1QFZ - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   PEA FNR Y308S MUTANT IN COMPLEX WITH NADPH

Authors :   Z. Deng, A. Aliverti, G. Zanetti, A. K. Arakaki, J. Ottado, E. G. Orellano, N. B. Calcaterra, E. A. Ceccarelli, N. Carrillo, P. A. Karplus

Date :   18 Apr 99 (Deposition) - 27 Apr 99 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

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

Keywords :   Flavoenzyme, Photosynthesis, Electron Transfer, Hydride Transfer, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Z. Deng, A. Aliverti, G. Zanetti, A. K. Arakaki, J. Ottado, E. G. Orellano, N. B. Calcaterra, E. A. Ceccarelli, N. Carrillo, P. A. Karplus
A Productive Nadp+ Binding Mode Of Ferredoxin-Nadp+ Reductase Revealed By Protein Engineering And Crystallographic Studies.
Nat. Struct. Biol. V. 6 847 1999
PubMed-ID: 10467097 | Reference-DOI: 10.1038/12307
(for further references see the PDB file header)

Molecule 1
	Chains	:	A, B
	EC Number	:	1.18.1.2
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Mutation	:	YES
	Organ	:	LEAF
	Organism Common	:	PEA
	Organism Scientific	:	PISUM SATIVUM
	Organism Taxid	:	3888
	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 (3, 5)

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

Biological Unit 1 (3, 3)

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

Biological Unit 2 (2, 2)

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

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:35 , SER A:137 , GLU A:138 , HOH A:1247 , HOH A:1258 , ARG B:535	BINDING SITE FOR RESIDUE SO4 A 311
2	AC2	SOFTWARE	ARG A:87 , LEU A:88 , TYR A:89 , SER A:90 , CYS A:108 , LYS A:110 , LEU A:112 , TYR A:114 , GLY A:124 , VAL A:125 , CYS A:126 , SER A:127 , THR A:166 , SER A:308 , NDP A:310 , HOH A:1003 , HOH A:1012 , HOH A:1028 , HOH A:1127 , HOH A:1209 , HOH A:1221 , HOH A:1280 , HOH A:1289 , HOH A:1528	BINDING SITE FOR RESIDUE FAD A 309
3	AC3	SOFTWARE	SER A:90 , LYS A:110 , GLY A:165 , THR A:166 , GLY A:167 , GLY A:197 , VAL A:198 , PRO A:199 , SER A:228 , ARG A:229 , LYS A:238 , TYR A:240 , GLN A:242 , CYS A:266 , GLY A:267 , LEU A:268 , GLY A:270 , MET A:271 , GLU A:306 , VAL A:307 , SER A:308 , FAD A:309 , HOH A:1004 , HOH A:1007 , HOH A:1029 , HOH A:1042 , HOH A:1125 , HOH A:1130 , HOH A:1148 , HOH A:1186 , HOH A:1208 , HOH A:1219 , HOH A:1299 , HOH A:1371 , HOH A:1723	BINDING SITE FOR RESIDUE NDP A 310
4	AC4	SOFTWARE	ARG B:587 , LEU B:588 , TYR B:589 , SER B:590 , CYS B:608 , LYS B:610 , LEU B:612 , TYR B:614 , GLY B:624 , VAL B:625 , CYS B:626 , SER B:627 , THR B:666 , SER B:808 , NDP B:810 , HOH B:1001 , HOH B:1009 , HOH B:1122 , HOH B:1239 , HOH B:1287 , HOH B:1377 , HOH B:1415	BINDING SITE FOR RESIDUE FAD B 809
5	AC5	SOFTWARE	SER B:590 , LYS B:610 , THR B:664 , GLY B:665 , THR B:666 , GLY B:667 , GLY B:697 , VAL B:698 , PRO B:699 , SER B:728 , ARG B:729 , LYS B:738 , TYR B:740 , ILE B:741 , GLN B:742 , CYS B:766 , GLY B:767 , LEU B:768 , GLY B:770 , MET B:771 , GLU B:806 , SER B:808 , FAD B:809 , HOH B:1024 , HOH B:1173 , HOH B:1272 , HOH B:1275 , HOH B:1343 , HOH B:1346 , HOH B:1367 , HOH B:1726	BINDING SITE FOR RESIDUE NDP B 810

(no "SS Bond" information available for 1QFZ)

Asymmetric Unit

No.	Residues
1	Gly A:143	-	Pro A:144
2	Gly B:643	-	Pro B:644

(no "SAP(SNP)/Variant" information available for 1QFZ)

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:29-151 B:529-651

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:29-151 -

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:529-651

(no "Exon" information available for 1QFZ)

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:308
 aligned with FENR1_PEA | P10933 from UniProtKB/Swiss-Prot  Length:360

