Type I pyridoxal 5′-phosphate dependent enzymatic domains embedded within multimodular nonribosomal peptide synthetase and polyketide synthase assembly lines

Milano, Teresa; Paiardini, Alessandro; Grgurina, Ingeborg; Pascarella, Stefano

doi:10.1186/1472-6807-13-26

Table 2 List of non redundant NRPS/PKS proteins containing type I PLP-dependent domains of the four families

From: Type I pyridoxal 5′-phosphate dependent enzymatic domains embedded within multimodular nonribosomal peptide synthetase and polyketide synthase assembly lines

UniProt code	Specie	B6db ^a)	Domain layout ^b)	Specificity ^c)	Cluster type ^d)	Product ^e)
Family: Aminotran_3
1. A1YBQ7	Sorangium cellulosum	?	CP–KS–CP–CP–ABHy6–PLP1	?	T1pks	Mmal-Mmal-Mal-Mmal-Mal-Mmal-Mal-Mal-Pk
2. C3AKA5	Bacillus mycoides	GSA	KS–CP–PLP1	?	Nrps-transatpks	Asn-Mal-Gly-Nrp-Nrp-Nrp-Thr-Gly
3. C5B3B9	Methylobacterium extorquens	TPA	CP–ABHy–PLP1– FMO	?	?	?
4. C6XWU5	Pedobacter heparinus	GSA	A–CP–KS–AT–CP–PLP1	Nrp	Nrps-t1pks	Nrp-Mal-Gly-Pk
5. C8RZN9	Rhodobacter sp. SW2	DAT	KS–AT–ADHN–ADHznN–KR–CP–PLP1	Mal	Terpene-t1pks	Mal
6. D3VEV4	Xenorhabdus nematophila	GSA	CP–PLP1– C–A–CP	Nrp	T1pks-nrps	Nrp-Mal-Nrp-Asn
7. D6KDX7	Streptomyces sp. e14	GSA	CP–PLP1– C	?	Nrps	Nrp-Mal-Nrp-Orn-Asp-Nrp-Nrp-Thr
8. E1TD76	Burkholderia sp.	DAT	CP–PLP1– SDH	?	?	?
9. F4CRB0	Pseudonocardia dioxanivorans	DOT	A–CP–PLP1	?	?	?
10. F5RC11	Methyloversatilis universalis	OAT	CP–ABHy6–PLP1–FMO	?	?	?
11. F7QBN5	Salinisphaera shabanensis E1L3A	GSA	C–A–CP–KS–AT–CP–PLP1– C–HxxPF–A–CP	Gly,-	Nrps-t1pks	Gly-Mal-Nrp
12. F9UAS6	Thiocapsa marina 5811	GSA	KS–AT–CP–PLP1	Mal	Nrps-t1pks	Nrp-Nrp-Mal-Gly
13. G0PR31	Streptomyces griseus	GSA	PLP1–Luc–C–HxxPF–CP–C	?	T1pks-nrps	Mal-Thr
14. G2E5C9	Thiorhodococcus drewsii AZ1	GSA	A–CP–KS–AT–CP–PLP1– C–CP–C–HxxPF–C–HxxPF–A–CP–C–HxxPF	Mal, Thr	Nrps-t1pks	Nrp-Tyr-Pk-Mal-Thr-Asp
15. Q2T5Z2	Burkholderia thailandensis	GSA	KS–AT–CP–PLP1– C–HxxPF–A–CP–C	Asp	Nrps-t1pks-hserlactone	Mal-Asp-Gln-Cys-Pk-Val-Mal-Ala
Family: Aminotran_1_2
1. A1ZVW4	Microscilla marina	AOS	A–CP–PLP2	Nrp	?	?
2. A3ZWL3	Blastopirellula marina	AOS	A–CP–PLP2	?	?	?
3. B3EYK4	Anabaena circinalis	AOS	CP–PLP2	?	?	?
4. B6VRQ8	Streptomyces griseoviridis	AOS	A–CP–KS–AT–PLP2	Mal	T1pks	Nrp-Pk-Mal
5. B6VRS3	Streptomyces griseoviridis	AOS	CP–CP–PLP2	?	T1-pks	Nrp-Pk-Mal
6. D6B3S9	Streptomyces albus J1074	AOS	KR–CP–PLP2	?	T1pks	Gly-Mal-Mal
7. K0EZM3	Nocardia brasiliensis	AOS	A–CP–Luc–PLP2	?	Terpene	?
Family: Beta_elim_lyase
1. D9T192	Micromonospora aurantiaca	TPL	CP–KR–KS–ECH–CP–KS–KR–MT–CP–KS–KR–CP–KS–CP–CP–DUF2156–PLP3–ABHy1	?	T2pks-nrps-transatpks	Nrp-Mal-Cys-Mal-Thr
2. C7PXR3	Catenulispora acidiphila	TPL	CP–KR–KS–ECH–CP–KS–KR–MT–CP–KS–KR–CP–KS–CP–DUF2156–PLP3–ABHy5	?	Nrps-transatpks-t1pks-t2pks	Nrp-Mal-Thr-Cys-Mal
3. Q8GGP2	Streptomyces atroolivaceus	TPL	CP–KR–KS–CP–KS–KR–CP–MT–CP–KS–KR–CP–KS–CP–CP–DUF2156–PLP3–ABHy1	?	Nrps-transatpks	Ser-Nrp-Thr-Pk-Ser-Mal-Cys-Ala-Nrp
4. A9ECY5	Kordia algicida	TPL	CP–DUF2156–PLP3–KS–KR–CP–KS	?	transatpks-t2pks	Pk-Mal
5. F2LI38	Burkholderia gladioli	TPL	CP–KS–KR–CP–PLP3–KS–CP–KS	?	T2pks-transatpks-nrps	Mal-Gly-Nrp
6. F8TUA6	Lysobacter sp. ATCC 53042	TPL	CP–DUF2156–PLP3–KS–KR–CP–KS–KR	?	Lantipeptide-nrps-transatpks	Leu-Leu-Phe-Leu-Leu-Nrp-Ile-Thr-Gly-Asn-Ser
Family: Pyridoxal_deC
1. Q6E7J8	Lyngbya majuscula	DDC	KS–AT–ADH–KR–CP–C–HxxPF–A–PLP4– A–CP	Mal, Nrp	T1pks-t2pks-nrps	Pk-Pk-Pk-Mal-Mal-Mal-Nrp-Mal-Ala-Mal
2. B6IZA3	Coxiella burnetii	GDC	A–CP–C–PLP4	Gly	Nrp	Gly

