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Biochemical Space

Processes

+ Cyanobacterium in its environment
o Environmental processes
+ Cellular processes
o Respiration and photosynthesis
o Carbon concentrating mechanism (CCM)
o Respiration
o Clock mechanism
o Metabolism

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thylakoid membrane [tlm]

A membrane enriched in complexes formed of reaction centers, accessory pigments and electron carriers, in which photosynthetic reactions take place.

Annotations
Models
Relations
Rules
Processes
+External links
go:0034357
+Respiration and photosynthesis
Details

Part of:

+cell

Contains:

+lumen
+plastoquinone
+plastoquinol
+heme f
+high potential hemes
+type I NADPH dehydrogenase, NDH1
+dehydrogenase complex, NDH1_3
+type II NADH dehydrogenase, NDH2
+succinate dehydrogenase, SDH
+plastoquinone oxidase, CydBD
+ATPase
+phycobilisome
+cytochrome b6/f complex
+photosystem I
+photosystem II
+chlorophyll exciton of the internal antenna of PSII migration 1
chlorophyll exciton of the internal antenna of PSII migrates to the primary chlorophyll donor of PSII that drives the charge separation between P680 and Pheo
Rule: ps2(chl{*}|p680{n}|pheo{n})::tlm <=> ps2(chl{n}|p680{+}|pheo{-})::tlm
Details
+plastoquinone reduction in the thylakoid membrane 1
oxidation of NADPH and reduction of plastoquinone in the thylakoid membrane
Rule: NADPH::cyt + 5 h{+}::cyt + pq::tlm => NADP{+}::cyt + 4 h{+}::lum + pqh2::tlm
modifier: NDH1
Details
+oxidation of S3-state of the oxygen-evolving complex OEC{3+} by Yz{+} in PSII RC
Oxygen evolving complex is oxidized from S3 to S4
Rule: ps2(oec{3+} | yz{+})::tlm <=> ps2(oec{4+} | yz{n})::tlm
Details
+oxidation of S2-state of the oxygen-evolving complex OEC{2+} by Yz{+} in PSII RC
Oxygen evolving complex is oxidized from S2 to S3
Rule: ps2(oec{2+}|yz{+})::tlm <=> ps2(oec{3+}|yz{n})::tlm
Details
+oxidation of SO-state of the oxygen-evolving complex OEC{n} by Yz{+} in PSII RC
Oxygen evolving complex is oxidized from S0 to S1
Rule: ps2(oec{n}|yz{+})::tlm <=> ps2(oec{+}|yz{n})::tlm
Details
+oxidation of S1-state of the oxygen-evolving complex OEC{+} by Yz{+} in PSII RC
Oxygen evolving complex is oxidized from S1 to S2
Rule: ps2(oec{+}|yz{+})::tlm <=> ps2(oec{2+}|yz{n})::tlm
Details
+reduction of P680{+} and oxidation of Yz{n} in PSII RC
thyrosin donor is oxidized by P680+
Rule: ps2(yz{n}|p680{+})::tlm <=> ps2(yz{+}|p680{n})::tlm
Details
+binding of PQ to the Qb site
a plastoquinone from the pool binds to the Qb-binding pocket of the PSII D1 protein
Rule: qb{empty}::ps2::tlm + pq::tlm <=> qb{n}::ps2::tlm
Details
+protonation Qb{2-} to pqh2
the double reduced secondary quinone acceptor Qb2- is protonated plastoquinol and released from the Qb-binding pocket of the PSII D1 protein to plastoquinon pool.
Rule: qb{2-}::ps2::tlm + 2 h{+}::cyt <=> qb{empty}::ps2::tlm + pqh2::tlm
Details
+oxidation of Qa{-} and reduction of Qb{-} in PSII RC
the electron from the reduced primary quinone acceptor of PSII Qa-
Rule: ps2(qa{-}|qb{-})::tlm <=> ps2(qa{n}|qb{2-})::tlm
Details
+oxidation of Qa{-} and reduction of Qb{n} in PSII RC
the electron from the reduced primary quinone acceptor of PSII Qa-
Rule: ps2(qa{-}|qb{n})::tlm <=> ps2(qa{n}|qb{-})::tlm
Details
+fluorescence emission from the chlorophyll of the internal PSI antenna
chlorophyll a (chl, pigment ligand) emits near infra-red {nir} fluorescence
Rule: chl{*}::ps1::tlm => chl{n}::ps1::tlm + photon{nir}::cell
Details
+oxidation of Pheo{-} and reduction of Qa{n} in PSII RC
chlorophyll exciton of the internal antenna of PSI migrates to the primary chlorophyll donor of PSI that drives the charge separation between P700 and A0
Rule: ps2(pheo{-}|qa{n})::tlm <=> ps2(pheo{n}|qa{-})::tlm
Details
