BGC0000455

BGC0000455: vancomycin biosynthetic gene cluster from Amycolatopsis orientalis HCCB10007 (ATCC43491)

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Location: 1 - 65,044 nt. (total: 65,044 nt).
This entry is originally from NCBI GenBank HQ679900.1.

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core biosynthetic genes

additional biosynthetic genes

transport-related genes

regulatory genes

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Gene details

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General

Compounds

Genes

Biosynthesis

History

KnownClusterBlast

NRPS/PKS domains

General information about the BGC

MIBiG accession	BGC0000455
Short description	vancomycin biosynthetic gene cluster from Amycolatopsis orientalis HCCB10007 (ATCC43491)
Status	Quality: questionable The quality level of this entry. Status: active The status of this entry. Completeness: complete Whether the entry covers everything needed for the pathway producing the compound(s)
Biosynthetic class(es)	saccharide (None) NRPS (Type I)
Loci	HQ679900.1 1 - 65044 via Knock-out studies
Compounds	vancomycin
Species	Amycolatopsis orientalis HCCB10007 (ATCC43491) [taxonomy]
References	[1] The Biosynthesis of Vancomycin-Type Glycopeptide Antibiotics-The Order of the Cyclization Steps. Bischoff, D et al., Angewandte Chemie International Edition (2001) DOI:10.1002/1521-3773(20011217)40:24<4688::aid-anie4688>3.0.co;2-m [2] An Oxidative Phenol Coupling Reaction Catalyzed by OxyB, a Cytochrome P450 from the Vancomycin‐Producing Microorganism. Zerbe, K et al., Angewandte Chemie International Edition (2004) DOI:10.1002/ANIE.200461278 [3] Incorporation of Glucose Analogs by GtfE and GtfD from the Vancomycin Biosynthetic Pathway to Generate Variant Glycopeptides. Losey, H et al., Chemistry & Biology (2002) DOI:10.1016/S1074-5521(02)00270-3 [4] Genetic analysis of the balhimycin (vancomycin-type) oxygenase genes. Stegmann, E et al., Journal of Biotechnology (2006) DOI:10.1016/j.jbiotec.2006.04.009 [5] In Vitro Reconstitution of OxyA Enzymatic Activity Clarifies Late Steps in Vancomycin Biosynthesis. Forneris, C et al., ACS Chemical Biology (2017) DOI:10.1021/acschembio.7b00456 [6] Tandem Action of Glycosyltransferases in the Maturation of Vancomycin and Teicoplanin Aglycones: Novel Glycopeptides,. Losey, H et al., Biochemistry (2001) DOI:10.1021/bi010050w [7] Crystal Structure of Vancosaminyltransferase GtfD from the Vancomycin Biosynthetic Pathway: Interactions with Acceptor and Nucleotide Ligands,. Mulichak, A et al., Biochemistry (2004) DOI:10.1021/bi036130c [8] Vancomycin: structure and transformation to CDP-I. Harris, C et al., Journal of the American Chemical Society (1983) DOI:10.1021/ja00361a029 [9] Oxidative Phenol Coupling Reactions Catalyzed by OxyB: A Cytochrome P450 from the Vancomycin Producing Organism. Implications for Vancomycin Biosynthesis. Woithe, K et al., Journal of the American Chemical Society (2007) DOI:10.1021/ja071038f [10] Bis-chlorination of a hexapeptide–PCP conjugate by the halogenase involved in vancomycin biosynthesis. Schmartz, P et al., Org. Biomol. Chem. (2014) DOI:10.1039/C4OB00474D [11] Chemical probes reveal the timing of early chlorination in vancomycin biosynthesis. Leng, D et al., Chemical Communications (2021) DOI:10.1039/D0CC07421G [12] Identification and Analysis of the Balhimycin Biosynthetic Gene Cluster and Its Use for Manipulating Glycopeptide Biosynthesis in Amycolatopsis mediterranei DSM5908. Pelzer, S et al., Antimicrobial Agents and Chemotherapy (1999) DOI:10.1128/AAC.43.7.1565 [13] Complete genome sequence and comparative genomic analyses of the vancomycin-producing Amycolatopsis orientalis. Xu, L et al., BMC Genomics (2014) DOI:10.1186/1471-2164-15-363 [14] Structural characterization of OxyD, a cytochrome P450 involved in beta-hydroxytyrosine formation in vancomycin biosynthesis. Cryle MJ et al., J Biol Chem (2010) PMID:20519494 [15] Complete genome sequence and comparative genomic analyses of the vancomycin-producing Amycolatopsis orientalis. Xu L et al., BMC Genomics (2014) PMID:24884615

