Coding

Part:BBa_K1998013

Designed by: Shauna Winchester   Group: iGEM16_Macquarie_Australia   (2016-10-13)
Revision as of 23:42, 18 October 2016 by SWinchester (Talk | contribs) (→‎Biology & Literature)


MgPPIX to Chlorophyll a plasmid


Sequence and Features


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal BglII site found at 912
    Illegal BglII site found at 2365
    Illegal BglII site found at 5647
    Illegal BglII site found at 6136
    Illegal BamHI site found at 316
    Illegal BamHI site found at 3128
    Illegal BamHI site found at 5416
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal AgeI site found at 1904
    Illegal AgeI site found at 1955
  • 1000
    INCOMPATIBLE WITH RFC[1000]
    Illegal BsaI site found at 478
    Illegal BsaI.rc site found at 4018


Overview

This composite part makes up one of our operons in the chlorophyll biosynthesis pathway. It is composed of YCF54, ChlM, POR, DVR1, ChlP and ChlG. These genes are Mg-protoporphyrin IX monomethyl ester (oxidative) cyclase (YCF54) and Magnesium-protoporphyrin O-methyltransferase (ChlM), Light-dependent protochlorophyllidereductase (POR), 3,8-divinyl, Geranylgeranyl reductase(ChlP), protochlorophyllidea 8-vinyl reductase (DVR1) and Chlorophyll synthetase (ChlG).
These genes are part of the chlorophyll biosynthetic pathway and are involved in converting Mg-protoporphyrin IX to chlorophyll

ChlorophyllBiosynthesisDiagram

Biology & Literature

These two genes within this part are used within an operon in the biosynthesis pathway. YCF54 works with the CTH1 gene and Plastocyanin within the oxidative cyclase pathway. It's interaction with other genes results in the catalysis of the biosynthesis pathway from Mg-protoporphyrin IX to Protochlorophyllide [1]. Deletion studies have detected the importance of YCF54 in maintaining levels of Mg-protoporphyrin IX methyl ester indicating that the YCF54 gene is critical to both the assembly and function of the cyclase complex [1].
The second gene in this part is ChlM. ChlM encodes for a magnesium protoporhyrin IX methytransferase. ChlM's role in the pathway is to methylate Mg-protoporphyrin IX which then aids the catalysis of Mg-cheltase [2]. This then facilitates the formation of the final protochlorophyllide. Involved in the second step of the pathway, the ChlM gene is involved in the transfer of a methyl group onto one of the rings of magnesium protoporphyrin which forms the magnesium prootoporhyrin IX monomethylester [3, 4].
The POR gene is a light dependent protochlorophyllidereductase. It's role is to convert protochlorophyllide to chlorophyllide using NADPH and light as the reductant. Formation of the POR protein in plants is important as without it the chloroplasts do not function [5, 6]. The protochlorophyllide reduces to chlorophyllide by being excited through light functioning as a catalysis. The excitation of the POR molecule and therefore the transformation of it to chlorophyllide cause the conversion of the membranes from an inactive state into active chloroplast [7]. Through this transformation into active chloroplasts, energy is produced and now able to be used by the plant.

Geranylgeranyl reductase - ChlP is a hydrogenase enzyme that reduces the double bonds of geranylgeranyl diphosphate to form phytol pyrophosphate

3,8-divinyl protochlorophyllidea 8-vinyl reductase - DVR1 reduces divinyl protochlorophyllide a to monovinyl protochlorophyllide a

Reaction: DVR1_reaction_image.png

Chlorophyll synthetase - ChlG catalyses the esterification of chlorophyllide with phytyl-pyrophosphate or geranyl-geranyl pyrophosphate in chloroplasts, producing chlorophyll

Protein information

YCF54
Mass: 17.08kDa
Sequence: MAPAAASADKATAAEYYALVCNAEWFFMDPQNESVAEQLREKVRFFKEQNKERDFFIVPNPKWLDAKFPEQAKQVKRPCVALVSTDKMWITFMKLRLDRVLKIDLKSM PASEVLAAGEALPDFKPDGKWTAPYARYTPGWWNVFLPNH

