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Vanco_00100 : CDS information

close this sectionLocation

Organism
StrainATCC 19795 (=NBRC 12806)
Entry nameVancomycin
Contig
Start / Stop / Direction31,323 / 36,914 / + [in whole cluster]
31,323 / 36,914 / + [in contig]
Location31323..36914 [in whole cluster]
31323..36914 [in contig]
TypeCDS
Length5,592 bp (1,863 aa)
Click on the icon to see Genetic map.

close this sectionAnnotation

Category1.2 NRPS
Productnon-ribosomal peptide synthetase
Product (GenBank)non-ribosomal peptide synthetase C
Gene
Gene (GenBank)vpsC
EC number
Keyword
Note
Note (GenBank)
Reference
ACC
comment
A. orientalis ATCC 19795でのvancomycin生合成 gene clusterとして配列が登録されているが、cluster報告論文なし。個々のタンパクなどでの続報もなし。
Related Reference
ACC
R4T047
PmId
[24884615] Complete genome sequence and comparative genomic analyses of the vancomycin-producing Amycolatopsis orientalis. (BMC Genomics. , 2014)
comment
BLAST id89%
Amycolatopsis orientalis HCCB10007_(AORI_1480)

vancomycinの大量産生に使用されているA. orientalis ATCC 43491由来工業用菌株HCCB10007の完全ゲノムシークエンス。そこからvcm cluster(AORI_1471-1505)を同定し、いくつかの遺伝子のmutantsを作製してin vivo機能を特徴づけている。

AORI_1480(vcmC): Non-ribosomal peptide synthetase

vcmCに関しては配列解析のみ。
Figure 5でのVcmCのドメイン構造は、
M7: C-A-T-C-TE (Dpg7)
ACC
Q939Y9
NITE
Balhi_00090
PmId
[11932455] Nonribosomal biosynthesis of vancomycin-type antibiotics: a heptapeptide backbone and eight peptide synthetase modules. (Microbiology. , 2002)
[15651041] The biosynthesis of vancomycin-type glycopeptide antibiotics--a model for oxidative side-chain cross-linking by oxygenases coupled to the action of peptide synthetases. (Chembiochem. , 2005)
[17506888] Phylogenetic analysis of condensation domains in NRPS sheds light on their functional evolution. (BMC Evol Biol. , 2007)
comment
BLAST id87%
Amycolatopsis balhimycina_bpsC
Peptide synthetase

---
[PMID: 11932455](2002)
balhimycin生合成gene clusterにおけるbpsA, bpsB, bpsC, bpsD, orf1の同定。

BpsCのドメイン構造は、
module 7: C-A-T-C-TE
adenylation(A) domainのselectivity-conferring codeを確認している。

bpsC in-frame deletion mutantは抗菌活性のある化合物を産生しなかった。
module 7 は L-3,5-dihydroxyphenylglycine(Dpg)を活性化することが、異種性発現して得たA domainのATP/PP(i) exchange assaysによって測定された。

thiolation(T) domainとthioesterase(TE) domainの間にあるC domainに似た配列に割り当てられるペプチド骨格構築での機能はない。

---
[PMID: 15651041](2005)
dpgA mutantではbicyclic hexapeptide、bpsC mutantではmonocyclic hexapeptideの蓄積があることから、OxyBによるCD ring形成はBpsB_module 6からBpsC_module 7へのhexapeptideの移動中かその少し前に起こるはずだと述べている。bpsC mutantでbicyclic hexapeptideが検出されないのは、BpsCでのdeletionのせいでOxyAとNRPS複合体の間の相互作用に必須な部位がないからであると説明されうる。

また、dpgA mutantにおいて、7つめのAAとしてDpgの代わりにL-4-hydroxyphenylglycine(Hpg)を含むtricyclic heptapeptideが得られたことから、BpsCとoxygenasesはいくらかの基質寛容性を示す。

---
[PMID: 17506888](2007)
NRPS C domain subtypesの系統発生関係の再構築をしている報告。

グリコペプチド系抗生物質のNRPSに含まれるC domain様区域(X*)は、2つのL-AAsの間のペプチド結合を触媒するC domainのsubtypeに関係し、祖先では追加のmoduleがあったと暗示される。

