7U7H | pdb_00007u7h

Cysteate acyl-ACP transferase from Alistipes finegoldii

PDB DOI: https://doi.org/10.2210/pdb7U7H/pdb

Classification: TRANSFERASE
Organism(s): Alistipes finegoldii DSM 17242
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-03-07 Released: 2023-01-18
Deposition Author(s): Radka, C.D., Miller, D.J., Frank, M.W., Rock, C.O.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free:
0.268 (Depositor), 0.246 (DCC)
R-Value Work:
0.218 (Depositor), 0.223 (DCC)
R-Value Observed:
0.221 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Biochemical characterization of the first step in sulfonolipid biosynthesis in Alistipes finegoldii.

Radka, C.D., Miller, D.J., Frank, M.W., Rock, C.O.

(2022) J Biological Chem 298: 102195-102195

PubMed: 35760102 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1016/j.jbc.2022.102195
Primary Citation Related Structures:
7U7H

PubMed Abstract:
Sulfonolipids are unusual lipids found in the outer membranes of Gram-negative bacteria in the phylum Bacteroidetes. Sulfonolipid and its deacylated derivative, capnine, are sulfur analogs of ceramide-1-phosphate and sphingosine-1-phosphate, respectively; thus, sulfonolipid biosynthesis is postulated to be similar to the sphingolipid biosynthetic pathway. Here, we identify the first enzyme in sulfonolipid synthesis in Alistipes finegoldii as the product of the alfi_1224 gene, cysteate acyl-acyl carrier protein (ACP) transferase (SulA). We show SulA catalyzes the condensation of acyl-ACP and cysteate (3-sulfo-alanine) to form 3-ketocapnine. Acyl-CoA is a poor substrate. We show SulA has a bound pyridoxal phosphate (PLP) cofactor that undergoes a spectral redshift in the presence of cysteate, consistent with the transition of the lysine-aldimine complex to a substrate-aldimine complex. Furthermore, the SulA crystal structure shows the same prototypical fold found in bacterial serine palmitoyltransferases (Spts), enveloping the PLP cofactor bound to Lys251. We observed the SulA and Spt active sites are identical except for Lys281 in SulA, which is an alanine in Spt. Additionally, SulA(K281A) is catalytically inactive but binds cysteate and forms the external aldimine normally, highlighting the structural role of the Lys281 side chain in walling off the active site from bulk solvent. Finally, the electropositive groove on the protein surface adjacent to the active site entrance provides a landing pad for the electronegative acyl-ACP surface. Taken together, these data identify the substrates, products, and mechanism of SulA, the PLP-dependent condensing enzyme that catalyzes the first step in sulfonolipid synthesis in a gut commensal bacterium.

Organizational Affiliation

Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, USA. Electronic address: christopher.radka@stjude.org.

Macromolecule Content

Total Structure Weight: 300.71 kDa
Atom Count: 18,499
Modeled Residue Count: 2,492
Deposited Residue Count: 2,658
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
7-keto-8-aminopelargonate synthetase-like enzyme	A, B, C, D, E A, B, C, D, E, F	443	Alistipes finegoldii DSM 17242	Mutation(s): 0 Gene Names: Alfi_1224
UniProt
Find proteins for I3YKQ4 (Alistipes finegoldii (strain DSM 17242 / JCM 16770 / CCUG 46020 / CIP 107999 / KCTC 15236 / AHN 2437)) Explore I3YKQ4 Go to UniProtKB: I3YKQ4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	I3YKQ4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PLP (Subject of Investigation/LOI) Query on PLP Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain G [auth A] MOL2 format, chain H [auth B] MOL2 format, chain G [auth A] mmCIF format, chain H [auth B] mmCIF format, chain G [auth A]	G [auth A], H [auth B]	PYRIDOXAL-5'-PHOSPHATE C₈ H₁₀ N O₆ P NGVDGCNFYWLIFO-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D, E A, B, C, D, E, F	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.268 (Depositor), 0.246 (DCC)
R-Value Work: 0.218 (Depositor), 0.223 (DCC)
R-Value Observed: 0.221 (Depositor)

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 127.516	α = 90
b = 127.516	β = 90
c = 177.3	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-01-18

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	1K99AI166116-01
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	5R01GM034496-38