Chemical products information

vancomycin Evidence: NMR [8]

Copy SMILES

C₆₆H₇₅Cl₂N₉O₂₄

Chemical database entries
PubCHEM

List of genes involved in compound(s) production

Identifiers	Position	Product	Functions	Evidence	Extra
AEI58859.1 vanH	1 - 1032 (+)	D-lactate dehydrogenase			copy AA seq copy Nt seq
AEI58860.1 vanA	1034 - 2080 (+)	D-alanyl-D-alanine ligase			copy AA seq copy Nt seq
AEI58861.1 vanX	2070 - 2678 (+)	D-alanyl-D-alanine dipeptidase			copy AA seq copy Nt seq
AEI58862.1 vtrR	3664 - 4638 (+)	StrR family transcriptional regulator			copy AA seq copy Nt seq
AEI58863.1 vcm1	4784 - 5635 (+)	prephenate dehydrogenase			copy AA seq copy Nt seq
AEI58864.1	5595 - 7733 (+)	ABC transporter			copy AA seq copy Nt seq
AEI58865.1 vcm2	7730 - 17188 (+)	peptide synthetase			copy AA seq copy Nt seq
AEI58866.1 vcm3	17541 - 29693 (+)	peptide synthetase			copy AA seq copy Nt seq
AEI58867.1 vcm4	29714 - 35290 (+)	peptide synthetase			copy AA seq copy Nt seq
AEI58868.1 vcm5	35584 - 36759 (+)	Cyclization\|Oxidation	Cyclization Oxidation	MITE0000038 [1], [4], [5], [12] MITE0000038 [1], [4], [5], [12]	copy AA seq copy Nt seq
AEI58869.1 vcm6	37090 - 38313 (+)	Cyclization\|Oxidation	Cyclization Oxidation	MITE0000041 [1], [2], [4], [9], [12] MITE0000041 [1], [2], [4], [9], [12]	copy AA seq copy Nt seq
AEI58870.1 vcm7	38440 - 39660 (+)	p450 monooxygenase			copy AA seq copy Nt seq
AEI58871.1 vcm8	39705 - 41180 (+)	Halogenase	Halogenation	MITE0000040 [10], [11], [13]	copy AA seq copy Nt seq
AEI58872.1 vcm9	41236 - 42462 (+)	Glycosyltransferase	Glycosylation	MITE0000042 [3], [6], [7], [13]	copy AA seq copy Nt seq
AEI58873.1 vcm10	42515 - 43741 (+)	Glycosyltransferase	Glycosylation	MITE0000037 [3], [6], [13]	copy AA seq copy Nt seq
AEI58874.1 vcm11	43767 - 44993 (+)	C-3 methyl transferanse			copy AA seq copy Nt seq
AEI58875.1	44999 - 45820 (+)	hypothetical protein			copy AA seq copy Nt seq
AEI58876.1 vcm12	45860 - 46702 (+)	Methyltransferase	Methylation	MITE0000039 [13]	copy AA seq copy Nt seq
AEI58877.1 vcm13	46683 - 47987 (-)	phenylglycine amino transferase			copy AA seq copy Nt seq
AEI58878.1 vcm14	48218 - 49048 (+)	hydrolase			copy AA seq copy Nt seq
AEI58879.1 vcm15	49099 - 50781 (+)	peptide synthetase			copy AA seq copy Nt seq
AEI58880.1 vcm16	50795 - 51985 (+)	p450 monooxygenase			copy AA seq copy Nt seq
AEI58881.1 vcm17	52104 - 53138 (+)	hydrooxyphenyl pyruvate dioxygenase			copy AA seq copy Nt seq
AEI58882.1 vcm18	53135 - 54214 (+)	phenylglycolate oxidase			copy AA seq copy Nt seq
AEI58883.1	54431 - 55618 (+)	putative antiporter			copy AA seq copy Nt seq
AEI58884.1 vcm19	55798 - 57204 (+)	NDP-hexose 2,3-dehydrolase			copy AA seq copy Nt seq
AEI58885.1 vcm20	57205 - 58176 (+)	4-ketoreductase			copy AA seq copy Nt seq
AEI58886.1 vcm21	58173 - 59282 (+)	C-3 amino transferase			copy AA seq copy Nt seq
AEI58887.1 vcm22	59306 - 59923 (+)	epimerase			copy AA seq copy Nt seq
AEI58888.1 vcm23	60011 - 61129 (+)	dihydrophenylactic synthase			copy AA seq copy Nt seq
AEI58889.1 vcm24	61156 - 61785 (+)	enoyl-CoA hydratase			copy AA seq copy Nt seq
AEI58890.1 vcm25	61782 - 63008 (+)	hydroxyacyl-dehydrogenase			copy AA seq copy Nt seq
AEI58891.1 vcm26	63005 - 63796 (+)	enoyl-CoA hydratase			copy AA seq copy Nt seq
AEI58892.1	63968 - 65044 (+)	putative aldolase			copy AA seq copy Nt seq

