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Structure paper

TitleEndowing homodimeric carbamoyltransferase GdmN with iterative functions through structural characterization and mechanistic studies.
Journal, issue, pagesNat Commun, Vol. 13, Page 6617-6617, Year 2022
Publish dateNov 12, 2021 (structure data deposition date)
AuthorsWei, J. / Zhang, X. / Zhou, Y. / Cheng, X. / Lin, Z. / Tang, M. / Zheng, J. / Wang, B. / Kang, Q. / Bai, L.
External linksNat Commun / PubMed:36329057
MethodsX-ray diffraction
Resolution1.98 - 2.88 Å
Structure data

PDB-7vx0:
The structure of GdmN complex with ATP
Method: X-RAY DIFFRACTION / Resolution: 2.0 Å

PDB-7vyj:
The structure of GdmN in complex with carbamoyl adenylate intermediate
Method: X-RAY DIFFRACTION / Resolution: 1.98 Å

PDB-7vyo:
The structure of GdmN
Method: X-RAY DIFFRACTION / Resolution: 2.25 Å

PDB-7vyp:
The structure of GdmN complex with the natural tetrahedral intermediate, carbamoylated derivative, and AMP
Method: X-RAY DIFFRACTION / Resolution: 2.88 Å

PDB-7vzn:
The structure of GdmN in complex with carbamoyl adenylate intermediate and 20-O-methyl-19-chloroproansamitocin
Method: X-RAY DIFFRACTION / Resolution: 2.1 Å

PDB-7vzq:
The structure of GdmN V24Y/G157A/R158A/G188R mutant in complex with carbamoyl adenylate intermediate
Method: X-RAY DIFFRACTION / Resolution: 2.1 Å

PDB-7vzu:
The structure of GdmN Y82F mutant
Method: X-RAY DIFFRACTION / Resolution: 2.3 Å

PDB-7vzy:
The structure of GdmN complex with AMP and 20-O-methyl-19-chloroproansamitocin
Method: X-RAY DIFFRACTION / Resolution: 2.81 Å

PDB-7vzz:
The structure of GdmN in complex with the natural tetrahedral intermediate, carbamoyl adenylate, and 20-O-methyl-19-chloroproansamitocin
Method: X-RAY DIFFRACTION / Resolution: 2.85 Å

Chemicals

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

ChemComp-FE:
Unknown entry

ChemComp-GOL:
GLYCEROL

ChemComp-SO4:
SULFATE ION

ChemComp-EDO:
1,2-ETHANEDIOL

ChemComp-CP:
PHOSPHORIC ACID MONO(FORMAMIDE)ESTER

ChemComp-PO4:
PHOSPHATE ION

ChemComp-HOH:
WATER

ChemComp-CA0:
5'-O-[(S)-(carbamoyloxy)(hydroxy)phosphoryl]adenosine

ChemComp-PEG:
DI(HYDROXYETHYL)ETHER

ChemComp-CL:
Unknown entry

ChemComp-82Z:
[(5S,6E,8S,9S,12R,13E,15E)-21-chloranyl-12,20-dimethoxy-6,8,16-trimethyl-5-oxidanyl-3,11-bis(oxidanylidene)-2-azabicyclo[16.3.1]docosa-1(21),6,13,15,18(22),19-hexaen-9-yl] carbamate

ChemComp-AMP:
ADENOSINE MONOPHOSPHATE / AMP*YM

ChemComp-8CW:
[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl [(~{S})-azanyl-[[(5~{S},6~{E},8~{S},9~{S},12~{R},13~{E},15~{E})-21-chloranyl-12,20-dimethoxy-6,8,16-trimethyl-5-oxidanyl-3,11-bis(oxidanylidene)-2-azabicyclo[16.3.1]docosa-1(21),6,13,15,18(22),19-hexaen-9-yl]oxy]-oxidanyl-methyl] hydrogen phosphate

ChemComp-83Z:
(5~{S},6~{E},8~{S},9~{S},12~{R},15~{E})-21-chloranyl-12,20-dimethoxy-6,8,16-trimethyl-5,9-bis(oxidanyl)-2-azabicyclo[16.3.1]docosa-1(21),6,15,18(22),19-pentaene-3,11-dione

Source
  • streptomyces hygroscopicus (bacteria)
KeywordsTRANSFERASE / Carbamoylation / Ansamycins antibiotics / Homodimer / Carbamoyltransferase

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