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Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE FERREDOXIN-FERREDOXIN REDUCTASE (BPHA3-BPHA4)COMPLEX

Authors :   T. Senda, M. Senda

Date :   12 Apr 07 (Deposition) - 23 Oct 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

Keywords :   Electron Transfer, Ferredoxin, Ferredoxin Reductase, Oxidoreductase/Electron Transport Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Senda, S. Kishigami, S. Kimura, M. Fukuda, T. Ishida, T. Senda
Molecular Mechanism Of The Redox-Dependent Interaction Between Nadh-Dependent Ferredoxin Reductase And Rieske-Type [2Fe-2S] Ferredoxin
J. Mol. Biol. V. 373 382 2007
PubMed-ID: 17850818 | Reference-DOI: 10.1016/J.JMB.2007.08.002
(for further references see the PDB file header)

Molecule 1 - FERREDOXIN REDUCTASE
	Chains	:	A, P
	EC Number	:	1.18.1.2
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	BPHA4
	Organism Scientific	:	PSEUDOMONAS SP.
	Organism Taxid	:	306
	Strain	:	STRAIN KKS102
	Synonym	:	FERREDOXIN REDUCTASE BPHA4

Molecule 2 - BIPHENYL DIOXYGENASE FERREDOXIN SUBUNIT
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	BPHA3
	Organism Scientific	:	PSEUDOMONAS SP.
	Organism Taxid	:	306
	Strain	:	STRAIN KKS102

		1	2	3
Asymmetric/Biological Unit	:	A	B	P

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 5)

No.	Name	Count	Type	Full Name
1	FAD	2	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
2	FES	1	Ligand/Ion	FE2/S2 (INORGANIC) CLUSTER
3	NAI	2	Ligand/Ion	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS B:43 , HIS B:45 , GLY B:46 , CYS B:63 , LEU B:65 , HIS B:66 , PRO B:82	BINDING SITE FOR RESIDUE FES B 500
2	AC2	SOFTWARE	GLY A:14 , GLY A:16 , LEU A:17 , ALA A:18 , GLY A:39 , ASP A:40 , GLU A:41 , ARG A:48 , PRO A:49 , ALA A:82 , ALA A:108 , THR A:109 , GLY A:110 , ARG A:130 , GLY A:272 , ASP A:273 , THR A:290 , TRP A:291 , SER A:292 , ALA A:294 , TYR A:319 , TRP A:320	BINDING SITE FOR RESIDUE FAD A 501
3	AC3	SOFTWARE	GLY P:14 , GLY P:16 , LEU P:17 , ALA P:18 , VAL P:38 , ASP P:40 , GLU P:41 , ARG P:48 , PRO P:49 , LYS P:53 , THR P:81 , ALA P:82 , ALA P:108 , THR P:109 , GLY P:110 , ARG P:130 , GLU P:159 , GLY P:272 , ASP P:273 , GLU P:289 , THR P:290 , TRP P:291 , ALA P:294 , TYR P:319 , TRP P:320 , NAI P:504 , HOH P:508 , HOH P:522 , HOH P:526 , HOH P:527 , HOH P:535	BINDING SITE FOR RESIDUE FAD P 502
4	AC4	SOFTWARE	VAL A:151 , GLY A:152 , GLY A:153 , GLY A:154 , VAL A:155 , ILE A:156 , VAL A:174 , GLU A:175 , THR A:176 , SER A:182 , ARG A:183 , GLY A:234 , ILE A:235 , GLY A:236 , VAL A:237 , GLU A:289	BINDING SITE FOR RESIDUE NAI A 503
5	AC5	SOFTWARE	ARG P:114 , GLY P:154 , VAL P:155 , ILE P:156 , GLU P:175 , THR P:176 , GLN P:177 , ARG P:183 , GLY P:234 , ILE P:235 , GLY P:236 , GLU P:289 , FAD P:502 , HOH P:519 , HOH P:531	BINDING SITE FOR RESIDUE NAI P 504

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

Asymmetric/Biological Unit

No.	Residues
1	Ala A:8	-	Pro A:9
2	Pro B:80	-	Pro B:81
3	Ala P:8	-	Pro P:9
4	Ser P:209	-	Val P:210

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

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RIESKE	PS51296	Rieske [2Fe-2S] iron-sulfur domain profile.	BPHA3_PSES1	4-100	1	B:4-100

(no "Exon" information available for 2YVJ)

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:402
 aligned with Q52437_PSES1 | Q52437 from UniProtKB/TrEMBL  Length:408

