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- PDB-3cr3: Structure of a transient complex between Dha-kinase subunits DhaM... -

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Basic information

Entry
Database: PDB / ID: 3cr3
TitleStructure of a transient complex between Dha-kinase subunits DhaM and DhaL from Lactococcus lactis
Components
  • PTS-dependent dihydroxyacetone kinase, ADP-binding subunit dhaL
  • PTS-dependent dihydroxyacetone kinase, phosphotransferase subunit dhaM
KeywordsTRANSFERASE / Transient Protein-protein complex TRANSFERASE complex PTS-DEPENDENT DIHYDROXYACETONE KINASE / ATP-binding / Glycerol metabolism / Nucleotide-binding / Phosphotransferase system
Function / homology
Function and homology information


phosphoenolpyruvate-glycerone phosphotransferase / phosphoenolpyruvate-glycerone phosphotransferase activity / glycerone kinase activity / phosphoenolpyruvate-dependent sugar phosphotransferase system / glycerol catabolic process / magnesium ion binding / ATP binding / membrane / cytosol
Similarity search - Function
Dihydroxyacetone kinase phosphotransferase subunit, N-terminal domain / Dihydroxyacetone kinase phosphotransferase subunit DhaM / Dihydroxyacetone kinase, subunit L / DhaL domain / Phosphotransferase system, mannose-type IIA component / DhaL domain / DhaL domain superfamily / DAK2 domain / DhaL domain profile. / Dak2 ...Dihydroxyacetone kinase phosphotransferase subunit, N-terminal domain / Dihydroxyacetone kinase phosphotransferase subunit DhaM / Dihydroxyacetone kinase, subunit L / DhaL domain / Phosphotransferase system, mannose-type IIA component / DhaL domain / DhaL domain superfamily / DAK2 domain / DhaL domain profile. / Dak2 / Phosphotransferase system, mannose-type IIA component / Phosphotransferase system, mannose-type IIA component superfamily / : / PTS system fructose IIA component / PTS_EIIA type-4 domain profile. / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / PTS-dependent dihydroxyacetone kinase, phosphotransferase subunit DhaM / PTS-dependent dihydroxyacetone kinase, ADP-binding subunit DhaL
Similarity search - Component
Biological speciesLactococcus lactis subsp. lactis (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsJeckelmann, J.M. / Zurbriggen, A. / Christen, S. / Baumann, U. / Erni, B.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: X-ray Structures of the Three Lactococcus lactis Dihydroxyacetone Kinase Subunits and of a Transient Intersubunit Complex.
Authors: Zurbriggen, A. / Jeckelmann, J.M. / Christen, S. / Bieniossek, C. / Baumann, U. / Erni, B.
History
DepositionApr 4, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _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.pdbx_leaving_atom_flag / _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.end_auth_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PTS-dependent dihydroxyacetone kinase, ADP-binding subunit dhaL
B: PTS-dependent dihydroxyacetone kinase, ADP-binding subunit dhaL
C: PTS-dependent dihydroxyacetone kinase, phosphotransferase subunit dhaM
D: PTS-dependent dihydroxyacetone kinase, phosphotransferase subunit dhaM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,49210
Polymers68,5404
Non-polymers9526
Water3,459192
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8130 Å2
ΔGint-48.1 kcal/mol
Surface area23780 Å2
MethodPISA
2
A: PTS-dependent dihydroxyacetone kinase, ADP-binding subunit dhaL
C: PTS-dependent dihydroxyacetone kinase, phosphotransferase subunit dhaM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7465
Polymers34,2702
Non-polymers4763
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: PTS-dependent dihydroxyacetone kinase, ADP-binding subunit dhaL
D: PTS-dependent dihydroxyacetone kinase, phosphotransferase subunit dhaM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7465
Polymers34,2702
Non-polymers4763
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
A: PTS-dependent dihydroxyacetone kinase, ADP-binding subunit dhaL
D: PTS-dependent dihydroxyacetone kinase, phosphotransferase subunit dhaM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7465
Polymers34,2702
Non-polymers4763
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
B: PTS-dependent dihydroxyacetone kinase, ADP-binding subunit dhaL
C: PTS-dependent dihydroxyacetone kinase, phosphotransferase subunit dhaM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7465
Polymers34,2702
Non-polymers4763
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.133, 146.842, 58.483
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D

