6VEB

Precorrin-2-bound S128A S. typhimurium siroheme synthase

PDB DOI: https://doi.org/10.2210/pdb6VEB/pdb

Classification: TRANSFERASE
Organism(s): Salmonella enterica subsp. enterica
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2019-12-31 Released: 2020-03-04
Deposition Author(s): Pennington, J.M., Stroupe, M.E.
Funding Organization(s): National Science Foundation (NSF, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.55 Å
R-Value Free: 0.245
R-Value Work: 0.164
R-Value Observed: 0.169

wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history.

Literature

Siroheme synthase orients substrates for dehydrogenase and chelatase activities in a common active site.

Pennington, J.M., Kemp, M., McGarry, L., Chen, Y., Stroupe, M.E.

(2020) Nat Commun 11: 864-864

PubMed: 32054833 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s41467-020-14722-1
Primary Citation of Related Structures:
6P5X, 6P5Z, 6P7C, 6P7D, 6PQZ, 6PR0, 6PR1, 6PR2, 6PR3, 6PR4, 6ULU, 6VEB

PubMed Abstract:
Siroheme is the central cofactor in a conserved class of sulfite and nitrite reductases that catalyze the six-electron reduction of sulfite to sulfide and nitrite to ammonia. In Salmonella enterica serovar Typhimurium, siroheme is produced by a trifunctional enzyme, siroheme synthase (CysG). A bifunctional active site that is distinct from its methyltransferase activity catalyzes the final two steps, NAD ⁺-dependent dehydrogenation and iron chelation. How this active site performs such different chemistries is unknown. Here, we report the structures of CysG bound to precorrin-2, the initial substrate; sirohydrochlorin, the dehydrogenation product/chelation substrate; and a cobalt-sirohydrochlorin product. We identified binding poses for all three tetrapyrroles and tested the roles of specific amino acids in both activities to give insights into how a bifunctional active site catalyzes two different chemistries and acts as an iron-specific chelatase in the final step of siroheme synthesis.

Organizational Affiliation

Department of Biological Science and Institute of Molecular Biophysics, Florida State University, 91 Chieftan Way, Tallahassee, FL, 32306, USA.

