3ZC3 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   FERREDOXIN-NADP REDUCTASE (MUTATION S80A) COMPLEXED WITH NADP BY COCRYSTALLIZATION

Authors :   M. Martinez-Julvez, R. Hurtado-Guerrero, B. Herguedas, A. Sanchez-A M. Hervas, J. A. Navarro, M. Medina

Date :   15 Nov 12 (Deposition) - 20 Nov 13 (Release) - 08 Jan 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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

Keywords :   Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Sanchez-Azqueta, B. Herguedas, R. Hurtado-Guerrero, M. Hervas, J. A. Navarro, M. Martinez-Julvez, M. Medina
A Hydrogen Bond Network In The Active Site Of Anabaena Ferredoxin-Nadp(+) Reductase Modulates Its Catalytic Efficiency.
Biochim. Biophys. Acta V. 1837 251 2013
PubMed-ID: 24200908 | Reference-DOI: 10.1016/J.BBABIO.2013.10.010

Molecule 1 - FERREDOXIN-NADP REDUCTASE
	Chains	:	A, B
	EC Number	:	1.18.1.2
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector	:	PET28A
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organism Scientific	:	NOSTOC SP. PCC7119
	Organism Taxid	:	1168
	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	GOL	1	Ligand/Ion	GLYCEROL
3	NAP	2	Ligand/Ion	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE

Biological Unit 1 (3, 3)

No.	Name	Count	Type	Full Name
1	FAD	1	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
2	GOL	1	Ligand/Ion	GLYCEROL
3	NAP	1	Ligand/Ion	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	FAD	1	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
2	GOL	-1	Ligand/Ion	GLYCEROL
3	NAP	1	Ligand/Ion	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:77 , LEU A:78 , TYR A:79 , ALA A:80 , CYS A:98 , VAL A:99 , ARG A:100 , LEU A:102 , TYR A:104 , PRO A:107 , GLY A:115 , VAL A:116 , CYS A:117 , SER A:118 , THR A:157 , TYR A:303 , HOH A:2040 , HOH A:2041 , HOH A:2049 , HOH A:2056 , HOH A:2080 , HOH A:2111 , PRO B:107 , FAD B:304	BINDING SITE FOR RESIDUE FAD A 304
2	AC2	SOFTWARE	LYS A:105 , PRO A:107 , FAD A:304 , ARG B:77 , LEU B:78 , TYR B:79 , ALA B:80 , CYS B:98 , VAL B:99 , ARG B:100 , LEU B:102 , TYR B:104 , GLY B:115 , VAL B:116 , CYS B:117 , SER B:118 , THR B:157 , TYR B:303 , HOH B:2013 , HOH B:2014 , HOH B:2016 , HOH B:2028 , HOH B:2056	BINDING SITE FOR RESIDUE FAD B 304
3	AC3	SOFTWARE	ARG A:100 , LEU A:102 , THR A:155 , GLY A:156 , THR A:157 , GLY A:192 , VAL A:193 , PRO A:194 , SER A:223 , ARG A:224 , ARG A:233 , TYR A:235 , GLN A:237 , GLY A:262 , LEU A:263 , TYR A:303 , HOH A:2051 , HOH A:2053 , HOH A:2081 , HOH A:2099 , HOH A:2112 , HOH A:2113 , HOH A:2114 , LYS B:105 , GLY B:110 , GLU B:111 , THR B:112	BINDING SITE FOR RESIDUE NAP A1304
4	AC4	SOFTWARE	LYS A:105 , GLU A:111 , THR A:112 , HOH A:2058 , ARG B:100 , LEU B:102 , THR B:155 , GLY B:156 , THR B:157 , GLY B:192 , VAL B:193 , PRO B:194 , SER B:223 , ARG B:224 , ARG B:233 , TYR B:235 , GLN B:237 , GLY B:262 , TYR B:303 , HOH B:2018 , HOH B:2030 , HOH B:2045	BINDING SITE FOR RESIDUE NAP B1304
5	AC5	SOFTWARE	LEU A:47 , GLY A:50 , ASN A:51 , LEU A:52 , LYS A:53 , ASP A:92	BINDING SITE FOR RESIDUE GOL A1305

(no "SS Bond" information available for 3ZC3)

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 3ZC3)

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.	FENR_NOSSO	155-279	2	A:18-142 B:18-142

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.	FENR_NOSSO	155-279	1	A:18-142 -

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.	FENR_NOSSO	155-279	1	- B:18-142

(no "Exon" information available for 3ZC3)

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:295
 aligned with FENR_NOSSO | P21890 from UniProtKB/Swiss-Prot  Length:440