+chlorophyll exciton of the internal antenna of PSII migration 3
chlorophyll exciton of the internal antenna of PSII migrates to the primary chlorophyll donor of PSII that drives the charge separation between P680 and Pheo
Rule: ps2(chl{*} | p680{n} | pheo{n})::tlm <=> ps2(chl{n} | p680{+} | pheo{-})::tlm
Details
+fluorescence emission from the chlorophyll of the internal PSII antenna
chlorophyll a (chl, pigment ligand) emits near infra-red {nir} fluorescence
Rule: chl{*}::ps2::tlm => chl{n}::ps2::tlm + photon{nir}::cell
Details
+light absorption in the chlorophyll of the internal PSII antenna
chlorophyll a (chl, pigment ligand) is excited by absorption of a photon in the internal antenna of PSII (PSII, pigment-protein complex)
Rule: photon{blue_red}::cell + chl{n}::ps2::tlm => chl{*}::ps2::tlm
Details
+exciton transfer from phycobilisome to PSII
Exciton is transferred from the phycocyanobilin (PCB) in the phycobilisome (PBS) to chlorophyll (chl) in the
Rule: pcb{*}::pbs::tlm + chl{n}::ps2::tlm => pcb{n}::pbs::tlm + chl{*}::ps2::tlm
Details
+plastoquinole oxidation in the thylakoid membrane
oxidation of plastoquinole in the thylakoid membrane
Rule: pqh2::tlm + O2::lum + 2 h{+}::lum => pq::tlm + 2 H2O::lum
modifier: CydBD
Details
+plastoquinone reduction in the thylakoid membrane 2
oxidation of succinate and reduction of plastoquinone in the thylakoid membrane
Rule: succinate::cyt + pq::tlm => fumarate::cyt + pqh2::tlm
modifier: SDH
Details
+plastoquinone reduction in the thylakoid membrane 3
oxidation of NADH and reduction of plastoquinone in the thylakoid membrane
Rule: NADH::cyt + h{+}::cyt + pq::tlm => NAD+::cyt + pqh2::tlm
modifier: NDH2
Details
+plastoquinone reduction in the thylakoid membrane 4
oxidation of NADPH and reduction of plastoquinone in the thylakoid membrane
Rule: NADPH::cyt + 4 h{+}::cyt + pq::tlm + H2O::cyt + CO2::lum => NADP{+}::cyt + 4 h{+}::lum + pqh2::tlm + HCO3{-}::cyt
modifier: NDH1_3
Details
+charge recombination between oxidized P700 and reduced Fa
Rule: ps1(p700{+} | fa{-})::tlm => ps1(p700{n} | fa{n})::tlm + photon{red}::cell
modifier: As the recombination is considred as subsequent backward electron transport from Fa- to P700+ through Fx, A1, A0 and aChl, these enities must be in neutral state to accept the electron and hence they are modifiers of the recombination-
Details
+charge recombination between oxidized P700 and reduced Fx
Rule: ps1(p700{+} | fx{-})::tlm => ps1(p700{n} | fx{n})::tlm + photon{red}::cell
modifier: As the recombination is considred as subsequent backward electron transport from Fx- to P700+ through A1, A0 and aChl, these enities must be in neutral state to accept the electron and hence they are modifiers of the recombination-
Details
+charge recombination between oxidized P700 and reduced A1
Rule: ps1(p700{+} | a1{-})::tlm => ps1(p700{n} | a1{n})::tlm
modifier: As the recombination is considred as subsequent backward electron transport from A1- to P700+ through A0 and aChl, these enities must be in neutral state to accept the electron and hence they are modifiers of the recombination.
Details
+reduction of oxidized primary electron donor in photosystem I
Rule: ps1(p700{n} | achl{+})::tlm <=> ps1(p700{+} | achl{n})::tlm
Details
+reduction of oxidized P700
Rule: pc{n}::cell + p700{+}::ps1::tlm <=> pc{+}::cell + p700{n}::ps1::tlm
Details
+electron transport from Fb to Ferredoxin
Rule: fb{-}::ps1::tlm + fd{n}::cell <=> fb{n}::ps1::tlm + fd{-}::cell
Details
+electron transport from Fx to Fa
Rule: ps1(fx{-} | fa{n})::tlm => ps1(fx{n} | fa{-})::tlm
Details
+electron transport from Fa to Fb
Rule: ps1(fa{-} | fb{n})::tlm <=> ps1(fa{n} | fb{-})::tlm
Details
+electron transport from A0 to A1
Rule: ps1(a0{-} | a1{n})::tlm => ps1(a0{n} | a1{-})::tlm
Details
+electron transport from A1 to Fx
