7V4F

Unique non-heme hydroxylase in biosynthesis of nucleoside antibiotic pathway uncover mechanism of reaction

PDB DOI: https://doi.org/10.2210/pdb7V4F/pdb

Classification: ANTIBIOTIC
Organism(s): Streptomyces sp. MK730-62F2
Expression System: Escherichia coli-Pichia pastoris shuttle vector pPpGUT1
Mutation(s): No

Deposited: 2021-08-13 Released: 2022-02-23
Deposition Author(s): Li, T.L., Saeid, M.Z.
Funding Organization(s): Academia Sinica (Taiwan)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.98 Å
R-Value Free: 0.251
R-Value Work: 0.191
R-Value Observed: 0.196

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

beta-Hydroxylation of alpha-amino-beta-hydroxylbutanoyl-glycyluridine catalyzed by a nonheme hydroxylase ensures the maturation of caprazamycin

Zadeh, S.M., Chen, M.H., Wang, Z.C., Astani, E.K., Lo, I.W., Lin, K.H., Hsu, N.S., Adhikari, K., Lyu, S.Y., Tsai, H.Y., Terasawa, Y., Yabe, M., Yamamoto, K., Ichikawa, S., Li, T.L.

(2022) Commun Chem 5: 87

DOI: https://doi.org/10.1038/s42004-022-00703-6

Macromolecule Content

Total Structure Weight: 42.88 kDa
Atom Count: 2,947
Modelled Residue Count: 334
Deposited Residue Count: 364
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-hydroxylase	A [auth B], B [auth A]	182	Streptomyces sp. MK730-62F2	Mutation(s): 0 Gene Names: cpz10
UniProt
Find proteins for C4NCJ7 (Streptomyces sp. MK730-62F2) Explore C4NCJ7 Go to UniProtKB: C4NCJ7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	C4NCJ7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
5KC (Subject of Investigation/LOI) Query on 5KC Download Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B]	C [auth B]	(2S,3S)-2-azanyl-4-(2-hydroxy-2-oxoethylamino)-3-oxidanyl-butanoic acid C₆ H₁₂ N₂ O₅ ITNGKQLAUYSKRS-UCORVYFPSA-N		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]
SIN Query on SIN Download Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain H [auth A] MOL2 format, chain D [auth B] MOL2 format, chain H [auth A]	D [auth B], H [auth A]	SUCCINIC ACID C₄ H₆ O₄ KDYFGRWQOYBRFD-UHFFFAOYSA-N		Interactions Focus chain D [auth B] Focus chain H [auth A] Interactions & Density Focus chain D [auth B] Focus chain H [auth A]
FE Query on FE Download Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain G [auth B] SDF format, chain I [auth A] SDF format, chain J [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth B] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A]	F [auth B], G [auth B], I [auth A], J [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain F [auth B] Focus chain G [auth B] Focus chain I [auth A] Focus chain J [auth A] Interactions & Density Focus chain F [auth B] Focus chain G [auth B] Focus chain I [auth A] Focus chain J [auth A]
CO2 Query on CO2 Download Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B]	E [auth B]	CARBON DIOXIDE C O₂ CURLTUGMZLYLDI-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]