    Alignment length:295
                                   155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435     
           FENR_NOSSO   146 DVPVNLYRPNAPFIGKVISNEPLVKEGGIGIVQHIKFDLTGGNLKYIEGQSIGIIPPGVDKNGKPEKLRLYSIASTRHGDDVDDKTISLCVRQLEYKHPESGETVYGVCSTYLTHIEPGSEVKITGPVGKEMLLPDDPEANVIMLATGTGIAPMRTYLWRMFKDAERAANPEYQFKGFSWLVFGVPTTPNILYKEELEEIQQKYPDNFRLTYAISREQKNPQGGRMYIQDRVAEHADELWQLIKNQKTHTYICGLRGMEEGIDAALSAAAAKEGVTWSDYQKDLKKAGRWHVETY 440
               SCOP domains d3zc3a1 A:9-141 automated matches                                                                                                    d3zc3a2 A:142-303 automated matches                                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeeeeeeee.........eeeeeee............eeeee.............eeee.............eeeeeee..eee......eeehhhhhhhhh.....eeeeeeee............eeeeeee..hhhhhhhhhhhhhhhhhhhhh........eeeeeee.hhhhh.hhhhhhhhhhhh...eeeeeee............hhhhhhhhhhhhhhhhhh...eeeeeee.hhhhhhhhhhhhhhhhh...hhhhhhhhhhhh..eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------FAD_FR  PDB: A:18-142 UniProt: 155-279                                                                                       ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zc3 A   9 DVPVNLYRPNAPFIGKVISNEPLVKEGGIGIVQHIKFDLTGGNLKYIEGQSIGIIPPGVDKNGKPEKLRLYAIASTRHGDDVDDKTISLCVRQLEYKHPESGETVYGVCSTYLTHIEPGSEVKITGPVGKEMLLPDDPEANVIMLATGTGIAPMRTYLWRMFKDAERAANPEYQFKGFSWLVFGVPTTPNILYKEELEEIQQKYPDNFRLTYAISREQKNPQGGRMYIQDRVAEHADELWQLIKNEKTHTYICGLRGMEEGIDAALSAAAAKEGVTWSDYQKDLKKAGRWHVETY 303
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298

Chain B from PDB  Type:PROTEIN  Length:295
 aligned with FENR_NOSSO | P21890 from UniProtKB/Swiss-Prot  Length:440

    Alignment length:295
                                   155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435     
           FENR_NOSSO   146 DVPVNLYRPNAPFIGKVISNEPLVKEGGIGIVQHIKFDLTGGNLKYIEGQSIGIIPPGVDKNGKPEKLRLYSIASTRHGDDVDDKTISLCVRQLEYKHPESGETVYGVCSTYLTHIEPGSEVKITGPVGKEMLLPDDPEANVIMLATGTGIAPMRTYLWRMFKDAERAANPEYQFKGFSWLVFGVPTTPNILYKEELEEIQQKYPDNFRLTYAISREQKNPQGGRMYIQDRVAEHADELWQLIKNQKTHTYICGLRGMEEGIDAALSAAAAKEGVTWSDYQKDLKKAGRWHVETY 440
               SCOP domains d3zc3b1 B:9-141 automated matches                                                                                                    d3zc3b2 B:142-303 automated matches                                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeeeeeeee.........eeeeeee............eeeee.............eeee.............eeeeeee..eee......eeehhhhhhhhh.....eeeeeeee............eeeeeee..hhhhhhhhhhhhhhhhhhhhh........eeeeeee.hhhhh.hhhhhhhhhhhh...eeeeeee............hhhhhhhhhhhhhhhhhhh..eeeeeeehhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh..eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------FAD_FR  PDB: B:18-142 UniProt: 155-279                                                                                       ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zc3 B   9 DVPVNLYRPNAPFIGKVISNEPLVKEGGIGIVQHIKFDLTGGNLKYIEGQSIGIIPPGVDKNGKPEKLRLYAIASTRHGDDVDDKTISLCVRQLEYKHPESGETVYGVCSTYLTHIEPGSEVKITGPVGKEMLLPDDPEANVIMLATGTGIAPMRTYLWRMFKDAERAANPEYQFKGFSWLVFGVPTTPNILYKEELEEIQQKYPDNFRLTYAISREQKNPQGGRMYIQDRVAEHADELWQLIKNEKTHTYICGLRGMEEGIDAALSAAAAKEGVTWSDYQKDLKKAGRWHVETY 303
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298

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 3ZC3)

(no "Pfam Domain" information available for 3ZC3)

Asymmetric Unit(hide GO term definitions)

Chain A,B (FENR_NOSSO | P21890)

molecular function
	GO:0050661	NADP binding	Interacting selectively and non-covalently with nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NADP+, or the reduced form, NADPH.
	GO:0004324	ferredoxin-NADP+ reductase activity	Catalysis of the reaction: reduced ferredoxin + NADP+ = oxidized ferredoxin + NADPH + H+.
	GO:0050660	flavin adenine dinucleotide binding	Interacting selectively and non-covalently with FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.
	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.
cellular component
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0030089	phycobilisome	Any of the granules, approximately 32 nm x 48 nm and consisting of highly aggregated phycobiliproteins, that are attached in arrays to the external face of a thylakoid membrane in algae of the phyla Cyanophyta and Rhodophyta, where they function as light-harvesting devices in photosynthesis. Excitation energy in the phycobilisome flows in the sequence: phycoerythrin, phycocyanin, allophycocyanin before passing to the antenna chlorophyll of photosystem II.
	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.
	GO:0042651	thylakoid membrane	The pigmented membrane of any thylakoid.

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
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

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	3zc3
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	1.18.1.2
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3zbt	FERREDOXIN-NADP REDUCTASE MUTANT WITH SER 59 REPLACED BY ALA (S59A)
3zbu	FERREDOXIN-NADP REDUCTASE MUTANT WITH SER 80 REPLACED BY ALA (S80A)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 5)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (2, 4)

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Gene Ontology (10, 10)

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