Rule: ps1(a1{-} | fx{n})::tlm <=> ps1(a1{n} | fx{-})::tlm
Details
+primary charge separation between the primary electron donor and the primary electron acceptor in ph
Rule: ps1(achl{*} | a0{n})::tlm <=> ps1(achl{+} | a0{-})::tlm
Details
+energy transfer from chlorophyll-containing light-harvesting antenna of photosystem I to the primary
Rule: ps1(chl{*} | achl{n})::tlm <=> ps1(chl{n} | achl{*})::tlm
Details
+non-radiative deactivation of excited states in chlorophyll-containing light-harvesting antenna of p
Rule: chl{*}::ps1::tlm => chl{n}::ps1::tlm
Details
+radiative deactivation of excited states in chlorophyll-containing light-harvesting antenna of photo
Rule: chl{*}::ps1::tlm => chl{n}::ps1::tlm + photon{red}::cell
Details
+absorption of blue/red photon by chlorophyll-containing light-harvesting antenna of photosystem I
Rule: chl{n}::ps1::tlm + photon{blue_red}::cell => chl{*}::ps1::tlm
Details
+energy transfer from phycobilin-containing phycobilisome to chlorophyll-containing light-harvesting
Rule: pcb{*}::pbs::tlm + chl{n}::ps1::tlm <=> pcb{n}::pbs::tlm + chl{*}::ps1::tlm
Details
+radiative deactivation of excited states in phycobilin-containing phycobilisome by fluorescence emis
Rule: pcb{*}::pbs::tlm => pcb{n}::pbs::tlm + photon{red}::cell
Details
+absorption of orange photon by phycobilin-containing phycobilisome
Rule: pcb{n}::pbs::tlm + photon{orange}::cell => pcb{*}::pbs::tlm
Details
+non-radiative deactivation of excited states in phycobilin-containing phycobilisome by non-regulated
Rule: pcb{*}::pbs::tlm => pcb{n}::pbs::tlm
Details
+plastoquinone reduction
Rule: pq{n}::tlm + 2 h{+}::cyt + bhc{2-}::cytb6f::tlm <=> pqh2::tlm + bhc{n}::cytb6f::tlm
Details
+reduction of oxidized high potential hemes by ferredoxin-dependent cyclic electron transport
Rule: bhc{n}::cytb6f::tlm + fd{-}::cyt <=> bhc{-}::cytb6f::tlm + fd{n}::cyt
Details
+reduction of singly reduced high potential hemes by ferredoxin-dependent cyclic electron transport
Rule: bhc{-}::cytb6f::tlm + fd{-}::cyt <=> bhc{2-}::cytb6f::tlm + fd{n}::cyt
Details
+reduction of singly reduced high potential hemes by low potential heme b
Rule: cytb6f(bl{-} | bhc{-})::tlm <=> cytb6f(bl{n} | bhc{2-})::tlm
Details
+plastoquinol oxidation
Rule: pqh2{n}::tlm + cytb6f(bl{n} | f{n})::tlm <=> pq::tlm + 2 h{+}::lum + cytb6f(bl{-} | f{-})::tlm
Details
+plastocyanin reduction
Rule: f{-}::cytb6f::tlm + pc{+}::lum <=> f{n}::cytb6f::tlm + pc{n}::lum
Details
+reduction of oxidized high potential hemes by low potential heme b
Rule: cytb6f(bl{-} | bhc{n})::tlm <=> cytb6f(bl{n} | bhc{-})::tlm
Details
+chlorophyll excitaton of the internal antenna PSII2 migration 2
chlorophyll exciton of the internal antenna of PSII migrates to the primary chlorophyll donor of PSII that drives the charge separation between P680 and Pheo
Rule: chl{*}::ps2::tlm + ps2(p680{n} | pheo{n})::tlm <=> chl{n}::ps2::tlm + ps2(p680{+} | pheo{-})::tlm
Details
+proline dehydrogenase (enzyme name) R34
Rule: C00148::cyt + pq::tlm => C03912::cyt + pqh2{n}::tlm
modifier: 1-5-5-2
Details
+monoamine oxidase (enzyme name) R54
Rule: C00062::cyt + pq::tlm + H2O::cyt => C03771::cyt + C00014::cyt + pqh2{n}::tlm
modifier: 1-4-3-4
Details
+glycerol-3-phosphate dehydrogenase (enzyme name) R264
Rule: C00093::cyt + pq::tlm => C00111::cyt + pqh2{n}::tlm
modifier: 1-1-5-3
Details
+1-3-99-1 (enzyme name) R513
Rule: succinate::cyt + pq::tlm => pqh2{n}::tlm + fumarate::cyt
modifier: 1-3-99-1
Details
+R726
Rule: pq::cyt => pq::tlm
Details
Please use the following reference to cite this web site:
M. Trojak, D. Safranek, J. Hrabec, J. Salagovic, F. Romanovska, J. Cerveny: E-Cyanobacterium.org: A Web-Based Platform for Systems Biology of Cyanobacteria. In: Computational Methods in Systems Biology, CMSB 2016, Vol. 9859 of LNCS, pp. 316-322. Springer, 2016. DOI