Macromolecule Content

Total Structure Weight: 102.93 kDa
Atom Count: 7,493
Modelled Residue Count: 900
Deposited Residue Count: 914
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Siroheme synthase	A, B	457	Salmonella enterica subsp. enterica	Mutation(s): 1 Gene Names: cobA, cysG, A4O23_22680, A4O45_23495, A5895_10260, ACK40_21915, AH543_24340, AL864_13490, B9C63_23695, CC394_23355... cobA, cysG, A4O23_22680, A4O45_23495, A5895_10260, ACK40_21915, AH543_24340, AL864_13490, B9C63_23695, CC394_23355, CC828_23245, CPY04_23335, CQF73_24090, CQH69_23770, CQM83_24035, CQM91_23950, CWG97_04420, D4392_23335, D4408_24080, D4427_23490, D4428_23600, D4507_23395, D4515_23795, D4E09_23835, D4E59_23545, D4E64_23910, D4E70_23615, D4E75_22760, D4F17_23250, D4F20_23570, D4F29_23000, D4F49_23820, D4F54_21825, D4F87_23560, D4G07_23810, D4G50_23805, D4X67_23945, D4Y38_22995, D4Y42_23265, D4Y96_23470, D4Z75_23120, D5782_23070, D5836_24310, D5881_23125, D5A65_24210, D5B23_24060, D5C00_23760, D5C21_23840, D5O45_24060, D5O48_24255, D5P09_24125, D5P22_23765, D5P36_21245, D5P54_19825, D5P71_21870, D5Q05_23505, D5X20_22850, D5Y01_23010, D5Y08_23660, D6379_23290, D6429_21865, D6J55_23675, D6J74_23505, D6P41_23695, D6Q63_23855, D6R58_22975, D6R98_23865, D6S02_23370, D6S45_23570, D6S74_23640, D6S82_23760, D6T18_23595, D7N15_23195, D7N26_23945, D7N30_23525, D7N52_23575, D7O25_23820, D7O77_23450, D8Q64_21745, D8S35_24215, D8S62_23725, D8S66_24520, D9O71_23255, D9P12_23260, D9P13_23305, D9P51_22965, DFQ85_08280, DK030_07475, DK113_22975, DK687_23375, DKT04_23460, DKT40_22680, DKU65_22440, DKV20_24340, DL110_23435, DL115_21645, DL130_23925, DL146_23455, DL163_23880, DLB18_22580, DLB43_23490, DLC24_22825, DLF22_23220, DLF29_24400, DLF33_23155, DLF36_23470, DLM10_23710, DLM26_23890, DLQ73_23465, DLQ92_22925, DLR05_23380, DM006_23485, DM323_23285, DM367_24075, DM371_23830, DM705_23905, DMA96_24030, DMB04_23395, DML85_20570, DMM43_23865, DMO61_22925, DMO65_23235, DMV32_23255, DN092_21835, DN096_17090, DN123_18420, DN182_24420, DN282_24210, DN317_23660, DN319_23985, DN362_23995, DNI00_21425, DNI67_22410, DNI82_24175, DNJ17_23520, DNM80_24185, DNU17_23255, DNU67_23755, DNU84_23130, DNV04_23575, DNV18_24435, DNV28_23830, DNV55_23115, DNV59_23205, DNV93_24240, DNY86_24000, DNZ02_24100, DNZ29_23620, DO557_23340, DO565_23090, DO591_24015, DO596_23880, DO617_23890, DO630_23685, DO638_23100, DO681_24120, DO731_24105, DO981_16865, DOA55_23120, DOA87_24295, DOA98_24055, DOB00_23930, DOC25_23595, DOC31_12165, DOH04_23240, DOH41_23555, DOH63_23205, DOH69_23565, DOH81_23800, DOI78_23195, DOJ02_24430, DOJ11_19160, DOR51_23145, DOV77_22745, DOV78_22375, DOW52_23180, DOX30_23900, DP688_24205, DP693_23150, DP698_23535, DP703_24195, DP713_24390, DP736_24050, DP778_23450, DP800_23450, DP859_23875, DPA01_22585, DPA36_23285, DPB61_23630, DPD61_23230, DPE40_23250, DPE76_21335, DPE98_22330, DPP34_22980, DPP41_24295, DPP49_23850, DPP70_23140, DPS71_23220, DPT22_23580, DPT74_23805, DPU13_22980, DPY81_22995, DPZ65_20145, DQ076_23430, DQ082_23395, DQ880_23785, DQ933_23705, DQC12_20050, DQC81_21240, DQC88_22075, DQD11_23435, DQD59_15735, DQE08_19980, DQE20_22815, DQE42_23995, DQJ22_22855, DQK43_23325, DQQ27_23480, DQR39_23575, DQR74_22755, DQS55_23550, DQS89_23430, DQT21_24150, DQT40_20085, DQT67_24145, DQZ89_22730, DRA21_23780, DRA26_23910, DRA37_23360, DRD40_23755, DRD55_22850, DRE12_23690, DRE69_22130, DRE92_22615, DRK49_23400, DRL53_23670, DRL65_24040, DRL96_23465, DRM39_23520, DRM43_23115, DRT45_23760, DRT76_23250, DRU07_22490, DRV17_23930, DRV44_23300, DRY30_24240, DS168_23130, DS336_23415, DS372_23280, DS485_23475, DS493_23550, DS572_23890, DS605_22630, DS651_22985, DS666_23240, DS688_24580, DS708_23885, DSA90_23105, DSB20_24505, DSB26_23530, DSB29_23215, DSB36_23820, DSF03_22695, DSF23_12440, DSF57_23350, DSF93_23505, DSG69_23455, DSM73_23875, DSM81_23920, DSM96_23930, DSN18_23205, DSR78_24250, DSR92_21190, DSS12_22290, DSS37_23620, DSS62_22775, DSS75_23430, DSS77_24315, DST25_23085, DT168_23620, DTE69_22625, DTG45_23495, DTG68_22565, DTG80_23765, DTT99_19805, DTV63_23440, DTW19_23225, DU084_22390, DU129_23835, DU131_22825, DU159_23825, DU165_23925, DU205_24120, DU207_23795, DU257_24320, DU750_19160, DU762_23420, DU854_22090, DU873_23310, DU916_20895, DU947_24440, DUB79_23050, DUB80_23255, DUB82_23235, DUP91_23210, DUQ41_22935, DUQ55_23840, DUQ58_20775, DUR69_18130, DUR90_22210, DUU54_20070, DUU71_24500, DUU80_23985, DUU92_23505, DUV51_23775, DV01_23265, DVF71_23695, DVG21_22945, E5N87_17725, EBJ71_23145, EBJ89_23915, EBK43_23020, EBK48_23810, EBO89_23265, EBO94_22695, EBP12_23765, EC422_22620, EC429_22615, EC434_22830, EC491_23745, EC492_18880, ECA94_23540, ECD30_24635, ED477_23805, EDK87_23895, EDL36_23455, EDL46_24280, EEA59_23510, EEA93_23330, EER72_21930, EES08_23010, EF649_23005, EGM25_23675, EH130_23450, EHB46_23510, EHB61_21570, EHD20_23630, EIE60_23400, EIL32_22805, EIW55_23130, EIW93_23605, FD75_21980, PK95_22395, S639_25165 EC: 2.1.1.107 (PDB Primary Data), 1.3.1.76 (PDB Primary Data), 4.99.1.4 (PDB Primary Data)
UniProt
Find proteins for P25924 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore P25924 Go to UniProtKB: P25924
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P25924
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PQ2 (Subject of Investigation/LOI) Query on PQ2 Download Ideal Coordinates CCD File SDF format, chain K [auth B] MOL2 format, chain K [auth B]	K [auth B]	3,3',3'',3'''-[(7S,8S,12S,13S)-3,8,13,17-tetrakis(carboxymethyl)-8,13-dimethyl-7,8,12,13,20,24-hexahydroporphyrin-2,7,1 2,18-tetrayl]tetrapropanoic acid C₄₂ H₄₈ N₄ O₁₆ CSWLXNNNLVVXKD-ORDMNHKBSA-N		Interactions Focus chain K [auth B] Interactions & Density Focus chain K [auth B]
NAD Query on NAD Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A]	D [auth A]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
SAH Query on SAH Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain J [auth B] MOL2 format, chain C [auth A] MOL2 format, chain J [auth B]	C [auth A], J [auth B]	S-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		Interactions Focus chain C [auth A] Focus chain J [auth B] Interactions & Density Focus chain C [auth A] Focus chain J [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B]	E [auth A] F [auth A] G [auth A] H [auth A] I [auth A] E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], L [auth B], M [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth B] Focus chain M [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth B] Focus chain M [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.55 Å
R-Value Free: 0.245
R-Value Work: 0.164
R-Value Observed: 0.169
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.682	α = 90
b = 99.489	β = 90
c = 146.037	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2020-03-04

Deposition Author(s):

Pennington, J.M.

Stroupe, M.E.

Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	MCB1149763

Revision History (Full details and data files)

Version 1.0: 2020-03-04
Type: Initial release
Version 1.1: 2023-10-11
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary