Username:
Password:
Register
Reset password

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

Navigation
Below is displayed the entity view of the selected entity. Entity view is shown in the form of scheme expressing relations part of (green), contains (orange), substrate of rule (red) and product of rule (blue). The navigation panel on the left shows the entity in corresponding model and allows you to browse the biological structure of the model. Manipulation with the navigation panel is realized by unfolding the items in the navigation tree and clicking on a requested system level.

Annotations Tab
All the annotation links to relevant databases for the currently selected entity are displayed on the Annotation Tab below the scheme.

Models Tab
The Models Tab displays all models containing selected entity.

Relations Tab
Relations Tab contains information about relations in which selected entity figures. There are several types of relations: part of, contains, partial composition items and full composition items. This tab also contains organism info which is optional.

Rules Tab
Rules tab contains list of rules which contains selected entity.

Processes Tab
This tab contains set of processes in which selected entity is present.

photosystem II [ps2]

A photosystem that contains a pheophytin-quinone reaction center with associated accessory pigments and electron carriers. In cyanobacteria and chloroplasts, in the presence of light, PSII functions as a water-plastoquinone oxidoreductase, transferring electrons from water to plastoquinone, whereas other photosynthetic bacteria carry out anoxygenic photosynthesis and oxidize other compounds to re-reduce the photoreaction center.

Annotations
Models
Relations
Rules
Processes
+External links
go:0009523
+Plyusnina et al. (in prep.)
+Respiration and photosynthesis
Details

Part of:

+thylakoid membrane

Definition in BCS:

qb|qa|chl|p680|pheo|oec|yz
+quinone b
+quinone a
+chlorophyl
+photosystem II reaction center
+pheophytin
+oxygen-evolving complex
+yz
+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
+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
+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
+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
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