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Asym./Biol. Unit (Jmol Viewer)

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Title :   CRYSTAL STRUCTURE OF SEMET-RED CHLOROPHYLL CATABOLITE REDUCTASE

Authors :   M. Sugishima, Y. Kitamori, K. Fukuyama

Date :   29 Dec 08 (Deposition) - 05 May 09 (Release) - 02 Jun 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

Chains :   Asym./Biol. Unit : A,B

Keywords :   Alpha-Beta-Alpha Sandwich, Chlorophyll Catabolism, Chloroplast, Coiled Coil, Nadp, Oxidoreductase, Plastid, Transit Peptide (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Sugishima, Y. Kitamori, M. Noguchi, T. Kohchi, K. Fukuyama
Crystal Structure Of Red Chlorophyll Catabolite Reductase: Enlargement Of The Ferredoxin-Dependent Bilin Reductase Family
J. Mol. Biol. V. 389 376 2009
PubMed-ID: 19374909 | Reference-DOI: 10.1016/J.JMB.2009.04.017
(for further references see the PDB file header)

Molecule 1 - RED CHLOROPHYLL CATABOLITE REDUCTASE, CHLOROPLASTIC
	Chains	:	A, B
	EC Number	:	1.3.1.80
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX-6P-1
	Expression System Strain	:	C41(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	TRUNCATED THE CHLOROPLAST TRANSIT PEPTIDE
	Gene	:	RCCR
	Organism Common	:	MOUSE-EAR CRESS, THALE-CRESS
	Organism Scientific	:	ARABIDOPSIS THALIANA
	Organism Taxid	:	3702
	Synonym	:	RCC REDUCTASE, ATRCCR, ACCELERATED CELL DEATH PROTEIN 2

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 14)

No.	Name	Count	Type	Full Name
1	MSE	12	Mod. Amino Acid	SELENOMETHIONINE
2	NA	2	Ligand/Ion	SODIUM ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LEU A:199 , LEU A:201 , VAL A:204 , HOH A:320	BINDING SITE FOR RESIDUE NA A 1
2	AC2	SOFTWARE	LEU B:199 , LEU B:201 , VAL B:204 , HOH B:320	BINDING SITE FOR RESIDUE NA B 2

(no "SS Bond" information available for 2ZXK)

(no "Cis Peptide Bond" information available for 2ZXK)

(no "SAP(SNP)/Variant" information available for 2ZXK)

(no "PROSITE Motif" information available for 2ZXK)

(no "Exon" information available for 2ZXK)

Asymmetric/Biological Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:266
 aligned with RCCR_ARATH | Q8LDU4 from UniProtKB/Swiss-Prot  Length:319

    Alignment length:270
                                    59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319
           RCCR_ARATH    50 RKFMEFPYVSPTRKQLMVDLMSTVENRLQSQLLPCNLPPDVRNFNNPNGSAEASLHIRSGDKSSPIDFVIGSWIHCKIPTGVSLNITSISGFLNSSTKAPNFVVELIQSSSKSLVLILDLPHRKDLVLNPDYLKEYYQDTALDSHRQSLLKLPEVNPYVSPSLFVRSAFSPTASMLKIDAEEEDKLEEILRDHVSPAAKEVLEVWLERCVKEEEEKIVVGEEERMELERRDKSFRRKSIEDDLDLQFPRMFGEEVSSRVVHAIKEAFGVL 319
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhh...hhhhhhhhhhhhhhhhhhh.........hhhhheee.....eeeeeeeee......eeeeeeeeeeee.....eeeeeeeeeee........eeeeeee....eeeeeee.........hhhhhhhhh....hhhhhhhhhhh..eee....hhhhhhhh....eeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhh...----....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2zxk A  50 RKFmEFPYVSPTRKQLmVDLmSTVENRLQSQLLPCNLPPDVRNFNNPNGSAEASLHIRSGDKSSPIDFVIGSWIHCKIPTGVSLNITSISGFLNSSTKAPNFVVELIQSSSKSLVLILDLPHRKDLVLNPDYLKEYYQDTALDSHRQSLLKLPEVNPYVSPSLFVRSAFSPTASmLKIDAEEEDKLEEILRDHVSPAAKEVLEVWLERCVKE----IVVGEEERmELERRDKSFRRKSIEDDLDLQFPRmFGEEVSSRVVHAIKEAFGVL 319
                               |    59      | 69|       79        89        99       109       119       129       139       149       159       169       179       189       199       209       219    |  229       239       249       259 |    |269    |  279       289       299       309       319
                               |           66-MSE                                                                                                                                                       224-MSE                              261  266     274-MSE                  299-MSE                
                              53-MSE           70-MSE

Chain B from PDB  Type:PROTEIN  Length:253
 aligned with RCCR_ARATH | Q8LDU4 from UniProtKB/Swiss-Prot  Length:319

