5ZW7

FAD-PigA complex at 1.3 A

PDB DOI: https://doi.org/10.2210/pdb5ZW7/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Prodigiosinella confusarubida
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2018-05-14 Released: 2018-09-05
Deposition Author(s): Lee, C.-C., Ko, T.-P., Wang, A.H.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.30 ?
R-Value Free: 0.127
R-Value Work: 0.114
R-Value Observed: 0.114

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystal Structure of PigA: A Prolyl Thioester-Oxidizing Enzyme in Prodigiosin Biosynthesis.

Lee, C.-C., Ko, T.-P., Chen, C.T., Chan, Y.T., Lo, S.Y., Chang, J.Y., Chen, Y.W., Chung, T.F., Hsieh, H.J., Hsiao, C.D., Wang, A.H.J.

(2019) Chembiochem 20: 193-202

PubMed: 30095206 Search on PubMed
DOI: https://doi.org/10.1002/cbic.201800409
Primary Citation of Related Structures:
5ZW0, 5ZW2, 5ZW7, 5ZW8, 6AF6

PubMed Abstract:
Prodigiosin is an intensely red pigment comprising three pyrroles. The biosynthetic pathway includes a two-step proline oxidation catalyzed by phosphatidylinositol N-acetylglucosaminyltransferase subunit?A (PigA), with flavin adenine dinucleotide (FAD) as its cofactor. The enzyme is crystallized in the apo form and in complex with FAD and proline. As an acyl coenzyme?A dehydrogenase (ACAD) family member, the protein folds into a β-sheet flanked by two α-helical domains. PigA forms a tetramer, which is consistent with analytical ultracentrifugation results. FAD binds to PigA in a similar way to that in the other enzymes of the ACAD family. The variable conformations of loop β4-β5 and helix αG correlate well with the structural flexibility required for substrate entrance to the Re side of FAD. Modeling with PigG, the acyl carrier protein, suggests a reasonable mode of interaction with PigA. The structure helps to explain the proline oxidation mechanism, in which Glu244 plays a central role by abstracting the substrate protons. It also reveals a plausible pocket for oxygen binding to the Si side of FAD.

Organizational Affiliation

Institute of Biological Chemistry, Academia Sinica, 128 Academia Road Section 2, Taipei, 11529, Taiwan.

Macromolecule Content

Total Structure Weight: 45.5 kDa
Atom Count: 3,885
Modelled Residue Count: 383
Deposited Residue Count: 402
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-prolyl-[peptidyl-carrier protein] dehydrogenase	A	402	Prodigiosinella confusarubida	Mutation(s): 0 Gene Names: pigA EC: 1.3.8.14
UniProt
Find proteins for Q5W271 (Serratia sp. (strain ATCC 39006)) Explore Q5W271 Go to UniProtKB: Q5W271
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5W271
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD 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]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
O4B Query on O4B 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]	1,4,7,10,13,16-HEXAOXACYCLOOCTADECANE C₁₂ H₂₄ O₆ XEZNGIUYQVAUSS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
GOL Query on GOL 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 H [auth A] 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 H [auth A] 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 H [auth A]	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A]
CL Query on CL 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]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.30 ?
R-Value Free: 0.127
R-Value Work: 0.114
R-Value Observed: 0.114
Space Group: I 2 2 2

Unit Cell:

Length ( ? )	Angle ( ? )
a = 85.228	α = 90
b = 85.624	β = 90
c = 145.928	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2018-09-05

Deposition Author(s):

Lee, C.-C.

Ko, T.-P.

Wang, A.H.J.

Funding Organization	Location	Grant Number
	Taiwan	--

Revision History (Full details and data files)

Version 1.0: 2018-09-05
Type: Initial release
Version 1.1: 2019-02-06
Changes: Data collection, Database references
Version 1.2: 2023-11-22
Changes: Data collection, Database references, Refinement description
Version 1.3: 2024-11-06
Changes: Structure summary