^a)Family assignment with B6db. Abbreviations mean: GSA = Glutamate-1-semialdehyde 2,1-aminomutase; TPA = Taurine--pyruvate aminotransferase; DAT = Diamine aminotransferase; DOT = Diaminobutyrate-2-oxoglutarate transaminase; OAT = Ornithine--oxo-acid aminotransferase; AOS = 8-amino-7-oxononanoate synthase, TPL = Tyrosine phenol-lyase; DDC = Diaminobutyrate decarboxylase; GDC = Glutamate decarboxylase. Question mark means “not assigned”.
^b)Domain codes with Pfam id code in parentheses: A = AMP–binding enzyme (PF00501); CP = Phosphopantetheine attachment site (PF00550); KS = beta–ketoacyl synthase (PF00109); AT = Acyltransferase domain (PF00698); MT = Methyltransferase domain (PF13489); C = Condensation domain (PF00668); HxxPF = HxxPF–repeated domain (PF13745); Luc = Luciferase (PF00296); ABHyX = Alpha/beta hydrolase fold where X is the subgroup number; FMO = Flavin–containing monooxygenase (PF00743); ADHN = Alcohol dehydrogenase GroES–like domain (PF08240); ADHZnN = Zinc–binding dehydrogenase (PF00107); KR = Ketoreductase domain (PF08659); DUF4009 = Domain of unknown function (PF13193); SDH = Shikimate/quinate 5–dehydrogenase (PF01488); ECH = Enoyl–CoA hydratase/isomerase family (PF00378). Type-I domains are: PLP1 = Aminotran_3 (PF00202); PLP2 = Aminotran_1_2 (PF00155); PLP3 = Beta_elim_lyase (PF01212); PLP4 = Pyridoxal_deC (PF00282).
^c)Predicted specificity of the AT or A domains of the chain containing the type-I domain. Nrp means generic amino acid (no consensus among the predictive methods). Question mark denotes no prediction. Mal and Pk represent malonyl and a generic polyketide, respectively.
^d)Gene cluster type as predicted by antiSMASH. Pks and Nrps stand for Polyketide synthase and Non-ribosomal polypeptide synthetase, respectively. T1pks, T2pks, transatpks refer to Type-I, Type-II and trans-AT pks, respectively. Question mark denotes no prediction.
^e) Predicted cluster product. Monomers incorporated by the module containing the type-I domain are boldfaced. Question mark denotes no prediction.

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ISSN: 1472-6807

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