Difference between revisions of "Part:BBa K1080010"

Revision as of 02:29, 16 October 2014

YCF54

Usage and Biology

The structure of the chlorophyll molecule is the isocyclic ring. The formation of the ring is dependent by the action of enzyme Mg-protoporphyrin IX monomethyl ester (oxidative) cyclase. The catalysis of this enzyme to divinyl protochlorophyllide.

A crucial regulatory step in the biosynthesis of chlorophyll in higher plants and algae is the reduction of protochlorophyllide to chlorophyllide. POR is unique in its formation as it directly utilizes light for catalysis. POR is a major protein in the membrane of plants, without it, the chloroplasts would remain inactive. The protochlorophyllide absorbs light, excites the molecule and is reduced by NADPH to form chlorophyllide. The illumination of POR and its conversion of protochlorophyllide to chlorophyllide transforms etiolated membranes to active chloroplasts, which in turn provides energy to the plant once chlorophyll is produced. The absorption of light by the co-enzyme complex developed from the interaction of POR and NADPH induces hydrogen transfer resulting in the formation of chlorophyllide and NADP+

Essential for the formation of protochlorophyllide is the catalysis of Protoporphyrin Monomethylester Oxidative Cyclase. This is achieved by the interaction YCF 54 with other components integral in the formation, XanL or CTH1 and plastocyanin. The activity and stability of the Protoporphyrin Monomethylester Oxidative Cyclase is dependent on the YCF54 component when forming protochlorophyllide.

Sequence and Features

Assembly Compatibility:

10
COMPATIBLE WITH RFC[10]
12
COMPATIBLE WITH RFC[12]
21
INCOMPATIBLE WITH RFC[21]
Illegal BamHI site found at 108
23
COMPATIBLE WITH RFC[23]
25
COMPATIBLE WITH RFC[25]
1000
INCOMPATIBLE WITH RFC[1000]
Illegal BsaI site found at 270

Amino acid sequence

MAPAAASADK ATAAEYYALV CNAEWFFMDP QNESVAEQLR EKVRFFKEQN KERDFFIVPN
PKWLDAKFPE QAKQVKRPCV ALVSTDKMWI TFMKLRLDRV LKIDLKSMPA SEVLAAGEAL
PDFKPDGKWT APYARYTPGW WNVFLPNH

References and documentation are available. Please note the modified algorithm for extinction coefficient.

Number of amino acids: 148

Molecular weight: 17073.7

Theoretical pI: 8.50

Amino acid composition:
Ala (A) 20 13.5%
Arg (R) 7 4.7%
Asn (N) 6 4.1%
Asp (D) 9 6.1%
Cys (C) 2 1.4%
Gln (Q) 5 3.4%
Glu (E) 10 6.8%
Gly (G) 3 2.0%
His (H) 1 0.7%
Ile (I) 3 2.0%
Leu (L) 11 7.4%
Lys (K) 14 9.5%
Met (M) 5 3.4%
Phe (F) 10 6.8%
Pro (P) 12 8.1%
Ser (S) 5 3.4%
Thr (T) 5 3.4%
Trp (W) 6 4.1%
Tyr (Y) 4 2.7%
Val (V) 10 6.8%
Pyl (O) 0 0.0%
Sec (U) 0 0.0%

(B)   0	  0.0%
(Z)   0	  0.0%
(X)   0	  0.0%

Total number of negatively charged residues (Asp + Glu): 19 Total number of positively charged residues (Arg + Lys): 21

Atomic composition:

Carbon C 785 Hydrogen H 1190 Nitrogen N 202 Oxygen O 212 Sulfur S 7

Formula: C785H1190N202O212S7 Total number of atoms: 2396

Extinction coefficients:

Extinction coefficients are in units of M-1 cm-1, at 280 nm measured in water.

Ext. coefficient 39085 Abs 0.1% (=1 g/l) 2.289, assuming all pairs of Cys residues form cystines

Ext. coefficient 38960 Abs 0.1% (=1 g/l) 2.282, assuming all Cys residues are reduced

Estimated half-life:

The N-terminal of the sequence considered is M (Met).

The estimated half-life is:

                            30 hours (mammalian reticulocytes, in vitro).
                           >20 hours (yeast, in vivo).
                           >10 hours (Escherichia coli, in vivo).

Instability index:

The instability index (II) is computed to be 35.64 This classifies the protein as stable.

Aliphatic index: 70.00

Grand average of hydropathicity (GRAVY): -0.385

Source

Chlamydomonas reinhardtii

@@ Line 5: / Line 5: @@
 The structure of the chlorophyll molecule is the isocyclic ring. The formation of the ring is dependent by the action of enzyme Mg-protoporphyrin IX monomethyl ester (oxidative) cyclase. The catalysis of this enzyme to divinyl protochlorophyllide.
+A crucial regulatory step in the biosynthesis of chlorophyll in higher plants and algae is the reduction of protochlorophyllide to chlorophyllide. POR is unique in its formation as it directly utilizes light for catalysis. POR is a major protein in the membrane of plants, without it, the chloroplasts would remain inactive. The protochlorophyllide absorbs light, excites the molecule and is reduced by NADPH to form chlorophyllide. The illumination of POR and its conversion of protochlorophyllide to chlorophyllide transforms etiolated membranes to active chloroplasts, which in turn provides energy to the plant once chlorophyll is produced. The absorption of light by the co-enzyme complex developed from the interaction of POR and NADPH induces hydrogen transfer resulting in the formation of chlorophyllide and NADP+
+Essential for the formation of protochlorophyllide is the catalysis of Protoporphyrin Monomethylester Oxidative Cyclase. This is achieved by the interaction YCF 54 with other components integral in the formation, XanL or CTH1 and plastocyanin. The activity and stability of the Protoporphyrin Monomethylester Oxidative Cyclase is dependent on the YCF54 component when forming protochlorophyllide.
 [[File:The structure of the chlorophyll molecule is the isocyclic ring. The formation of the ring is dependent by the action of enzyme Mg-protoporphyrin IX monomethyl ester (oxidative) cyclase. The catalysis of this enzyme to divinyl protochlorophyllide.png]]