Figure 4の系統樹にこのentryも含まれる。
ACC
Q70AZ6
NITE
Teicp2_00210
PmId
[25686610] X-domain of peptide synthetases recruits oxygenases crucial for glycopeptide biosynthesis. (Nature. , 2015)
[26549530] Sequential In Vitro Cyclization by Cytochrome P450 Enzymes of Glycopeptide Antibiotic Precursors Bearing the X-Domain from Nonribosomal Peptide Biosynthesis. (Angew Chem Int Ed Engl. , 2015)
[27213615] Regulation of the P450 Oxygenation Cascade Involved in Glycopeptide Antibiotic Biosynthesis. (J Am Chem Soc. , 2016)
comment
BLAST id77%
Actinoplanes teichomyceticus ATCC 31121株_tcp ORF12
Non-ribosomal peptide synthetase

---
[PMID: 25686610](2015)
SUPPLEMENTARY INFORMATION内のリストにこのUniProt entryの記載があるが、同グループの他論文(PMID: 25358800, 25586301)ではDSM43866株を使用してATCC 31121株由来のgene nameを採用している混乱があるため、同様の可能性あり。

X-domainの結晶構造解析や相互作用の実験から、X-domainがcytochrome P450(oxy genesでコードされる)による架橋形成に関与することがわかった。

---
[PMID: 26549530](2015) abstract + supporting information
PMID: 25686610の続報。同様にsupporting informationでこのUniProt entryの記載あり。その他タンパクもATCC 31121株のentriesを採用している。

close this sectionPKS/NRPS Module

A7 L-3,5-dihydroxyphenylglycine(Dpg)
C15..313
A496..891
PCP974..1041
X1055..1354
TE1627..1844

