4UFQ

Structure of a novel Hyaluronidase (Hyal_Sk) from Streptomyces koganeiensis.

PDB DOI: https://doi.org/10.2210/pdb4UFQ/pdb

Classification: HYDROLASE
Organism(s): Streptomyces koganeiensis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2015-03-18 Released: 2016-04-13
Deposition Author(s): Gavira, J.A., Messina, L., Pernagallo, S., Unciti-Broceta, J.D., Conejero-Muriel, M., Diaz-Mochon, J.J., Vaccaro, S., Caruso, S., Musumeci, L., Bisicchia, S., Di Pasquale, R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free: 0.174
R-Value Work: 0.149
R-Value Observed: 0.151

wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

Identification and Characterization of a Bacterial Hyaluronidase and its Production in Recombinant Form.

Messina, L., Gavira, J.A., Pernagallo, S., Unciti-Broceta, J.D., Sanchez Martin, R.M., Diaz-Mochon, J.J., Vaccaro, S., Conejero-Muriel, M., Pineda-Molina, E., Caruso, S., Musumeci, L., Di Pasquale, R., Pontillo, A., Sincinelli, F., Pavan, M., Secchieri, C.

(2016) FEBS Lett 590: 2180

PubMed: 27311405 Search on PubMed
DOI: https://doi.org/10.1002/1873-3468.12258
Primary Citation of Related Structures:
4UFQ

PubMed Abstract:
Hyaluronidases (Hyals) are broadly used in medical applications to facilitate the dispersion and/or absorption of fluids or medications. This study reports the isolation, cloning, and industrial-scale recombinant production, purification and full characterization, including X-ray structure determination at 1.45 Å, of an extracellular Hyal from the nonpathogenic bacterium Streptomyces koganeiensis. The recombinant S. koganeiensis Hyal (rHyal_Sk) has a novel bacterial catalytic domain with high enzymatic activity, compared with commercially available Hyals, and is more thermostable and presents higher proteolytic resistance, with activity over a broad pH range. Moreover, rHyal_Sk exhibits remarkable substrate specificity for hyaluronic acid (HA) and poses no risk of animal cross-infection.

Organizational Affiliation

Local Unit Fidia Research Sud, Fidia Farmaceutici S.p.A., Noto, Italy.

Macromolecule Content

Total Structure Weight: 44.84 kDa
Atom Count: 3,605
Modelled Residue Count: 423
Deposited Residue Count: 434
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hyaluronidase	A, B	217	Streptomyces koganeiensis	Mutation(s): 0
UniProt
Find proteins for A0A0U2E2J7 (Streptomyces koganeiensis) Explore A0A0U2E2J7 Go to UniProtKB: A0A0U2E2J7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0U2E2J7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A]	J [auth A], K [auth A], L [auth A], M [auth A], N [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain P [auth B] SDF format, chain Q [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B]	C [auth A], D [auth A], E [auth A], P [auth B], Q [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain P [auth B] Focus chain Q [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain P [auth B] Focus chain Q [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain S [auth B] SDF format, chain T [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B]	S [auth B], T [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain S [auth B] Focus chain T [auth B] Interactions & Density Focus chain S [auth B] Focus chain T [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A]	I [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain O [auth A] SDF format, chain R [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain O [auth A] MOL2 format, chain R [auth B]	F [auth A], G [auth A], H [auth A], O [auth A], R [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain O [auth A] Focus chain R [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain O [auth A] Focus chain R [auth B]