5YNU | pdb_00005ynu

Crystal structure of an aromatic prenyltransferase FAMD1 from Fischerella ambigua UTEX 1903 in complex with INN

PDB DOI: https://doi.org/10.2210/pdb5YNU/pdb

Classification: TRANSFERASE
Organism(s): Fischerella ambigua UTEX 1903
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2017-10-25 Released: 2018-08-29
Deposition Author(s): Wang, J., Liu, W.D., Chen, C.C., Guo, R.T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.166 (Depositor), 0.168 (DCC)
R-Value Work:
0.112 (Depositor), 0.117 (DCC)
R-Value Observed:
0.115 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Structural insight into a novel indole prenyltransferase in hapalindole-type alkaloid biosynthesis.

Wang, J., Chen, C.C., Yang, Y., Liu, W., Ko, T.P., Shang, N., Hu, X., Xie, Y., Huang, J.W., Zhang, Y., Guo, R.T.

(2018) Biochem Biophys Res Commun 495: 1782-1788

PubMed: 29229390 Search on PubMed
DOI: https://doi.org/10.1016/j.bbrc.2017.12.039
Primary Citation Related Structures:
5YNT, 5YNU, 5YNV, 5YNW

PubMed Abstract:
FamD1 is a novel CloQ/NphB-family indole prenyltransferase which involves in hapalindole-type alkaloid biosynthesis. Here the native FamD1 structure and three protein-ligand complexes are analyzed to investigate the molecular basis of substrate binding and catalysis. FamD1 adopts a typical ABBA architecture of aromatic prenyltransferase, in which the substrate-binding chamber is found in the central β-barrel. The indole-containing acceptor substrate is bound adjacent to the prenyl donor. Based on the complex structures, a catalytic mechanism of FamD1 is proposed. Functional implications on the sister enzyme FamD2 are also discussed.

Organizational Affiliation

Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.

Macromolecule Content

Total Structure Weight: 75.17 kDa
Atom Count: 5,697
Modeled Residue Count: 607
Deposited Residue Count: 658
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
aromatic prenyltransferase	A, B	329	Fischerella ambigua UTEX 1903	Mutation(s): 0 Gene Names: ambP3 EC: 2.5.1.159
UniProt
Find proteins for V5TDY7 (Fischerella ambigua (strain UTEX 1903)) Explore V5TDY7 Go to UniProtKB: V5TDY7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	V5TDY7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DMA Query on DMA Download:Ideal Coordinates CCD File SDF format, chain J [auth B] MOL2 format, chain J [auth B] mmCIF format, chain J [auth B]	J [auth B]	DIMETHYLALLYL DIPHOSPHATE C₅ H₁₂ O₇ P₂ CBIDRCWHNCKSTO-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Interactions & Density Focus chain J [auth B]
POP Query on POP Download:Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	PYROPHOSPHATE 2- H₂ O₇ P₂ XPPKVPWEQAFLFU-UHFFFAOYSA-L		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
8XL Query on 8XL Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain K [auth B] MOL2 format, chain C [auth A] MOL2 format, chain K [auth B] mmCIF format, chain C [auth A] mmCIF format, chain K [auth B]	C [auth A], K [auth B]	3-[(Z)-2-isocyanoethenyl]-1H-indole C₁₁ H₈ N₂ JQMYMZZLIOIXEO-SREVYHEPSA-N		Interactions Focus chain C [auth A] Focus chain K [auth B] Interactions & Density Focus chain C [auth A] Focus chain K [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
IMD Query on IMD Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain L [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain L [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain L [auth B]	D [auth A], E [auth A], F [auth A], G [auth A], L [auth B]	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain L [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain L [auth B]