4NTD | pdb_00004ntd

Crystal structure of HlmI

PDB DOI: https://doi.org/10.2210/pdb4NTD/pdb

Classification: OXIDOREDUCTASE
Organism(s): Streptomyces clavuligerus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2013-12-02 Released: 2014-03-05
Deposition Author(s): Scharf, D.H., Groll, M., Habel, A., Heinekamp, T., Hertweck, C., Brakhage, A.A., Huber, E.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.159 (Depositor), 0.161 (DCC)
R-Value Work:
0.146 (Depositor), 0.148 (DCC)
R-Value Observed:
0.147 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Flavoenzyme-Catalyzed Formation of Disulfide Bonds in Natural Products

Scharf, D.H., Groll, M., Habel, A., Heinekamp, T., Hertweck, C., Brakhage, A.A., Huber, E.M.

(2014) Angew Chem Int Ed Engl 53: 2221-2224

PubMed: 24446392 Search on PubMed
DOI: https://doi.org/10.1002/anie.201309302
Primary Citation Related Structures:
4NTC, 4NTD, 4NTE

PubMed Abstract:
Nature provides a rich source of compounds with diverse chemical structures and biological activities, among them, sulfur-containing metabolites from bacteria and fungi. Some of these compounds bear a disulfide moiety that is indispensable for their bioactivity. Specialized oxidoreductases such as GliT, HlmI, and DepH catalyze the formation of this disulfide bridge in the virulence factor gliotoxin, the antibiotic holomycin, and the anticancer drug romidepsin, respectively. We have examined all three enzymes by X-ray crystallography and activity assays. Despite their differently sized substrate binding clefts and hence, their diverse substrate preferences, a unifying reaction mechanism is proposed based on the obtained crystal structures and further supported by mutagenesis experiments.

Organizational Affiliation

Departments of Molecular and Applied Microbiology and Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, and Friedrich Schiller University Jena, Beutenbergstrasse 11a, 07745 Jena (Germany).

Macromolecule Content

Total Structure Weight: 37.3 kDa
Atom Count: 3,036
Modeled Residue Count: 318
Deposited Residue Count: 340
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thioredoxin reductase	A	340	Streptomyces clavuligerus	Mutation(s): 0 Gene Names: SCLAV_5275
UniProt
Find proteins for E2PZ87 (Streptomyces clavuligerus) Explore E2PZ87 Go to UniProtKB: E2PZ87
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	E2PZ87
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
GSH Query on GSH Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	Glutathione C₁₀ H₁₇ N₃ O₆ S RWSXRVCMGQZWBV-WDSKDSINSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_002593 (GSH) Query on PRD_002593	B [auth A]	Glutathione	Peptide-like / Oxidation-reduction		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.159 (Depositor), 0.161 (DCC)
R-Value Work: 0.146 (Depositor), 0.148 (DCC)
R-Value Observed: 0.147 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.35	α = 90
b = 96.35	β = 90
c = 133.49	γ = 120

Software Package:

Software Name	Purpose
XDS	data scaling
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2014-03-05

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-03-05
Type: Initial release
Version 1.1: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description