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Title :   CRYSTAL STRUCTURE OF AN ENGINEERED FERREDOXIN NADP REDUCTASE (FNR) FROM PISUM SATIVUM

Authors :   H. Botti, M. A. Musumeci, E. A. Ceccarelli, A. Buschiazzo

Date :   02 Aug 10 (Deposition) - 23 Feb 11 (Release) - 28 Jun 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.90

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)

Keywords :   Chloroplast, Flavoprotein, Oxidoreductase, Transport, Photosynthesis, Electron Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. A. Musumeci, H. Botti, A. Buschiazzo, E. A. Ceccarelli
Swapping Fad Binding Motifs Between Plastidic And Bacterial Ferredoxin-Nadp(H) Reductases.
Biochemistry V. 50 2111 2011
PubMed-ID: 21306142 | Reference-DOI: 10.1021/BI101772A

Molecule 1 - FERREDOXIN--NADP REDUCTASE, LEAF ISOZYME, CHLOROPLASTIC
	Chains	:	A, B
	EC Number	:	1.18.1.2
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET32B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Variant	:	PLYSS
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organism Common	:	PEA
	Organism Scientific	:	PISUM SATIVUM
	Organism Taxid	:	3888
	Other Details	:	THE LOOP BETWEEN WILD-TYPE RESIDUES 115-123 (INCLUSIVE) HAS BEEN DELETED AND A C-TERMINAL TRP HAS BEEN INSERTED (W300)
	Synonym	:	FNR

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 6)

No.	Name	Count	Type	Full Name
1	FAD	2	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
2	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 4)

No.	Name	Count	Type	Full Name
1	FAD	1	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
2	SO4	3	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	FAD	1	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
2	SO4	1	Ligand/Ion	SULFATE ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:79 , ARG A:87 , LEU A:88 , TYR A:89 , SER A:90 , CYS A:108 , VAL A:109 , LYS A:110 , VAL A:112 , PRO A:113 , ASP A:114 , GLY A:115 , VAL A:116 , CYS A:117 , SER A:118 , THR A:157 , GLU A:297 , TYR A:299 , HOH A:2011	BINDING SITE FOR RESIDUE FAD A 1301
2	AC2	SOFTWARE	ARG A:35 , SER A:128 , GLU A:129 , HOH A:2001 , ARG B:35	BINDING SITE FOR RESIDUE SO4 A 1302
3	AC3	SOFTWARE	SER A:219 , ARG A:220 , TYR A:231	BINDING SITE FOR RESIDUE SO4 A 1303
4	AC4	SOFTWARE	LYS A:229 , TYR A:231 , GLU B:263	BINDING SITE FOR RESIDUE SO4 A 1304
5	AC5	SOFTWARE	ARG B:87 , LEU B:88 , TYR B:89 , SER B:90 , CYS B:108 , VAL B:109 , LYS B:110 , ASP B:114 , GLY B:115 , VAL B:116 , CYS B:117 , SER B:118 , THR B:157 , LYS B:260 , GLU B:297 , TYR B:299 , TRP B:300 , HOH B:2010 , HOH B:2011 , HOH B:2012	BINDING SITE FOR RESIDUE FAD B 1301
6	AC6	SOFTWARE	ARG A:286 , SER B:219 , ARG B:220 , LYS B:229 , TYR B:231	BINDING SITE FOR RESIDUE SO4 B 1302

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

Asymmetric Unit

No.	Residues
1	Gly A:134	-	Pro A:135
2	Gly B:134	-	Pro B:135

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

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FAD_FR	PS51384	Ferredoxin reductase-type FAD binding domain profile.	FENR1_PEA	81-203	2	A:29-142 B:29-142

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FAD_FR	PS51384	Ferredoxin reductase-type FAD binding domain profile.	FENR1_PEA	81-203	1	A:29-142 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FAD_FR	PS51384	Ferredoxin reductase-type FAD binding domain profile.	FENR1_PEA	81-203	1	- B:29-142

(no "Exon" information available for 2XNC)

Asymmetric 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:287
 aligned with FENR1_PEA | P10933 from UniProtKB/Swiss-Prot  Length:360

    Alignment length:296
                                                                                                                                                                                                                                                                                                                                360 
                                    75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355    | 
            FENR1_PEA    66 SKKQDENIVVNKFKPKEPYVGRCLLNTKITGDDAPGETWHMVFSTEGEVPYREGQSIGIVPDGIDKNGKPHKLRLYSIASSAIGDFGDSKTVSLCVKRLVYTNDAGEVVKGVCSNFLCDLKPGSEVKITGPVGKEMLMPKDPNATVIMLGTGTGIAPFRSFLWKMFFEKHEDYQFNGLAWLFLGVPTSSSLLYKEEFEKMKEKAPENFRLDFAVSREQVNDKGEKMYIQTRMAQYAEELWELLKKDNTFVYMCGLKGMEKGIDDIMVSLAAKDGIDWIEYKRTLKKAEQWNVEVY-   -
               SCOP domains d2xnca1 A:14-139 automated matches                                                                                                     d2xnca2 A:140-300 automated matches                                                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................eeeeeeeeee.........eeeeeee...........eeeee.............eeee.............eeeeeee.---------...hhhhhhhhhh....eeeeeeee............eeeeeee...hhhhhhhhhhhhh..........eeeeeeee.hhhhh.hhhhhhhhhhhh...eeeeeee............hhhhhhhhhhhhhhhhhh...eeeeeeee.hhhhhhhhhhhhhhhhh..hhhhhhhhhhhh..eeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------FAD_FR  PDB: A:29-142 UniProt: 81-203                                                                                      -------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xnc A  14 SKKQDENIVVNKFKPKEPYVGRCLLNTKITGDDAPGETWHMVFSTEGEVPYREGQSIGIVPDGIDKNGKPHKLRLYSIASSAIGDFGDSKTVSLCVKR---------VPDGVCSNFLCDLKPGSEVKITGPVGKEMLMPKDPNATVIMLGTGTGIAPFRSFLWKMFFEKHEDYQFNGLAWLFLGVPTSSSLLYKEEFEKMKEKAPENFRLDFAVSREQVNDKGEKMYIQTRMAQYAEELWELLKKDNTFVYMCGLKGMEKGIDDIMVSLAAKDGIDWIEYKRTLKKAEQWNVEVYW 300
                                    23        33        43        53        63        73        83        93       103       | -       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294      
                                                                                                                           111       112

