2PUK - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE BINARY COMPLEX BETWEEN FERREDOXIN: THIOREDOXIN REDUCTASE AND THIOREDOXIN M

Authors :   S. Dai, R. Friemann, P. Schurmann, H. Eklund

Date :   09 May 07 (Deposition) - 10 Jul 07 (Release) - 18 Sep 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.00

Chains :   Asym. Unit : A,B,C,E,F,G
Biol. Unit 1: A,B,C  (1x)
Biol. Unit 2: E,F,G  (1x)

Keywords :   Thioredoxin, Protein-Protein Complex, Redox, Iron-Sulfur, Electron Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Dai, R. Friemann, D. A. Glauser, F. Bourquin, W. Manieri, P. Schurmann, H. Eklund
Structural Snapshots Along The Reaction Pathway Of Ferredoxin-Thioredoxin Reductase.
Nature V. 448 92 2007
PubMed-ID: 17611542 | Reference-DOI: 10.1038/NATURE05937

Molecule 1 - FERREDOXIN-THIOREDOXIN REDUCTASE, CATALYTIC CHAIN
	Chains	:	A, E
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Plasmid	:	PET-3C
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Gene	:	FTRC
	Organism Scientific	:	SYNECHOCYSTIS SP.
	Organism Taxid	:	1143

Molecule 2 - FERREDOXIN-THIOREDOXIN REDUCTASE, VARIABLE CHAIN
	Chains	:	B, F
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Plasmid	:	PET-3C
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Gene	:	FTRV
	Mutation	:	YES
	Organism Scientific	:	SYNECHOCYSTIS SP.
	Organism Taxid	:	1143
	Synonym	:	FTR-V, FERREDOXIN- THIOREDOXIN REDUCTASE SUBUNIT A

Molecule 3 - THIOREDOXIN M-TYPE, CHLOROPLAST (TRX-M)
	Chains	:	C, G
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Plasmid	:	PET-3C
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Organism Common	:	SPINACH
	Organism Scientific	:	SPINACIA OLERACEA
	Organism Taxid	:	3562

		1	2	3	4	5	6
Asymmetric Unit	:	A	B	C	E	F	G
Biological Unit 1 (1x)	:	A	B	C
Biological Unit 2 (1x)	:				E	F	G

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	SF4	2	Ligand/Ion	IRON/SULFUR CLUSTER

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	SF4	1	Ligand/Ion	IRON/SULFUR CLUSTER

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	SF4	1	Ligand/Ion	IRON/SULFUR CLUSTER

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:55 , CYS A:74 , CYS A:76 , MET A:79 , CYS A:85 , HIS A:86 , CYS A:87 , PHE A:90	BINDING SITE FOR RESIDUE SF4 A 1000
2	AC2	SOFTWARE	CYS E:55 , CYS E:74 , CYS E:76 , MET E:79 , CYS E:85 , HIS E:86 , CYS E:87	BINDING SITE FOR RESIDUE SF4 E 1000

Asymmetric Unit

No.	Residues
1	A:57	-	C:37
2	E:57	-	G:37

Asymmetric Unit

No.	Residues
1	Cys A:74	-	Pro A:75
2	Ile C:80	-	Pro C:81
3	Cys E:74	-	Pro E:75
4	Ile G:80	-	Pro G:81

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

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THIOREDOXIN_1	PS00194	Thioredoxin family active site.	TRXM_SPIOL	96-114	2	C:29-47 G:29-47

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THIOREDOXIN_1	PS00194	Thioredoxin family active site.	TRXM_SPIOL	96-114	1	C:29-47 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THIOREDOXIN_1	PS00194	Thioredoxin family active site.	TRXM_SPIOL	96-114	1	- G:29-47

(no "Exon" information available for 2PUK)

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:108
 aligned with FTRC_SYNY3 | Q55389 from UniProtKB/Swiss-Prot  Length:118

    Alignment length:108
                                    18        28        38        48        58        68        78        88        98       108        
           FTRC_SYNY3     9 NKTLAAMKNFAEQYAKRTDTYFCSDLSVTAVVIEGLARHKEELGSPLCPCRHYEDKEAEVKNTFWNCPCVPMRERKECHCMLFLTPDNDFAGDAQDIPMETLEEVKAS 116
               SCOP domains d2puka_ A: Ferredoxin thioredoxin reductase (FTR), catalytic beta chain                                      SCOP domains
               CATH domains 2pukA00 A:8-115 Ferredoxin Thioredoxin Reductase                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh..........hhhhhhhhh.....hhhhhhh......................hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 2puk A   8 NKTLAAMKNFAEQYAKRTDTYFCSDLSVTAVVIEGLARHKEELGSPLCPCRHYEDKEAEVKNTFWNCPCVPMRERKECHCMLFLTPDNDFAGDAQDIPMETLEEVKAS 115
                                    17        27        37        47        57        67        77        87        97       107

Chain B from PDB  Type:PROTEIN  Length:73
 aligned with FTRV_SYNY3 | Q55781 from UniProtKB/Swiss-Prot  Length:75

    Alignment length:73
                                    10        20        30        40        50        60        70   
           FTRV_SYNY3     1 MNVGDRVRVTSSVVVYHHPEHKKTAFDLQGMEGEVAAVLTEWQGRPISANLPVLVKFEQRFKAHFRPDEVTLI  73
               SCOP domains d2pukb_ B: Ferredoxin thioredoxin reductase (FTR), alpha (variable) chain SCOP domains
               CATH domains 2pukB00 B:1-73  [code=2.30.30.50, no name defined]                        CATH domains
               Pfam domains ------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee....ee..hhhhh...ee....eeeeeee..ee..ee......eeee.hhh.eeeehhh.eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------- Transcript
                 2puk B   1 MNVGDRVRVTSSVVVYHHPEHKKTAFDLQGMEGEVAAVLTEWQGRPISANLPVLVKFEQRFKAHFRPDEVTLI  73
                                    10        20        30        40        50        60        70

Chain C from PDB  Type:PROTEIN  Length:106
 aligned with TRXM_SPIOL | P07591 from UniProtKB/Swiss-Prot  Length:181

    Alignment length:106
                                    84        94       104       114       124       134       144       154       164       174      
           TRXM_SPIOL    75 EVQDVNDSSWKEFVLESEVPVMVDFWAPWCGPCKLIAPVIDELAKEYSGKIAVYKLNTDEAPGIATQYNIRSIPTVLFFKNGERKESIIGAVPKSTLTDSIEKYLS 180
               SCOP domains d2pukc_ C: automated matches                                                                               SCOP domains
               CATH domains 2pukC00 C:8-113 Glutaredoxin                                                                               CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee....hhhhhh......eeeeee...hhhhhhhhhhhhhhhhhh....eeeeee...hhhhhhhh......eeeeee..eeeeeee...hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------THIOREDOXIN_1      ------------------------------------------------------------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 2puk C   8 EVQDVNDSSWKEFVLESEVPVMVDFWAPWCGPSKLIAPVIDELAKEYSGKIAVYKLNTDEAPGIATQYNIRSIPTVLFFKNGERKESIIGAVPKSTLTDSIEKYLS 113
                                    17        27        37        47        57        67        77        87        97       107

Chain E from PDB  Type:PROTEIN  Length:109
 aligned with FTRC_SYNY3 | Q55389 from UniProtKB/Swiss-Prot  Length:118

    Alignment length:109
                                    17        27        37        47        57        67        77        87        97       107         
           FTRC_SYNY3     8 NNKTLAAMKNFAEQYAKRTDTYFCSDLSVTAVVIEGLARHKEELGSPLCPCRHYEDKEAEVKNTFWNCPCVPMRERKECHCMLFLTPDNDFAGDAQDIPMETLEEVKAS 116
               SCOP domains d2puke_ E: Ferredoxin thioredoxin reductase (FTR), catalytic beta chain                                       SCOP domains
               CATH domains 2pukE00 E:7-115 Ferredoxin Thioredoxin Reductase                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh..........hhhhhhhhh.....hhhhhhhh.....................hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------- Transcript
                 2puk E   7 NNKTLAAMKNFAEQYAKRTDTYFCSDLSVTAVVIEGLARHKEELGSPLCPCRHYEDKEAEVKNTFWNCPCVPMRERKECHCMLFLTPDNDFAGDAQDIPMETLEEVKAS 115
                                    16        26        36        46        56        66        76        86        96       106

Chain F from PDB  Type:PROTEIN  Length:73
 aligned with FTRV_SYNY3 | Q55781 from UniProtKB/Swiss-Prot  Length:75

    Alignment length:73
                                    10        20        30        40        50        60        70   
           FTRV_SYNY3     1 MNVGDRVRVTSSVVVYHHPEHKKTAFDLQGMEGEVAAVLTEWQGRPISANLPVLVKFEQRFKAHFRPDEVTLI  73
               SCOP domains d2pukf_ F: Ferredoxin thioredoxin reductase (FTR), alpha (variable) chain SCOP domains
               CATH domains 2pukF00 F:1-73  [code=2.30.30.50, no name defined]                        CATH domains
           Pfam domains (1) --FeThRed_A-2pukF01 F:3-69                                           ---- Pfam domains (1)
           Pfam domains (2) --FeThRed_A-2pukF02 F:3-69                                           ---- Pfam domains (2)
         Sec.struct. author .....eeee....ee..........ee....eeeeeee..ee..ee......eeeee...eeeeehhh.ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------- Transcript
                 2puk F   1 MNVGDRVRVTSSVVVYHHPEHKKTAFDLQGMEGEVAAVLTEWQGRPISANLPVLVKFEQRFKAHFRPDEVTLI  73
                                    10        20        30        40        50        60        70