    Alignment length:268
                                    60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310        
           RCCR_ARATH    51 KFMEFPYVSPTRKQLMVDLMSTVENRLQSQLLPCNLPPDVRNFNNPNGSAEASLHIRSGDKSSPIDFVIGSWIHCKIPTGVSLNITSISGFLNSSTKAPNFVVELIQSSSKSLVLILDLPHRKDLVLNPDYLKEYYQDTALDSHRQSLLKLPEVNPYVSPSLFVRSAFSPTASMLKIDAEEEDKLEEILRDHVSPAAKEVLEVWLERCVKEEEEKIVVGEEERMELERRDKSFRRKSIEDDLDLQFPRMFGEEVSSRVVHAIKEAFGV 318
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----------RCC_reductase-2zxkB01 B:61-316                                                                                                                                                                                                                                  -- Pfam domains (1)
           Pfam domains (2) ----------RCC_reductase-2zxkB02 B:61-316                                                                                                                                                                                                                                  -- Pfam domains (2)
         Sec.struct. author hhhhh...hhhhhhhhhhhhhhhhhhh.........hhhhheee.....eeeeeeeee......eeeeeeeeeee.------.eeeeeeeee........eeeeeee....eeeeeee.........hhhhhhhhh....hhhhhhhhhh...eee....hhhhhhhh....eeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhh..---------.hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh.hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zxk B  51 KFmEFPYVSPTRKQLmVDLmSTVENRLQSQLLPCNLPPDVRNFNNPNGSAEASLHIRSGDKSSPIDFVIGSWIHCK------LNITSISGFLNSSTKAPNFVVELIQSSSKSLVLILDLPHRKDLVLNPDYLKEYYQDTALDSHRQSLLKLPEVNPYVSPSLFVRSAFSPTASmLKIDAEEEDKLEEILRDHVSPAAKEVLEVWLERC---------VGEEERmELERRDKSFRRKSIEDDLDLQFPRmFGEEVSSRVVHAIKEAFGV 318
                              |     60     |  70        80        90       100       110       120     |   -  |    140       150       160       170       180       190       200       210       220   |   230       240       250       | -       270   |   280       290       300       310        
                             53-MSE       66-MSE                                                     126    133                                                                                        224-MSE                           258       268     |                      299-MSE               
                                              70-MSE                                                                                                                                                                                                     274-MSE

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

(no "SCOP Domain" information available for 2ZXK)

(no "CATH Domain" information available for 2ZXK)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: RCC_reductase] (2)

Family: RCC_reductase (2)

Arabidopsis thaliana (Mouse-ear cress) (2)

1a	RCC_reductase-2zxkB01	B:61-316
1b	RCC_reductase-2zxkB02	B:61-316

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (RCCR_ARATH | Q8LDU4)

molecular function
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0051743	red chlorophyll catabolite reductase activity	Catalysis of the reaction: red chlorophyll catabolite + reduced ferredoxin + 2 H+ = primary fluorescent catabolite + oxidized ferredoxin. This reaction is the reduction of the C20/C1 double bond in the pyrrole system of red chlorophyll catabolite (RCC) to a colorless tetrapyrrole (pFCC) with a strong blue fluorescence.
biological process
	GO:0015996	chlorophyll catabolic process	The chemical reactions and pathways resulting in the breakdown of chlorophyll, any compound of magnesium complexed in a porphyrin (tetrapyrrole) ring and which functions as a photosynthetic pigment, into less complex products.
	GO:0009814	defense response, incompatible interaction	A response of a plant to a pathogenic agent that prevents the occurrence or spread of disease.
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
	GO:0010363	regulation of plant-type hypersensitive response	Any endogenous process that modulates the frequency, rate or extent of the plant hypersensitive response.
	GO:0043067	regulation of programmed cell death	Any process that modulates the frequency, rate or extent of programmed cell death, cell death resulting from activation of endogenous cellular processes.
cellular component
	GO:0009507	chloroplast	A chlorophyll-containing plastid with thylakoids organized into grana and frets, or stroma thylakoids, and embedded in a stroma.
	GO:0009941	chloroplast envelope	The double lipid bilayer enclosing the chloroplast and separating its contents from the rest of the cytoplasm; includes the intermembrane space.
	GO:0009570	chloroplast stroma	The space enclosed by the double membrane of a chloroplast but excluding the thylakoid space. It contains DNA, ribosomes and some temporary products of photosynthesis.
	GO:0009535	chloroplast thylakoid membrane	The pigmented membrane of a chloroplast thylakoid. An example of this component is found in Arabidopsis thaliana.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005739	mitochondrion	A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
	GO:0009536	plastid	Any member of a family of organelles found in the cytoplasm of plants and some protists, which are membrane-bounded and contain DNA. Plant plastids develop from a common type, the proplastid.
	GO:0009579	thylakoid	A membranous cellular structure that bears the photosynthetic pigments in plants, algae, and cyanobacteria. In cyanobacteria thylakoids are of various shapes and are attached to, or continuous with, the plasma membrane. In eukaryotes they are flattened, membrane-bounded disk-like structures located in the chloroplasts; in the chloroplasts of higher plants the thylakoids form dense stacks called grana. Isolated thylakoid preparations can carry out photosynthetic electron transport and the associated phosphorylation.

Asymmetric/Biological Unit
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	RCCR_ARATH \| Q8LDU4	:	2zxl 3aga 3agb 3agc

Description

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Ligands, Modified Residues, Ions (2, 14)

Sites (2, 2)

SS Bonds (0, 0)

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