close this sectionSequence

selected fasta
>non-ribosomal peptide synthetase [non-ribosomal peptide synthetase C]
MTVDDTRAKPRSSVEDVWPLSPLQEGMLFHTVLDKEGPDTYTVQTVYGIDGPLDAGLLKR
SWQALVDRHAALRACFRYVSGAQMVQVIARNAEIPWRETDLSGLPGDGADGVESAVDRLA
ADEVAERLSIESAPLMKLHLIRLGPESHRLVHTLHHVLVDGWSMPILHRELAEIYAAGGD
ASGLPPTVSYRDYLAWLGRQDKEAARAAWRAEFAGLETPTTVVPADPTRIPDIHTEVVEL
SAELTDGLARLARGNGLTLNTVVQGAWAVVLSQLAGRTDVVFGATASGRPADLPGVESMV
GQLLNTLPVRVRLDGARRAVELFADLQRDQAALMAHQYLGLQDVRTVAGPGAVFDTLVIY
ENFPRTGLDRPSDGGLNLRPVKRGSNSSHYPFTLVTGPGERMPLILDYDHGLFDRTAAES
VVGAMARVLERLVAEPDVLIGRLPTVSEAERALVLNDFNATAGPVPGESVPALFARRVAA
APEAVAIVDAHGANLTYAEIDQASDRLAGHLAGRGVGRGDRVGVAMERSPELIIAFLAIW
KAGAAYVPVDVEYPAERISFILEDSGVSTVLCTEATRAVAFSGLNAIVLDAPETRAAVDV
CAAPEIRLSADDLAYVMYTSGSTGLPKGVGIPHGAVAGLAGDEGWQIGAGDGVLMHATHV
FDPSLYAMWVPLVSGARVLLTEPGVLDAAGVRQAVRRGATYVHLTAGTFRALAETSPECF
DGLVEIGTGGDIVPLQSVENLRRAQPGLRVRNTYGPTETTLCATWLPIEPGDVLDRELPI
GHPMTNRRIYILDAFLRPVAPGVAGELYIAGTGLARGYLNAPGLTAGRFVACPFAAGERM
YRTGDLARWTRDGEVVFLGRADDQVKIRGYRVELGEVEAVLAAQPGVVEAVLLAREDQPG
EKRLVGYFVSDGGDAGPEEIRRQMAKVLPDYMVPIAVVALPGLPVTPNGKVDRRALPAPD
LAGGSSEKAPENETEKVLCALFAEILSVDQVGVDDAFQDLGGSSALAMRLVARIREELGE
DLPIRQLFSSPTPAGLARALAAKSRPVLEVAQRPERVPLTARQLRAWLLADPGGETASLT
TSVALRLHGRLDVPALTAALGDVAARHELLRTTFPGDAQSVHQHVHDTLAVELTPVAATE
DDLPGLLAELRESVFDLTREVPWRCDLFALSEKEHVLHLRVHRILADDDSLDVFFRDLAA
AYGARREGRVPQRAPLALQFADYSLWERRLLEDEDEPGSLVNEQVAFWRDNLAGIDGETV
LPFDRPRPAVPSRRAGSVALRLDAGPHARLAETAESAGAETLQLVHAALAMLLTRSGSGD
DVVIGTTLPRDEELFDLEPMVGPFTRPLALRTDVSGDPTFLEVVTRVQEAVQATNQHLDV
PFERIVELLDLPASLSRHPVFQVGLEVDEEDIDGWSTAELPALRTGVEPAGTDAMELDLA
VKLTEHFDDDDEAGGLEGALRYATDLFDQATAESVARRLVRVLEQVAEDPRRRVSELDLF
LDDFERGRPPIAPARWAGAVPAVVAELAGDDPVGALVLDELMRPVAPGAVGDLYVTGPAV
DTAPAGLPTVPCPFGEEGHRMLPTGLLARKTPAKTLVVVGERRRASTAVKTGDFEILLPL
RVGGDRPPLFCVHASGGLSWNYEPLLRYLPANQPVYGVQARGLARTEPLPGSVEEMAADY
LAQIRAVQPSGPYHLLGWSLGGRIAQAMARLLEQEGEKVGLLALLDAYPVYMGRKTTGAA
SEEAALSKRNQADLDLAGQLVKSEAARARLEAVMRNLWDIGPRHVSSPFAGDILLFVATV
DRPEHLPVSVAKASWKEFTTGTIEAHDIPSNHYDMVQTAALGQIGSIVAEKLRQRPEGER
TQR
selected fasta
>non-ribosomal peptide synthetase [non-ribosomal peptide synthetase C]
GTGACCGTTGACGACACTCGTGCGAAGCCTCGCTCCAGCGTGGAAGACGTCTGGCCGCTT
TCCCCGCTGCAAGAAGGGATGCTCTTCCACACCGTCCTGGACAAGGAGGGACCGGACACC
TACACGGTCCAGACCGTCTACGGGATCGACGGCCCGCTCGACGCGGGGCTGCTGAAGAGG
TCGTGGCAGGCGCTCGTGGACCGGCATGCCGCGCTGCGGGCCTGTTTCCGCTACGTCAGC
GGCGCCCAGATGGTGCAGGTGATCGCGCGGAACGCCGAAATTCCTTGGCGCGAAACGGAT
CTTTCCGGGCTGCCCGGCGACGGTGCCGATGGCGTCGAGAGCGCGGTGGACCGCCTGGCC
GCGGACGAGGTGGCCGAACGGCTGAGCATCGAGTCGGCGCCACTGATGAAACTGCACCTG
ATCCGGCTCGGCCCGGAAAGCCACCGGCTCGTGCACACGCTGCACCACGTCCTCGTGGAC
GGCTGGTCGATGCCGATCCTGCACCGGGAACTCGCCGAGATCTACGCCGCGGGCGGTGAC
GCCTCCGGGCTCCCGCCCACCGTGTCCTATCGGGACTACCTCGCCTGGCTGGGGCGGCAG