Chain G from PDB  Type:PROTEIN  Length:105
 aligned with TRXM_SPIOL | P07591 from UniProtKB/Swiss-Prot  Length:181

    Alignment length:105
                                    84        94       104       114       124       134       144       154       164       174     
           TRXM_SPIOL    75 EVQDVNDSSWKEFVLESEVPVMVDFWAPWCGPCKLIAPVIDELAKEYSGKIAVYKLNTDEAPGIATQYNIRSIPTVLFFKNGERKESIIGAVPKSTLTDSIEKYL 179
               SCOP domains d2pukg_ G: automated matches                                                                              SCOP domains
               CATH domains 2pukG00 G:8-112 Glutaredoxin                                                                              CATH domains
           Pfam domains (1) Thioredoxin-2pukG01 G:8-111                                                                             - Pfam domains (1)
           Pfam domains (2) Thioredoxin-2pukG02 G:8-111                                                                             - Pfam domains (2)
         Sec.struct. author ..ee....hhhhhh......eeeeee....hhhhhhhhhhhhhhhhh....eeeeee...hhhhhhhh......eeeeee..eeeeeee...hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------THIOREDOXIN_1      ----------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------- Transcript
                 2puk G   8 EVQDVNDSSWKEFVLESEVPVMVDFWAPWCGPSKLIAPVIDELAKEYSGKIAVYKLNTDEAPGIATQYNIRSIPTVLFFKNGERKESIIGAVPKSTLTDSIEKYL 112
                                    17        27        37        47        57        67        77        87        97       107

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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	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(hide GO term definitions)

Chain A,E (FTRC_SYNY3 | Q55389)

molecular function
	GO:0051539	4 iron, 4 sulfur cluster binding	Interacting selectively and non-covalently with a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.
	GO:0009055	electron carrier activity	Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
	GO:0030385	ferredoxin:thioredoxin reductase activity	Catalysis of the two-electron reduction of the disulfide of thioredoxins with electrons from ferredoxin involving a 4Fe-4S cluster and an adjacent active-site disulfide.
	GO:0051536	iron-sulfur cluster binding	Interacting selectively and non-covalently with an iron-sulfur cluster, a combination of iron and sulfur atoms.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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:0016730	oxidoreductase activity, acting on iron-sulfur proteins as donors	Catalysis of an oxidation-reduction (redox) reaction in which an iron-sulfur protein acts as a hydrogen or electron donor and reduces a hydrogen or electron acceptor.
	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.

Chain B,F (FTRV_SYNY3 | Q55781)

molecular function
	GO:0051539	4 iron, 4 sulfur cluster binding	Interacting selectively and non-covalently with a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.
	GO:0016992	lipoate synthase activity	Catalysis of the reaction: protein N6-(octanoyl)lysine + 2 sulfur + 2 S-adenosyl-L-methionine = protein N6-(lipoyl)lysine + 2 L-methionine + 2 5'-deoxyadenosyl.
	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:0009107	lipoate biosynthetic process	The chemical reactions and pathways resulting in the formation of lipoate, 1,2-dithiolane-3-pentanoate, the anion derived from lipoic acid.
	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.

Chain C,G (TRXM_SPIOL | P07591)

molecular function
	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:0015035	protein disulfide oxidoreductase activity	Catalysis of the reaction: a protein with reduced sulfide groups = a protein with oxidized disulfide bonds.
biological process
	GO:0045454	cell redox homeostasis	Any process that maintains the redox environment of a cell or compartment within a cell.
	GO:0006662	glycerol ether metabolic process	The chemical reactions and pathways involving glycerol ethers, any anhydride formed between two organic hydroxy compounds, one of which is glycerol.
	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:0009507	chloroplast	A chlorophyll-containing plastid with thylakoids organized into grana and frets, or stroma thylakoids, and embedded in a stroma.
	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.

Asymmetric Unit
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	Cis Peptide Bonds
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		Ile C:80 - Pro C:81	[ RasMol ]
		Ile G:80 - Pro G:81	[ RasMol ]

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	2puk
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	FTRV_SYNY3 \| Q55781
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UniProtKB/Swiss-Prot
	FTRC_SYNY3 \| Q55389	:	1dj7 2pu9 2puo 2pvd 2pvg 2pvo
	FTRV_SYNY3 \| Q55781	:	1dj7 2pu9 2puo 2pvd 2pvg 2pvo
	TRXM_SPIOL \| P07591	:	1fb0 1fb6 1gl8

2pu9	THE SAME FERREDOXIN:THIOREDOXIN REDUCTASE COMPLEXED WITH THIOREDOXIN M

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (2, 2)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

Sequences/Alignments

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SCOP Domains (3, 6)

CATH Domains (3, 6)

Pfam Domains (2, 4)

Gene Ontology (17, 24)

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Related Entries Specified in the PDB File