4ZWV

Crystal Structure of Aminotransferase AtmS13 from Actinomadura melliaura

PDB DOI: https://doi.org/10.2210/pdb4ZWV/pdb
Entry: 4ZWV supersedes: 4RXK

Classification: TRANSFERASE
Organism(s): Actinomadura melliaura
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2015-05-19 Released: 2015-06-03
Deposition Author(s): Kim, Y., Bigelow, L., Endres, M., Wang, F., Phillips Jr., G.N., Joachimiak, A., Enzyme Discovery for Natural Product Biosynthesis (NatPro), Midwest Center for Structural Genomics (MCSG)
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.167
R-Value Work: 0.146
R-Value Observed: 0.147

wwPDB Validation 3D Report Full Report

This is version 2.1 of the entry. See complete history.

Literature

Structural characterization of AtmS13, a putative sugar aminotransferase involved in indolocarbazole AT2433 aminopentose biosynthesis.

Singh, S., Kim, Y., Wang, F., Bigelow, L., Endres, M., Kharel, M.K., Babnigg, G., Bingman, C.A., Joachimiak, A., Thorson, J.S., Phillips, G.N.

(2015) Proteins 83: 1547-1554

PubMed: 26061967 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1002/prot.24844
Primary Citation of Related Structures:
4XAU, 4ZWV

PubMed Abstract:
AT2433 from Actinomadura melliaura is an indolocarbazole antitumor antibiotic structurally distinguished by its unique aminodideoxypentose-containing disaccharide moiety. The corresponding sugar nucleotide-based biosynthetic pathway for this unusual sugar derives from comparative genomics where AtmS13 has been suggested as the contributing sugar aminotransferase (SAT). Determination of the AtmS13 X-ray structure at 1.50-Å resolution reveals it as a member of the aspartate aminotransferase fold type I (AAT-I). Structural comparisons of AtmS13 with homologous SATs that act upon similar substrates implicate potential active site residues that contribute to distinctions in sugar C5 (hexose vs. pentose) and/or sugar C2 (deoxy vs. hydroxyl) substrate specificity.

Organizational Affiliation

Center for Pharmaceutical Research and Innovation, Pharmaceutical Sciences Division, University of Kentucky College of Pharmacy, Lexington, Kentucky, 40536-0596.

Macromolecule Content

Total Structure Weight: 84.24 kDa
Atom Count: 7,450
Modelled Residue Count: 740
Deposited Residue Count: 744
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative aminotransferase	A, B	372	Actinomadura melliaura	Mutation(s): 0 Gene Names: atS13
UniProt
Find proteins for Q0H2X1 (Actinomadura melliaura) Explore Q0H2X1 Go to UniProtKB: Q0H2X1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q0H2X1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth B] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth B] MOL2 format, chain F [auth B]	C [auth A], D [auth A], E [auth B], F [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth B]

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP Query on LLP	A, B	L-PEPTIDE LINKING	C₁₄ H₂₂ N₃ O₇ P		LYS
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.167
R-Value Work: 0.146
R-Value Observed: 0.147
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 204.137	α = 90
b = 73.025	β = 103.68
c = 58.607	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHENIX	phasing
SHELXDE	phasing
HKL-3000	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2015-06-03

Deposition Author(s):

Enzyme Discovery for Natural Product Biosynthesis (NatPro)

Midwest Center for Structural Genomics (MCSG)

This entry supersedes: 4RXK

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	U01GM098248
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	CA84374
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM094585

Revision History (Full details and data files)

Version 1.0: 2015-06-03
Type: Initial release
Version 1.1: 2015-06-24
Changes: Database references
Version 1.2: 2015-07-01
Changes: Structure summary
Version 1.3: 2015-07-29
Changes: Database references
Version 1.4: 2015-10-14
Changes: Data collection
Version 2.0: 2017-09-27
Changes: Author supporting evidence, Derived calculations, Non-polymer description, Structure summary
Version 2.1: 2019-12-04
Changes: Author supporting evidence