Structure of PaaZ, a bifunctional enzyme in complex with NADP+ and OCoA

2024-03-27 REL PDBj PDBj PDBj 2019-03-31 2019-09-11 2019-09-11 2024-03-27 Department of Biotechnology (India) DBT/PR12422/MED/31/287/2014 India Council of Scientific & Industrial Research CSIR/37/1606/13/EMR-II India Department of Biotechnology (India) BT/PR5081/INF/22/156/2012 India Medical Research Council (United Kingdom) U105184322 United Kingdom Structure of PaaZ, a bifunctional enzyme in complex with NADP+ and OCoA Gakher L Vinothkumar KR Katagihallimath N Sowdhamini R Sathyanarayanan N Cannone G substrate channeling, bi-functional enzyme, hydrolase, dehydrogenase Sathyanarayanan N Cannone G Gakhar L Katagihallimath N Sowdhamini R Ramaswamy S Vinothkumar KR Molecular basis for metabolite channeling in a ring opening enzyme of the phenylacetate degradation pathway. Nat Commun UK 10 4127 4127 2019 31511507 doi:10.1038/s41467-019-11931-1 2041-1723 EMD-9873 other EM volume

PaaZ Native enzyme

6jqn FULLOVERLAP PaaZ PaaZ 0 1

PaaZ is a bifunctional enzyme that has hydrolase and dehydrogenase activity.

Escherichia coli K-12 K-12 0.44 Bifunctional protein PaaZ Escherichia coli K-12 K-12 0.073969391 6 Escherichia coli BL21(DE3) LEVO MGHHHHHHQQLASFLSGTWQSGRGRSRLIHHAISGEALWEVTSEGLDMAAARQFAIEKGAPALRAMTFIERAAMLKAVAK HLLSEKERFYALSAQTGATRADSWVDIEGGIGTLFTYASLGSRELPDDTLWPEDELIPLSKEGGFAARHLLTSKSGVAVH INAFNFPCWGMLEKLAPTWLGGMPAIIKPATATAQLTQAMVKSIVDSGLVPEGAISLICGSAGDLLDHLDSQDVVTFTGS AATGQMLRVQPNIVAKSIPFTMEADSLNCCVLGEDVTPDQPEFALFIREVVREMTTKAGQKCTAIRRIIVPQALVNAVSD ALVARLQKVVVGDPAQEGVKMGALVNAEQRADVQEKVNILLAAGCEIRLGGQADLSAAGAFFPPTLLYCPQPDETPAVHA TEAFGPVATLMPAQNQRHALQLACAGGGSLAGTLVTADPQIARQFIADAARTHGRIQILNEESAKESTGHGSPLPQLVHG GPGRAGGGEELGGLRAVKHYMQRTAVQGSPTMLAAISKQWVRGAKVEEDRIHPFRKYFEELQPGDSLLTPRRTMTEADIV NFACLSGDHFYAHMDKIAAAESIFGERVVHGYFVLSAAAGLFVDAGVGPVIANYGLESLRFIEPVKPGDTIQVRLTCKRK TLKKQRSAEEKPTGVVEWAVEVFNQHQTPVALYSILTLVARQHGDFVD P77455 3.3.2.12 NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE 0.0007434049999999999 6 NAP OCTANOYL-COENZYME A 0.00089373 6 CO8 singleParticle particle 0.015 7.4 25.0 HEPES 50.0 NACL

Protein was purified and kept in 25mM Hepes buffer and 50 mM NaCl

Quantifoil, UltrAuFoil, R1.2/1.3 GOLD 300 GRAPHENE OXIDE CONTINUOUS GLOW DISCHARGE 300 AIR 0.02

Grids were glow discharged for 5 minutes and then graphene oxide was applied. Subsequently, grids were washed with water 3 times and dried. The graphene oxide grids were then used for freezing.

ETHANE 100 283.15 FEI VITROBOT MARK IV

blotting force 10, blotting time 4 sec, waiting time 15 sec, drying time 0, blotting times 1..

The peak fraction from gel filtration was used for grid preparation. NADP+ and OCoA were added 10 fold excess and incubated for 15 minutes before freezing.

FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 50.0 2.7 2.2 3.2 75000.0 132075.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN 80.0 80.0

Data was collected with EPU software

FEI FALCON III (4k x 4k) COUNTING 4096 4096 1 667 60.0 27.0

The 60 second exposure was saved into 75 frames with each frame ~0.36 e-. The frames were then grouped into 3 for alignment and summed images were used for data processing

counting mode was used

179346

The map from native enzyme (D_13000114900) was low pass filtered to 60A and used as reference.

1 C3 BACK PROJECTION 3.1 FSC 0.143 CUT-OFF RELION 2.0 101503 MAXIMUM LIKELIHOOD RELION 2.0 MAXIMUM LIKELIHOOD RELION 2.0 RELION 2.0 emd_9875.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 412 412 412 0 0 0 412 412 412 436.71997 436.71997 436.71997 90.0 90.0 90.0 X Y Z -0.3496194 0.79728407 0.0001101211 0.016257212 1.06 1.06 1.06 0.085 AUTHOR ::::EMDATABANK.org::::EMD-9875:::: This map is of PaaZ in complex with NADP+ and Octanoyl CoA used for interpretation. OTHER

Real space refinement with secondary structure enabled, minimization and adp

REAL 59.899999999999999 emd_9875_additional_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 412 412 412 0 0 0 412 412 412 436.71997 436.71997 436.71997 90.0 90.0 90.0 X Y Z -0.022296049 0.10229283 0.000055612378 0.0030943002 1.06 1.06 1.06 AUTHOR ::::EMDATABANK.org::::EMD-9875:::: This map is one of the half-maps after refinement. emd_9875_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 412 412 412 0 0 0 412 412 412 436.71997 436.71997 436.71997 90.0 90.0 90.0 X Y Z -0.024177857 0.10037431 0.000054503216 0.003096786 1.06 1.06 1.06 AUTHOR ::::EMDATABANK.org::::EMD-9875:::: This map is one of the half-maps after refinement.