GACAAGGAAGCGGCCCGGGCGGCCTGGCGGGCCGAGTTCGCCGGGCTGGAGACCCCCACC
ACGGTCGTCCCCGCCGATCCCACCCGGATACCGGACATCCACACCGAAGTCGTCGAGCTG
TCCGCGGAGCTGACGGACGGCCTCGCCCGGCTGGCGCGCGGCAACGGGCTCACCCTGAAC
ACCGTCGTGCAGGGCGCGTGGGCCGTCGTGCTGTCGCAGCTCGCCGGCCGCACCGACGTG
GTGTTCGGCGCGACCGCCTCGGGGCGGCCCGCCGATCTGCCCGGCGTGGAGTCGATGGTC
GGCCAGCTGCTCAACACCCTGCCGGTGCGGGTCCGGCTCGACGGCGCGCGGCGGGCCGTC
GAGCTGTTCGCCGACCTGCAGCGCGACCAGGCGGCGCTCATGGCGCACCAGTATCTCGGC
CTCCAGGACGTGCGGACCGTCGCCGGACCCGGAGCGGTCTTCGACACGCTCGTCATCTAC
GAGAACTTCCCCCGCACGGGACTCGACCGGCCGTCGGACGGCGGCCTGAACCTGCGCCCG
GTGAAACGGGGGAGCAACTCCTCGCACTATCCGTTCACCCTGGTGACCGGTCCGGGCGAA
CGGATGCCGCTCATCCTCGACTACGACCACGGCCTGTTCGACCGGACGGCCGCCGAATCG
GTCGTCGGCGCGATGGCGCGCGTGCTGGAGCGGCTGGTCGCCGAGCCCGACGTCCTCATC
GGCCGTCTGCCGACAGTGAGCGAGGCCGAGCGCGCCTTGGTGCTGAACGACTTCAATGCG
ACCGCGGGTCCGGTGCCGGGGGAGTCCGTCCCCGCCTTGTTCGCCCGTCGGGTGGCCGCG
GCGCCGGAGGCGGTGGCGATCGTCGATGCCCACGGTGCGAACCTGACCTACGCCGAGATC
GACCAGGCGTCGGATCGGCTGGCGGGCCACCTCGCCGGTCGGGGCGTCGGCCGCGGTGAC
CGCGTCGGCGTGGCCATGGAGAGGTCACCGGAGCTGATCATCGCGTTCCTGGCGATCTGG
AAGGCGGGCGCCGCCTACGTTCCGGTGGACGTCGAGTACCCGGCCGAGCGGATCTCGTTC
ATCCTCGAGGACTCCGGCGTCTCGACCGTCCTGTGCACCGAAGCCACCCGCGCGGTCGCG
TTTAGCGGGCTAAACGCGATCGTGCTCGACGCGCCGGAAACGCGCGCGGCCGTCGACGTC
TGTGCCGCGCCGGAGATCCGGCTGTCCGCGGACGACCTCGCGTATGTCATGTACACCTCC
GGATCCACCGGTCTCCCGAAGGGCGTGGGAATCCCGCACGGTGCAGTCGCCGGGCTGGCG
GGCGACGAGGGCTGGCAGATCGGCGCGGGCGACGGCGTGCTGATGCACGCGACGCACGTC
TTCGACCCGTCGCTCTACGCGATGTGGGTGCCGCTCGTCTCCGGGGCGCGAGTCCTGCTC
ACCGAACCGGGAGTGCTGGACGCGGCCGGGGTCCGGCAGGCCGTGCGCCGCGGCGCGACC
TACGTCCACCTCACCGCCGGTACCTTCCGCGCGCTGGCGGAGACGTCGCCGGAATGCTTC
GACGGCCTGGTCGAGATCGGTACCGGCGGCGACATCGTCCCCCTGCAGTCGGTGGAGAAC
CTGCGGCGGGCCCAGCCCGGTTTGCGGGTGCGCAACACCTACGGTCCGACCGAGACCACC
CTGTGCGCGACGTGGCTGCCGATCGAACCCGGAGACGTACTCGACCGGGAGCTGCCGATC
GGGCATCCGATGACCAACCGCCGGATCTACATCCTCGACGCCTTCCTGCGCCCGGTCGCG
CCGGGTGTGGCGGGCGAGCTGTACATCGCGGGCACGGGCCTGGCCCGGGGGTACCTGAAC
GCGCCGGGCCTGACTGCCGGCCGCTTCGTGGCTTGCCCGTTCGCCGCCGGGGAACGCATG
TACCGCACCGGCGACCTGGCGCGCTGGACCCGTGACGGCGAAGTCGTGTTCCTCGGCCGT
GCGGACGACCAGGTGAAGATCCGCGGTTACCGGGTCGAACTCGGCGAGGTGGAGGCCGTG
CTGGCCGCCCAGCCGGGAGTCGTCGAGGCCGTCCTGCTGGCACGGGAAGACCAGCCCGGC
GAAAAGCGACTGGTCGGCTATTTCGTTTCGGACGGCGGCGACGCGGGACCGGAGGAGATC
CGGCGGCAGATGGCCAAGGTGCTGCCCGACTACATGGTCCCGATCGCGGTCGTCGCGCTG
CCCGGCCTGCCCGTCACCCCCAACGGGAAGGTGGATCGCCGGGCCCTGCCCGCCCCGGAT
CTCGCCGGAGGCTCGTCGGAGAAGGCGCCGGAGAACGAGACCGAAAAGGTGCTGTGCGCG
CTGTTCGCCGAGATCCTCAGCGTCGACCAGGTGGGCGTCGACGACGCCTTCCAGGACCTC
GGCGGCAGTTCGGCGCTGGCCATGCGGCTCGTCGCGCGGATCCGGGAGGAACTCGGCGAA
GACCTGCCCATCCGGCAGTTGTTCTCCTCGCCGACGCCCGCGGGGCTGGCCAGGGCGCTC
GCCGCGAAGTCCCGCCCCGTCCTGGAAGTCGCCCAGCGACCGGAGCGGGTACCGCTCACC
