99.8190591074
3.0765-3.18640.3620809252621430.3353303590196549X-RAY DIFFRACTION99.9104210212
3.1864-3.31380.3337999044281450.3075552918786518X-RAY DIFFRACTION99.910031489
3.3138-3.46450.3364304655451460.2947731017326542X-RAY DIFFRACTION99.8954443615
3.4645-3.6470.3096769486861450.2947030246796539X-RAY DIFFRACTION99.9252504111
3.647-3.87520.3395892148661480.2882401237286539X-RAY DIFFRACTION99.6275327771
3.8752-4.17390.3135478418221450.2961614207266507X-RAY DIFFRACTION99.7750112494
4.1739-4.59290.2944897034181360.2685645969936583X-RAY DIFFRACTION99.673638926
4.5929-5.25540.2875212899561460.2692815579836522X-RAY DIFFRACTION99.9700149925
5.2554-6.6130.3030121827951480.3033367473546578X-RAY DIFFRACTION99.9702734839
6.613-33.6410.3296518871141460.290048189916537X-RAY DIFFRACTION98.5547854299
Refinement TLS params.Method: refined / Origin x: 31.7341122869 Å / Origin y: -6.86298359013 Å / Origin z: 124.830700335 Å
111213212223313233
T0.220921450585 Å2-0.0141657873714 Å20.0471083326396 Å2-0.369893974163 Å2-0.00147899648028 Å2--0.206266872391 Å2
L0.493824097822 °2-0.10649695731 °20.172108302052 °2-0.0970561472104 °2-0.0188225904338 °2--0.353431178363 °2
S-0.000267176566091 Å °0.018763647809 Å °-0.0240364740366 Å °-0.0315391109778 Å °0.0425416908076 Å °0.0457396805039 Å °0.0399103429185 Å °0.0547447777063 Å °-0.0351803547499 Å °
Refinement TLS groupSelection details: all

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