NCS domain segments:

Component-ID: 1 / Refine code: 5

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUALAALAAA1 - 1921 - 192
21LEULEUALAALABB1 - 1921 - 192
12TYRTYRLYSLYSCC3 - 1231 - 121
22TYRTYRLYSLYSDD3 - 1231 - 121

NCS ensembles :
ID
1
2

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Components

#1: Protein PTS-dependent dihydroxyacetone kinase, ADP-binding subunit dhaL


Mass: 20909.639 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: lacI(q), oriR ColE1, bla
Source: (gene. exp.) Lactococcus lactis subsp. lactis (lactic acid bacteria)
Strain: IL1403 / Gene: dhaL / Plasmid: pMS-DhaKLM / Production host: Escherichia coli (E. coli) / Strain (production host): CB-delta-KLM
References: UniProt: Q9CIV7, Transferases; Transferring phosphorus-containing groups
#2: Protein PTS-dependent dihydroxyacetone kinase, phosphotransferase subunit dhaM / Phosphotransferase enzyme IIA component / PTS system EIIA component


Mass: 13360.600 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus lactis subsp. lactis (lactic acid bacteria)
Gene: dhaM / Plasmid: pMS-DhaKLM / Production host: Escherichia coli (E. coli) / Strain (production host): CB-delta-KLM
References: UniProt: Q9CIV6, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 192 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.32 Å3/Da / Density % sol: 47.03 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris/HCl, 0.2 M LiSO4, 36 % PEG 4000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 0.97885,0.97823,0.97240
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 8, 2006
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978851
20.978231
30.97241
ReflectionResolution: 2.1→147.442 Å / Num. all: 37982 / Num. obs: 37982 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Biso Wilson estimate: 26.5 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 22.2
Reflection shellResolution: 2.1→2.21 Å / % possible obs: 100 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.161 / Mean I/σ(I) obs: 8.1 / Num. unique all: 5440 / Rsym value: 0.214 / % possible all: 24.4

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.1→66.23 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.898 / SU B: 9.876 / SU ML: 0.144 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.261 / ESU R Free: 0.209 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.263 1897 5 %RANDOM
Rwork0.219 ---
all0.22168 37982 --
obs0.22168 37952 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.17 Å2
Baniso -1Baniso -2Baniso -3
1-3.31 Å20 Å20 Å2
2---2.51 Å20 Å2
3----0.79 Å2
Refinement stepCycle: LAST / Resolution: 2.1→66.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4726 0 58 192 4976
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0224840
X-RAY DIFFRACTIONr_angle_refined_deg1.2151.9956532
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8885622
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.48826.105190
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.55615890
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.1711514
X-RAY DIFFRACTIONr_chiral_restr0.0780.2768
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023482
X-RAY DIFFRACTIONr_nbd_refined0.2040.22520
X-RAY DIFFRACTIONr_nbtor_refined0.2930.23421
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2170.2266
X-RAY DIFFRACTIONr_metal_ion_refined0.1030.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1820.228
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1530.28
X-RAY DIFFRACTIONr_mcbond_it0.8121.53186
X-RAY DIFFRACTIONr_mcangle_it1.05824912
X-RAY DIFFRACTIONr_scbond_it2.06231887
X-RAY DIFFRACTIONr_scangle_it3.074.51620
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A768MEDIUM POSITIONAL0.150.5
1A673LOOSE POSITIONAL0.425
1A768MEDIUM THERMAL0.972
1A673LOOSE THERMAL1.4810
2C484MEDIUM POSITIONAL0.160.5
2C438LOOSE POSITIONAL0.645
2C484MEDIUM THERMAL0.712
2C438LOOSE THERMAL1.5610
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 140 -
Rwork0.218 2605 -
all-2745 -
obs-2745 100 %

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