GCCCGCCAGCTGCGCGCCTGGCTGCTGGCCGATCCGGGCGGGGAGACGGCGAGCCTGACC
ACGTCGGTCGCGCTGCGCCTGCACGGCAGGCTCGACGTGCCCGCGCTGACGGCCGCGCTC
GGCGACGTCGCGGCCCGGCACGAGCTTCTCCGCACGACCTTCCCCGGCGACGCGCAGAGC
GTCCACCAGCACGTCCACGACACCCTGGCGGTCGAGCTGACCCCGGTCGCGGCCACCGAG
GACGACCTCCCCGGCTTGCTCGCGGAGCTGCGTGAGTCGGTCTTCGACCTCACTCGGGAG
GTGCCGTGGCGGTGTGACCTTTTCGCGCTCTCGGAGAAGGAGCACGTGCTTCACCTGCGG
GTGCACCGGATCCTCGCCGACGACGACTCGCTGGACGTGTTCTTCCGCGACCTGGCGGCC
GCCTACGGGGCGCGGCGCGAGGGCCGGGTCCCGCAGCGGGCGCCCCTGGCCCTGCAGTTC
GCCGACTACTCGCTCTGGGAGCGGCGTCTGCTCGAGGACGAGGACGAGCCGGGCAGCCTG
GTCAACGAGCAGGTCGCCTTCTGGCGGGACAACCTGGCGGGCATCGACGGGGAGACGGTG
CTCCCGTTCGACCGCCCGCGGCCCGCGGTCCCGTCGCGGAGGGCGGGTTCGGTGGCGCTG
CGGCTGGACGCCGGCCCGCACGCCCGGCTGGCGGAGACGGCGGAGTCGGCGGGCGCGGAG
ACGCTCCAGCTGGTGCACGCCGCGCTCGCCATGCTGCTGACCAGATCCGGGTCGGGCGAC
GACGTGGTGATCGGCACGACGCTGCCGCGGGACGAGGAACTCTTCGACCTCGAACCGATG
GTCGGCCCGTTCACCCGGCCGCTCGCCCTGCGGACGGACGTCTCGGGCGATCCGACCTTC
CTGGAGGTCGTCACCCGGGTGCAGGAGGCCGTCCAGGCCACGAACCAGCACCTGGACGTG
CCCTTCGAACGGATCGTCGAGCTGCTGGATCTGCCTGCCTCGCTCTCCCGCCACCCGGTG
TTCCAGGTGGGACTGGAGGTGGACGAGGAGGACATCGACGGCTGGTCCACGGCGGAATTG
CCCGCGCTGCGCACCGGTGTCGAACCCGCCGGGACCGACGCGATGGAGCTGGATCTCGCG
GTCAAGCTCACCGAGCACTTCGATGACGACGACGAAGCGGGCGGCCTGGAAGGCGCGCTG
CGCTACGCCACCGATCTGTTCGATCAGGCCACGGCCGAATCGGTCGCCCGGCGGCTGGTC
CGCGTCCTCGAACAGGTGGCGGAGGATCCCCGGCGGCGGGTCAGCGAGCTGGACCTCTTC
CTGGACGACTTCGAACGCGGCCGTCCGCCGATCGCCCCGGCGCGGTGGGCGGGTGCCGTC
CCCGCGGTGGTCGCCGAGCTGGCCGGGGACGACCCGGTCGGCGCGCTGGTACTGGACGAG
CTGATGCGCCCCGTCGCGCCAGGCGCCGTCGGCGATCTCTACGTCACCGGTCCGGCGGTG
GACACGGCACCGGCCGGCCTGCCGACCGTGCCCTGTCCGTTCGGCGAGGAAGGGCACCGG
ATGCTGCCGACGGGCCTGCTCGCCCGCAAGACCCCCGCGAAGACCTTGGTCGTCGTGGGG
GAGCGGCGGCGGGCGAGCACCGCGGTGAAGACGGGTGACTTCGAAATCCTGTTGCCGCTC
CGCGTCGGCGGCGACCGCCCGCCGCTGTTCTGTGTCCACGCGAGCGGTGGCCTGAGCTGG
AACTACGAACCGTTGCTGCGGTATCTCCCGGCGAACCAGCCGGTCTACGGCGTGCAGGCA
CGCGGCCTGGCCAGGACGGAACCCCTGCCGGGCAGCGTCGAGGAGATGGCGGCCGACTAC
CTCGCGCAGATCCGCGCCGTGCAGCCGTCCGGGCCGTACCACCTCCTCGGCTGGTCCCTC
GGCGGCCGGATCGCGCAGGCGATGGCCAGGCTGCTGGAGCAGGAAGGGGAGAAGGTCGGC
CTGCTGGCGCTGCTCGACGCCTATCCCGTCTACATGGGACGCAAGACGACCGGCGCCGCG
AGCGAAGAAGCGGCCCTGTCGAAGCGGAACCAGGCGGATCTGGACCTCGCGGGTCAACTG
GTGAAGAGCGAGGCCGCCCGGGCGCGCCTCGAAGCCGTCATGCGGAACCTCTGGGACATC
GGGCCACGGCACGTTTCCTCGCCCTTCGCCGGCGACATCCTGCTCTTCGTGGCCACTGTG
GACCGTCCCGAACATCTTCCCGTCTCGGTGGCGAAAGCCAGCTGGAAGGAGTTCACCACC
GGGACCATCGAGGCCCACGACATCCCGTCCAACCACTACGACATGGTGCAAACCGCGGCG
CTGGGCCAGATTGGATCCATCGTCGCCGAGAAACTCCGGCAGCGGCCGGAAGGTGAAAGG
ACACAACGATGA
[7] C15..313
[7] A496..891
[7] L-3,5-dihydroxyphenylglycine(Dpg)662..762
[7] PCP974..1041
[7] X1055..1354
[7] TE1627..1844
[7] C43..939
[7] A1486..2673
[7] L-3,5-dihydroxyphenylglycine(Dpg)1984..2286
[7] PCP2920..3123
[7] X3163..4062
[7] TE4879..5532

