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- PDB-6wb7: Acarbose Kinase AcbK as a Complex with Acarbose and AMP-PNP -

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Basic information

Entry
Database: PDB / ID: 6wb7
TitleAcarbose Kinase AcbK as a Complex with Acarbose and AMP-PNP
ComponentsAcarbose 7(IV)-phosphotransferase
KeywordsTRANSFERASE / CARBOHYDRATE KINASE / ACARBOSE / NUCLEOTIDE BINDING / ATP BINDING / METAL ION BINDING / RIBOKINASE ACTIVITY / COMPLEX
Function / homology
Function and homology information


acarbose 7IV-phosphotransferase / phosphotransferase activity, alcohol group as acceptor / kinase activity
Similarity search - Function
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
alpha-acarbose / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / : / Acarbose 7(IV)-phosphotransferase
Similarity search - Component
Biological speciesActinoplanes sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.44 Å
AuthorsJeffrey, P.D. / Balaich, J.N. / Estrella, M.A. / Donia, M.S.
Funding support1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)
CitationJournal: Nature / Year: 2021
Title: The human microbiome encodes resistance to the antidiabetic drug acarbose.
Authors: Balaich, J. / Estrella, M. / Wu, G. / Jeffrey, P.D. / Biswas, A. / Zhao, L. / Korennykh, A. / Donia, M.S.
History
DepositionMar 26, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 8, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Dec 15, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Acarbose 7(IV)-phosphotransferase
B: Acarbose 7(IV)-phosphotransferase
C: Acarbose 7(IV)-phosphotransferase
D: Acarbose 7(IV)-phosphotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,72121
Polymers134,7474
Non-polymers4,97417
Water6,846380
1
A: Acarbose 7(IV)-phosphotransferase
B: Acarbose 7(IV)-phosphotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,83310
Polymers67,3742
Non-polymers2,4598
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8080 Å2
ΔGint-78 kcal/mol
Surface area21930 Å2
MethodPISA
2
C: Acarbose 7(IV)-phosphotransferase
D: Acarbose 7(IV)-phosphotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,88811
Polymers67,3742
Non-polymers2,5149
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7890 Å2
ΔGint-81 kcal/mol
Surface area22250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.545, 50.268, 127.794
Angle α, β, γ (deg.)89.060, 80.180, 71.810
Int Tables number1
Space group name H-MP1

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Components

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Protein / Sugars , 2 types, 8 molecules ABCD

#1: Protein
Acarbose 7(IV)-phosphotransferase / Acarbose 7-kinase


Mass: 33686.797 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Actinoplanes sp. (strain ATCC 31044 / CBS 674.73 / SE50/110) (bacteria)
Strain: ATCC 31044 / CBS 674.73 / SE50/110 / Gene: acbK, ACPL_3675 / Plasmid: pET28a / Production host: Escherichia coli (E. coli)
References: UniProt: Q8RMD4, acarbose 7IV-phosphotransferase
#2: Polysaccharide
4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D- ...4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-acarbose


Type: oligosaccharide, Oligosaccharide / Class: Inhibitor / Mass: 645.606 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-acarbose
DescriptorTypeProgram
WURCS=2.0/2,3,2/[a2122h-1a_1-5][a2122m-1a_1-5_4*NC^SC^SC^SC^RCCO/7=^ZC$3/6O/5O/4O]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-6-deoxy-Glcp4N]{[(4+1)][<C7O4>]{}}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 393 molecules

#3: Chemical
ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mn
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 380 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.12 Å3/Da / Density % sol: 41.99 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.25 M NaCl, 16% w/v PEG 3350, 10 mM MnCl2, 6 mM AMP-PNP, and 50 mM Acarbose

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9201 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Aug 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 2.44→28.533 Å / Num. obs: 40165 / % possible obs: 97.3 % / Redundancy: 2.4 % / Biso Wilson estimate: 31.29 Å2 / CC1/2: 0.983 / Rmerge(I) obs: 0.136 / Rpim(I) all: 0.106 / Rrim(I) all: 0.173 / Net I/σ(I): 5.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.44-2.52.40.665702028950.5620.5250.8521.492.4
10.91-28.532.60.0411394380.9960.0320.05218.493.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.5.21data scaling
PHASERphasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.25data extraction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6WB4

6wb4


Resolution: 2.44→28.532 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 27.93
RfactorNum. reflection% reflection
Rfree0.2498 2031 5.06 %
Rwork0.1867 --
obs0.19 40153 97.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 99.88 Å2 / Biso mean: 32.4481 Å2 / Biso min: 12.37 Å2
Refinement stepCycle: final / Resolution: 2.44→28.532 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8752 0 309 380 9441
Biso mean--34.15 30.63 -
Num. residues----1176
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0089313
X-RAY DIFFRACTIONf_angle_d0.7912741
X-RAY DIFFRACTIONf_chiral_restr0.0271505
X-RAY DIFFRACTIONf_plane_restr0.0031645
X-RAY DIFFRACTIONf_dihedral_angle_d13.433293
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.44-2.49650.33711290.267252093
2.4965-2.55880.33411210.2643246797
2.5588-2.6280.34771260.2567257997
2.628-2.70530.34111110.2456249497
2.7053-2.79250.33381510.2355256397
2.7925-2.89220.27831260.228249798
2.8922-3.00790.2991510.2319256098
3.0079-3.14460.29651240.2255259698
3.1446-3.31020.30151250.2031254498
3.3102-3.51720.26861330.1912255199
3.5172-3.78820.24511410.1729256898
3.7882-4.16840.21231520.1534255198
4.1684-4.76920.16491250.1315256998
4.7692-5.99950.20771520.1477253698
5.9995-28.5320.17871640.1399252798

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