6VEB

Precorrin-2-bound S128A S. typhimurium siroheme synthase


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 

Starting Model: experimental
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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

  • 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Siroheme synthase
A, B
457Salmonella enterica subsp. entericaMutation(s): 1 
Gene Names: 
cobAcysGA4O23_22680A4O45_23495A5895_10260ACK40_21915AH543_24340AL864_13490B9C63_23695CC394_23355CC828_23245CPY04_23335CQF73_24090CQH69_23770CQM83_24035CQM91_23950CWG97_04420D4392_23335D4408_24080D4427_23490D4428_23600D4507_23395D4515_23795D4E09_23835D4E59_23545D4E64_23910D4E70_23615D4E75_22760D4F17_23250D4F20_23570D4F29_23000D4F49_23820D4F54_21825D4F87_23560D4G07_23810D4G50_23805D4X67_23945D4Y38_22995D4Y42_23265D4Y96_23470D4Z75_23120D5782_23070D5836_24310D5881_23125D5A65_24210D5B23_24060D5C00_23760D5C21_23840D5O45_24060D5O48_24255D5P09_24125D5P22_23765D5P36_21245D5P54_19825D5P71_21870D5Q05_23505D5X20_22850D5Y01_23010D5Y08_23660D6379_23290D6429_21865D6J55_23675D6J74_23505D6P41_23695D6Q63_23855D6R58_22975D6R98_23865D6S02_23370D6S45_23570D6S74_23640D6S82_23760D6T18_23595D7N15_23195D7N26_23945D7N30_23525D7N52_23575D7O25_23820D7O77_23450D8Q64_21745D8S35_24215D8S62_23725D8S66_24520D9O71_23255D9P12_23260D9P13_23305D9P51_22965DFQ85_08280DK030_07475DK113_22975DK687_23375DKT04_23460DKT40_22680DKU65_22440DKV20_24340DL110_23435DL115_21645DL130_23925DL146_23455DL163_23880DLB18_22580DLB43_23490DLC24_22825DLF22_23220DLF29_24400DLF33_23155DLF36_23470DLM10_23710DLM26_23890DLQ73_23465DLQ92_22925DLR05_23380DM006_23485DM323_23285DM367_24075DM371_23830DM705_23905DMA96_24030DMB04_23395DML85_20570DMM43_23865DMO61_22925DMO65_23235DMV32_23255DN092_21835DN096_17090DN123_18420DN182_24420DN282_24210DN317_23660DN319_23985DN362_23995DNI00_21425DNI67_22410DNI82_24175DNJ17_23520DNM80_24185DNU17_23255DNU67_23755DNU84_23130DNV04_23575DNV18_24435DNV28_23830DNV55_23115DNV59_23205DNV93_24240DNY86_24000DNZ02_24100DNZ29_23620DO557_23340DO565_23090DO591_24015DO596_23880DO617_23890DO630_23685DO638_23100DO681_24120DO731_24105DO981_16865DOA55_23120DOA87_24295DOA98_24055DOB00_23930DOC25_23595DOC31_12165DOH04_23240DOH41_23555DOH63_23205DOH69_23565DOH81_23800DOI78_23195DOJ02_24430DOJ11_19160DOR51_23145DOV77_22745DOV78_22375DOW52_23180DOX30_23900DP688_24205DP693_23150DP698_23535DP703_24195DP713_24390DP736_24050DP778_23450DP800_23450DP859_23875DPA01_22585DPA36_23285DPB61_23630DPD61_23230DPE40_23250DPE76_21335DPE98_22330DPP34_22980DPP41_24295DPP49_23850DPP70_23140DPS71_23220DPT22_23580DPT74_23805DPU13_22980DPY81_22995DPZ65_20145DQ076_23430DQ082_23395DQ880_23785DQ933_23705DQC12_20050DQC81_21240DQC88_22075DQD11_23435DQD59_15735DQE08_19980DQE20_22815DQE42_23995DQJ22_22855DQK43_23325DQQ27_23480DQR39_23575DQR74_22755DQS55_23550DQS89_23430DQT21_24150DQT40_20085DQT67_24145DQZ89_22730DRA21_23780DRA26_23910DRA37_23360DRD40_23755DRD55_22850DRE12_23690DRE69_22130DRE92_22615DRK49_23400DRL53_23670DRL65_24040DRL96_23465DRM39_23520DRM43_23115DRT45_23760DRT76_23250DRU07_22490DRV17_23930DRV44_23300DRY30_24240DS168_23130DS336_23415DS372_23280DS485_23475DS493_23550DS572_23890DS605_22630DS651_22985DS666_23240DS688_24580DS708_23885DSA90_23105DSB20_24505DSB26_23530DSB29_23215DSB36_23820DSF03_22695DSF23_12440DSF57_23350DSF93_23505DSG69_23455DSM73_23875DSM81_23920DSM96_23930DSN18_23205DSR78_24250DSR92_21190DSS12_22290DSS37_23620DSS62_22775DSS75_23430DSS77_24315DST25_23085DT168_23620DTE69_22625DTG45_23495DTG68_22565DTG80_23765DTT99_19805DTV63_23440DTW19_23225DU084_22390DU129_23835DU131_22825DU159_23825DU165_23925DU205_24120DU207_23795DU257_24320DU750_19160DU762_23420DU854_22090DU873_23310DU916_20895DU947_24440DUB79_23050DUB80_23255DUB82_23235DUP91_23210DUQ41_22935DUQ55_23840DUQ58_20775DUR69_18130DUR90_22210DUU54_20070DUU71_24500DUU80_23985DUU92_23505DUV51_23775DV01_23265DVF71_23695DVG21_22945E5N87_17725EBJ71_23145EBJ89_23915EBK43_23020EBK48_23810EBO89_23265EBO94_22695EBP12_23765EC422_22620EC429_22615EC434_22830EC491_23745EC492_18880ECA94_23540ECD30_24635ED477_23805EDK87_23895EDL36_23455EDL46_24280EEA59_23510EEA93_23330EER72_21930EES08_23010EF649_23005EGM25_23675EH130_23450EHB46_23510EHB61_21570EHD20_23630EIE60_23400EIL32_22805EIW55_23130EIW93_23605FD75_21980PK95_22395S639_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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP25924
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PQ2 (Subject of Investigation/LOI)
Query on PQ2

Download Ideal Coordinates CCD File 
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
NAD
Query on NAD

Download Ideal Coordinates CCD File 
D [auth A]NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
SAH
Query on SAH

Download Ideal Coordinates CCD File 
C [auth A],
J [auth B]
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
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
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 = 59.682α = 90
b = 99.489β = 90
c = 146.037γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report

Currently 6VEB does not have a validation slider image.



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United StatesMCB1149763

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