close this sectionFeature

BLASTP
Database:UniProtKB:2011_09 		show BLAST table
InterPro
Database:interpro:38.0
IPR000873 AMP-dependent synthetase/ligase (Domain)
[496-891] 7.20000000000003e-106 PF00501
PF00501   AMP-binding
IPR001031 Thioesterase (Domain)
[1627-1844] 9.60000000000003e-38 PF00975
PF00975   Thioesterase
IPR001242 Condensation domain (Domain)
[15-313] 5.10000000000004e-63 PF00668 [1055-1354] 1.6e-49 PF00668
PF00668   Condensation
IPR009081 Acyl carrier protein-like (Domain)
[967-1042] 2.49999811956465e-19 SSF47336
SSF47336   ACP_like
[966-1044] 1.1e-25 G3DSA:1.10.1200.10
G3DSA:1.10.1200.10   ACP_like
[974-1041] PS50075
PS50075   ACP_DOMAIN
[977-1040] 5e-13 PF00550
PF00550   PP-binding
IPR010071 Amino acid adenylation domain (Domain)
[496-891] 1.10000000000001e-126 TIGR01733
TIGR01733   AA-adenyl-dom
IPR020845 AMP-binding, conserved site (Conserved_site)
[616-627] PS00455
PS00455   AMP_BINDING
SignalP No significant hit
TMHMM No significant hit
Vanco_00090 Vanco_00090   Vanco_00110 Vanco_00110
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