    Alignment length:308
                                    62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352        
            FENR1_PEA    53 QVTTEAPAKVVKHSKKQDENIVVNKFKPKEPYVGRCLLNTKITGDDAPGETWHMVFSTEGEVPYREGQSIGIVPDGIDKNGKPHKLRLYSIASSAIGDFGDSKTVSLCVKRLVYTNDAGEVVKGVCSNFLCDLKPGSEVKITGPVGKEMLMPKDPNATVIMLGTGTGIAPFRSFLWKMFFEKHEDYQFNGLAWLFLGVPTSSSLLYKEEFEKMKEKAPENFRLDFAVSREQVNDKGEKMYIQTRMAQYAEELWELLKKDNTFVYMCGLKGMEKGIDDIMVSLAAKDGIDWIEYKRTLKKAEQWNVEVY 360
               SCOP domains d1qfza1 A:1-153 Ferredoxin reductase (flavodoxin reductase) N-terminal domain                                                                            d1qfza2 A:154-308 Ferredoxin reductase (flavodoxin reductase)                                                                                               SCOP domains
               CATH domains ------------1qfzA01 A:13-145 Translation factors                                                                                                 1qfzA02 A:146-308 Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module                                                                               CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............................eeeeeeeeee.........eeeeeee...........eeeee.............eeee.............eeeeeee..eee.....eeehhhhhhhhhh....eeeeeeee............eeeeeee...hhhhhhhhhhhhh..........eeeeeeee.hhhhh.hhhhhhhhhhhh...eeeeeee............hhhhhhh.hhhhhhhhhhh..eeeeeeee.hhhhhhhhhhhhhhhhh..hhhhhhhhhhhh..eeeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------FAD_FR  PDB: A:29-151 UniProt: 81-203                                                                                      ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qfz A   1 QVTTEAPAKVVKHSKKQDENIVVNKFKPKEPYVGRCLLNTKITGDDAPGETWHMVFSTEGEVPYREGQSIGIVPDGIDKNGKPHKLRLYSIASSAIGDFGDSKTVSLCVKRLVYTNDAGEVVKGVCSNFLCDLKPGSEVKITGPVGKEMLMPKDPNATVIMLGTGTGIAPFRSFLWKMFFEKHEDYQFNGLAWLFLGVPTSSSLLYKEEFEKMKEKAPENFRLDFAVSREQVNDKGEKMYIQTRMAQYAEELWELLKKDNTFVYMCGLKGMEKGIDDIMVSLAAKDGIDWIEYKRTLKKAEQWNVEVS 308
                                    10        20        30        40        50        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

Chain B from PDB  Type:PROTEIN  Length:295
 aligned with FENR1_PEA | P10933 from UniProtKB/Swiss-Prot  Length:360

    Alignment length:295
                                    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 360
               SCOP domains d1qfzb1 B:514-653 Ferredoxin reductase (flavodoxin reductase) N-terminal domain                                                             d1qfzb2 B:654-808 Ferredoxin reductase (flavodoxin reductase)                                                                                               SCOP domains
               CATH domains 1qfzB01 B:514-645 Translation factors                                                                                               1qfzB02 B:646-808 Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module                                                                               CATH domains
           Pfam domains (1) -----------------------------------------------FAD_binding_6-1qfzB01 B:561-650                                                           ----------NAD_binding_1-1qfzB03 B:661-777                                                                                      ------------------------------- Pfam domains (1)
           Pfam domains (2) -----------------------------------------------FAD_binding_6-1qfzB02 B:561-650                                                           ----------NAD_binding_1-1qfzB04 B:661-777                                                                                      ------------------------------- Pfam domains (2)
         Sec.struct. author ..................eeeeeeeeee.........eeeeeee...........eeeee.............eeee.............eeeeeee..eee.....eeehhhhhhhhh.....eeeeeeee............eeeeeee...hhhhhhhhhhhhh..........eeeeeeee.hhhhh.hhhhhhhhhhhh...eeeeeee............hhhhhhhhhhhhhhhhhhh..eeeeeeee.hhhhhhhhhhhhhhhhh..hhhhhhhhhhhh..eeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------FAD_FR  PDB: B:529-651 UniProt: 81-203                                                                                     ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qfz B 514 SKKQDENIVVNKFKPKEPYVGRCLLNTKITGDDAPGETWHMVFSTEGEVPYREGQSIGIVPDGIDKNGKPHKLRLYSIASSAIGDFGDSKTVSLCVKRLVYTNDAGEVVKGVCSNFLCDLKPGSEVKITGPVGKEMLMPKDPNATVIMLGTGTGIAPFRSFLWKMFFEKHEDYQFNGLAWLFLGVPTSSSLLYKEEFEKMKEKAPENFRLDFAVSREQVNDKGEKMYIQTRMAQYAEELWELLKKDNTFVYMCGLKGMEKGIDDIMVSLAAKDGIDWIEYKRTLKKAEQWNVEVS 808
                                   523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723       733       743       753       763       773       783       793       803

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 '\|'

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module (85)

Pea (Pisum sativum) (4)

1a	1qfzA02	A:146-308
1b	1qfzB02	B:646-808

Class: Mainly Beta (13760)

Architecture: Beta Barrel (4804)

Topology: Elongation Factor Tu (Ef-tu); domain 3 (323)

Homologous Superfamily: Translation factors (223)

Pea (Pisum sativum) (4)

2a	1qfzB01	B:514-645
2b	1qfzA01	A:13-145

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: FAD_Lum_binding (30)

Family: FAD_binding_6 (24)

Pisum sativum (Garden pea) (6)

1a	FAD_binding_6-1qfzB01	B:561-650
1b	FAD_binding_6-1qfzB02	B:561-650

Clan: NAD_Ferredoxin (30)

Family: NAD_binding_1 (30)

Pisum sativum (Garden pea) (6)

2a	NAD_binding_1-1qfzB03	B:661-777
2b	NAD_binding_1-1qfzB04	B:661-777

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.

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

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