ChlM
Mass: 30.45kDa Sequence: MASEIAQTADVGSLTFAVGGVGAVVGLGALLVATDHQKRRSEQMKSFDGDEKEAVKDYFNTAGFERWRKIYGETDEVNKVQLDIRTGHAQTVDKVLRWVDEEGSVQGIT VADCGCGTGSLAIQLALRGAAVSASDISAAMASEAEQRYQQAVAAGQGKAPKVAPKFEALDLESVKGKYDTVTCLDVMIHYPQDKVDAMITHLAGLSDRRLIISFAPKTL SYSILKRIGELFPGPSKATRAYLHREEDVEAALKRAGFKVTKREMTATSFYFSRLLEAIRE

POR
Mass: 41.87kDa
Sequence:
MVVCAATATAPSPSLADKFKPNAIARVPATQQKQTAIITGASSGLGLNAAKALAATGEWHVVMACRDFLKAEQAAKKVGMPAGSYSILHLDLSSLESVRQFVQNFKASGR RLDALVCNAAVYLPTAKEPRFTADGFELSVGTNHLGHFLLTNLLLDDLKNAPNKQPRCIIVGSITGNTNTLAGNVPPKANLGDLSGLAAGVPAANPMMDGQEFNGAKAYK DSKVACMMTV RQMHQRFHDATGITFASLYPGCIAETGLFREHVPLFKTLFPPFQKYITKGYVSEEEAGRRLAAVISDPKLNKSGAYWSWSSTTGSFDNK

DVR1
Mass: 37kDa
Sequence:
MAMAASRQAVRVAAAVDADYRKREPKDVRVLVVGPTGYIGKFVVKELVSRGYNVVAFARENAGIKGKMGREDIVKEFHGAEVRFGSVLDPASLRDVAFKDPVDVVVSCLA SRTGGKKDSWLIDYTATKNSLDVARASGAKHFVLLSAICVQKPLLEFQKAKLQFESDLQAAGDITYSIVRPTAFFKSIAGQIDIVKKGNPYVMFGDGNLAACKPISEADLASF IADCVTEQNKVNKVLPIGGPSKAFTAKQQADLLFNITGLPPKYFPVPVALMDGMIGLFDSLAKLFPQLEDSAEFARIGKYYATESMLVYDEARGVYRKTKRLVTARTRWKTS SLVQ

ChlP
Mass: 47kDa
Sequence:
MVIGGGPSGACAAETLAKGGVETFLLERKLDNCKPCGGAIPLCMVEEFDLPMEIIDRRVTKMKMISPSNREVDVGKTLSETEWIGMCRREVFDDYLRNRAQKLGANIVNGL FMRSEQQSAEGPFTIHYNSYEDGSKMGKPATLEVDMIIGADGANSRIAKEIDAGEYDYAIAFQERIRIPDDKMKYYENLAEMYVGDDVSPDFYGWVFPKYDHVAVGTGTVVN KTAIKQYQQATRDRSKVKTEGGKIIRVEAHPIPEHPRPRRCKGRVALVGDAAGYVTKCSGEGIYFAAKSGRMAAEAIVEGSANGTKMCGEDAIRVYLDKWDRKYWTTYKVLD ILQKVFYRSNPAREAFVELCEDSYVQKMTFDSYLYKTVVPGNPLDDVKLLVRTVSSILRSNALRSVNSKSVNVSFGSKANEERVM AA

ChlG
Mass: 36.84kDa
Sequence:
MNQQATEEKSDTNSAARQMLGMKGAALETDIWKIRVQLTKPVTWIPLIWGVACGAAASGHYQWNNPTQIAQLLTCMMMSGPFLTGYTQTINDWYDREIDAINEPYRPIPS GRISERDVIVQIWVLLLGGIGLAYTLDQWAGHTTPVMLQLTIFGSFISYIYSAPPLKLKQSGWAGNYALGSSYIALPWWAGQALFGTLTLDVMALTIAYSLAGLGIAIVNDFKSI EGDRQ MGLQSLPVAFGVDTAKWICVSTIDVTQLGVAAYLAWGLHEELYGAVLLALILPQIYFQYKYFLPDPIANDVKYQASAQPFLVFGLLTAGLACGHHVNAVAA AASAAGAL

References

[1]

[edit]
Categories
Parameters
None