Biosynthesis information

Biosynthetic modules

Name

Unk01

Type

nrps-type1

Genes

vcm2

Substrates

leucine (evidence: Structure-based inference, ATP-PPi exchange assay)

Integrated Monomers

Domains

adenylation

Name

Unk02

Type

nrps-type1

Genes

vcm2

Substrates

R-beta-hydroxytyrosine (evidence: Structure-based inference [14])

Integrated Monomers

Domains

adenylation

Name

Unk03

Type

nrps-type1

Genes

vcm2

Substrates

asparagine (evidence: Structure-based inference)

Integrated Monomers

Domains

adenylation

Name

Unk04

Type

nrps-type1

Genes

vcm3

Substrates

4-hydroxyphenylglycine (evidence: Structure-based inference)

Integrated Monomers

Domains

adenylation

Name

Unk05

Type

nrps-type1

Genes

vcm3

Substrates

4-hydroxyphenylglycine (evidence: Structure-based inference)

Integrated Monomers

Domains

adenylation

Name

Unk06

Type

nrps-type1

Genes

vcm3

Substrates

R-beta-hydroxytyrosine (evidence: Structure-based inference)

Integrated Monomers

Domains

adenylation

Name

Unk07

Type

nrps-type1

Genes

vcm4

Substrates

3,5-dihydroxyphenylglycine (evidence: Structure-based inference)

Integrated Monomers

Domains

adenylation

Name

Unk08

Type

nrps-type1

Genes

vcm15

Substrates

tyrosine (evidence: Homology)

Integrated Monomers

Domains

adenylation

Annotation changelog

Entry version: 6

Date

Changes

Submitters

Reviewers

2024-06-14

MIBiG v4 annotathon

(ID: 37IOAS4X5OHP34DPN55OLFBF)

(ID: AAAAAAAAAAAAAAAAAAAAAAAA)

Entry version: next

Date

Changes

Submitters

Reviewers

2023-10-24

Added 'Saccharide' as additional biosynthetic class. Specified BGC evidence according to 'pubmed:24884615'. Added strain information.

(ID: C62OJVVH7XOTOTFZSJT727YU)

(ID: 25OPJFS6AQU3ROUADEVDYF5E)

Entry version: 4

Date

Changes

Submitters

Reviewers

2022-10-07

Update chemical activity to schema version 2.11

(ID: AAAAAAAAAAAAAAAAAAAAAAAA)

(ID: AAAAAAAAAAAAAAAAAAAAAAAA)

Entry version: 3

Date

Changes

Submitters

Reviewers

2022-09-15

Updated bioactivity data

(ID: AAAAAAAAAAAAAAAAAAAAAAAA)

(ID: AAAAAAAAAAAAAAAAAAAAAAAA)

2022-09-15

Added NRP substrate specificities

(ID: AAAAAAAAAAAAAAAAAAAAAAAA)

(ID: AAAAAAAAAAAAAAAAAAAAAAAA)

Entry version: 2

Date

Changes

Submitters

Reviewers

2019-10-16

Migrated from v1.4

(ID: AAAAAAAAAAAAAAAAAAAAAAAA)

(ID: AAAAAAAAAAAAAAAAAAAAAAAA)

Entry version: 1

Date

Changes

Submitters

Reviewers

2015-06-12

Submitted

(ID: AAAAAAAAAAAAAAAAAAAAAAAA)

(ID: AAAAAAAAAAAAAAAAAAAAAAAA)

Similar known clusters from MIBiG 4.0

Detailed domain annotation

Selected features only

Show module domains