Chain B from PDB  Type:PROTEIN  Length:288
 aligned with FENR1_PEA | P10933 from UniProtKB/Swiss-Prot  Length:360

    Alignment length:297
                                                                                                                                                                                                                                                                                                                                 360 
                                    74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354     | 
            FENR1_PEA    65 HSKKQDENIVVNKFKPKEPYVGRCLLNTKITGDDAPGETWHMVFSTEGEVPYREGQSIGIVPDGIDKNGKPHKLRLYSIASSAIGDFGDSKTVSLCVKRLVYTNDAGEVVKGVCSNFLCDLKPGSEVKITGPVGKEMLMPKDPNATVIMLGTGTGIAPFRSFLWKMFFEKHEDYQFNGLAWLFLGVPTSSSLLYKEEFEKMKEKAPENFRLDFAVSREQVNDKGEKMYIQTRMAQYAEELWELLKKDNTFVYMCGLKGMEKGIDDIMVSLAAKDGIDWIEYKRTLKKAEQWNVEVY-   -
               SCOP domains d2xncb1 B:13-139 automated matches                                                                                                      d2xncb2 B:140-300 automated matches                                                                                                                               SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------------------------------------------------FAD_binding_6-2xncB01 B:61-141                     ---------                              ----------NAD_binding_1-2xncB03 B:152-268                                                                                      -------------------------------- Pfam domains (1)
           Pfam domains (2) ------------------------------------------------FAD_binding_6-2xncB02 B:61-141                     ---------                              ----------NAD_binding_1-2xncB04 B:152-268                                                                                      -------------------------------- Pfam domains (2)
         Sec.struct. author ...................eeeeeeeeee.........eeeeeee...........eeeee.............eeee.............eeeeeee.---------....hhhhhhhhh....eeeeeeee............eeeeeee...hhhhhhhhhhhhh..........eeeeeeee.hhhhh.hhhhhhhhhhhh...eeeeeee............hhhhhhhhhhhhhhhhhh...eeeeeeee.hhhhhhhhhhhhhhhh...hhhhhhhhhhhh..eeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------FAD_FR  PDB: B:29-142 UniProt: 81-203                                                                                      -------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xnc B  13 HSKKQDENIVVNKFKPKEPYVGRCLLNTKITGDDAPGETWHMVFSTEGEVPYREGQSIGIVPDGIDKNGKPHKLRLYSIASSAIGDFGDSKTVSLCVKR---------VPDGVCSNFLCDLKPGSEVKITGPVGKEMLMPKDPNATVIMLGTGTGIAPFRSFLWKMFFEKHEDYQFNGLAWLFLGVPTSSSLLYKEEFEKMKEKAPENFRLDFAVSREQVNDKGEKMYIQTRMAQYAEELWELLKKDNTFVYMCGLKGMEKGIDDIMVSLAAKDGIDWIEYKRTLKKAEQWNVEVYW 300
                                    22        32        42        52        62        72        82        92       102        |-       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       
                                                                                                                            111       112

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 "CATH Domain" information available for 2XNC)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: FAD_Lum_binding (30)

Family: FAD_binding_6 (24)

Pisum sativum (Garden pea) (6)

1a	FAD_binding_6-2xncB01	B:61-141
1b	FAD_binding_6-2xncB02	B:61-141

Clan: NAD_Ferredoxin (30)

Family: NAD_binding_1 (30)

Pisum sativum (Garden pea) (6)

2a	NAD_binding_1-2xncB03	B:152-268
2b	NAD_binding_1-2xncB04	B:152-268

Asymmetric Unit(hide GO term definitions)

Chain A,B (FENR1_PEA | P10933)

molecular function
	GO:0004324	ferredoxin-NADP+ reductase activity	Catalysis of the reaction: reduced ferredoxin + NADP+ = oxidized ferredoxin + NADPH + H+.
	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).
biological process
	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:0015979	photosynthesis	The synthesis by organisms of organic chemical compounds, especially carbohydrates, from carbon dioxide (CO2) using energy obtained from light rather than from the oxidation of chemical compounds.
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: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:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	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 Unit
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	Cis Peptide Bonds
		Gly A:134 - Pro A:135	[ RasMol ]
		Gly B:134 - Pro B:135	[ RasMol ]

Biological Units
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	2xnc
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	1.18.1.2
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	FENR1_PEA \| P10933	:	1qfy 1qfz 1qg0 1qga 3mhp 4af6 4af7

1qfy	PEA FNR Y308S MUTANT IN COMPLEX WITH NADP+
1qfz	PEA FNR Y308S MUTANT IN COMPLEX WITH NADPH
1qg0	WILD-TYPE PEA FNR
1qga	PEA FNR Y308W MUTANT IN COMPLEX WITH NADP+

Description

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Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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