    Alignment length:402
                                    14        24        34        44        54        64        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       364       374       384       394       404  
         Q52437_PSES1     5 ALKAPVVVLGAGLASVSFVAELRQAGYQGLITVVGDEAERPYDRPPLSKDFMAHGDAEKIRLDCKRAPEVEWLLGVTAQSFDPQAHTVALSDGRTLPYGTLVLATGAAPRALPTLQGATMPVHTLRTLEDARRIQAGLRPQSRLLIVGGGVIGLELAATARTAGVHVSLVETQPRLMSRAAPATLADFVARYHAAQGVDLRFERSVTGSVDGVVLLDDGTRIAADMVVVGIGVLANDALARAAGLACDDGIFVDAYGRTTCPDVYALGDVTRQRNPLSGRFERIETWSNAQNQGIAVARHLVDPTAPGYAELPWYWSDQGALRIQVAGLASGDEEIVRGEVSLDAPKFTLIELQKGRIVGATCVNNARDFAPLRRLLAVGAKPDRAALADPATDLRKLAAAV 406
               SCOP domains d2yvja1 A:5-115,A:237-308 NADH-dependent ferredoxin reductase, BphA4                                           d2yvja2 A:116-236 NADH-dependent ferredoxin reductase, BphA4                                                             d2yvja1 A:5-115,A:237-308 NADH-dependent ferredoxin reductase, BphA4    d2yvja3 A:309-406 NADH-dependent ferredoxin reductase, BphA4                                       SCOP domains
               CATH domains 2yvjA01 A:5-110,A:239-317  [code=3.50.50.60, no name defined]                                             ---2yvjA02 A:114-236  [code=3.50.50.60, no name defined]                                                                      --2yvjA01 A:5-110,A:239-317  [code=3.50.50.60, no name defined]                  2yvjA03 A:318-406  [code=3.30.390.30, no name defined]                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeee..hhhhhhhhhhhhh......eeeee........hhhhhhhhhhhh...............eeee...eeeee....eeee....eee..eeee...eee............ee.....hhhhhhhh.....eeeeee..hhhhhhhhhhhhhhheeeeee...........hhhhhhhhhhhhhh..eeee....eeeee..eeee....eee...eee...eee.hhhhhhh.......ee...........eee....eeee......eee..hhhhhhhhhhhhhhhhhh..........eeeee....eeeeee.....eeeeeee......eeeeeeee..eeeeeeee.hhhhhhhhhhhhhh....hhhhhhh...hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2yvj A   5 ALKAPVVVLGAGLASVSFVAELRQAGYQGLITVVGDEAERPYDRPPLSKDFMAHGDAEKIRLDCKRAPEVEWLLGVTAQSFDPQAHTVALSDGRTLPYGTLVLATGAAPRALPTLQGATMPVHTLRTLEDARRIQAGLRPQSRLLIVGGGVIGLELAATARTAGVHVSLVETQPRLMSRAAPATLADFVARYHAAQGVDLRFERSVTGSVDGVVLLDDGTRIAADMVVVGIGVLANDALARAAGLACDDGIFVDAYGRTTCPDVYALGDVTRQRNPLSGRFERIETWSNAQNQGIAVARHLVDPTAPGYAELPWYWSDQGALRIQVAGLASGDEEIVRGEVSLDAPKFTLIELQKGRIVGATCVNNARDFAPLRRLLAVGAKPDRAALADPATDLRKLAAAV 406
                                    14        24        34        44        54        64        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       364       374       384       394       404

Chain B from PDB  Type:PROTEIN  Length:106
 aligned with BPHA3_PSES1 | Q52440 from UniProtKB/Swiss-Prot  Length:109

    Alignment length:106
                                    11        21        31        41        51        61        71        81        91       101      
          BPHA3_PSES1     2 TFTKACSVDEVPPGEALQVSHDAQKVAIFNVDGEFFATQDQCTHGEWSLSEGGYLDGDVVECSLHMGKFCVRTGKVKSPPPCEPLKVYPIRIEGRDVLVDFSRAAL 107
               SCOP domains d2yvjb_ B: automated matches                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains Rieske-2yvjB01 B:2-96                                                                          ----------- Pfam domains
         Sec.struct. author ..eeeee........eeeeee..eeeeeeee..eeeeee..............eee..eee......eee.....eee........ee.eee...eeee....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --RIESKE  PDB: B:4-100 UniProt: 4-100                                                              ------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 2yvj B   2 TFTKACSVDEVPPGEALQVSHDAQKVAIFNVDGEFFATQDQCTHGEWSLSEGGYLDGDVVECSLHMGKFCVRTGKVKSPPPCEPLKVYPIRIEGRDVLVDFSRAAL 107
                                    11        21        31        41        51        61        71        81        91       101

Chain P from PDB  Type:PROTEIN  Length:401
 aligned with Q52437_PSES1 | Q52437 from UniProtKB/TrEMBL  Length:408

    Alignment length:401
                                    15        25        35        45        55        65        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       365       375       385       395       405 
         Q52437_PSES1     6 LKAPVVVLGAGLASVSFVAELRQAGYQGLITVVGDEAERPYDRPPLSKDFMAHGDAEKIRLDCKRAPEVEWLLGVTAQSFDPQAHTVALSDGRTLPYGTLVLATGAAPRALPTLQGATMPVHTLRTLEDARRIQAGLRPQSRLLIVGGGVIGLELAATARTAGVHVSLVETQPRLMSRAAPATLADFVARYHAAQGVDLRFERSVTGSVDGVVLLDDGTRIAADMVVVGIGVLANDALARAAGLACDDGIFVDAYGRTTCPDVYALGDVTRQRNPLSGRFERIETWSNAQNQGIAVARHLVDPTAPGYAELPWYWSDQGALRIQVAGLASGDEEIVRGEVSLDAPKFTLIELQKGRIVGATCVNNARDFAPLRRLLAVGAKPDRAALADPATDLRKLAAAV 406
               SCOP domains d2yvjp1 P:6-115,P:237-308 NADH-dependent ferredoxin reductase, BphA4                                          d2yvjp2 P:116-236 NADH-dependent ferredoxin reductase, BphA4                                                             d2yvjp1 P:6-115,P:237-308 NADH-dependent ferredoxin reductase, BphA4    d2yvjp3 P:309-406 NADH-dependent ferredoxin reductase, BphA4                                       SCOP domains
               CATH domains 2yvjP01 P:6-110,P:239-317  [code=3.50.50.60, no name defined]                                            ---2yvjP02 P:114-236  [code=3.50.50.60, no name defined]                                                                      --2yvjP01 P:6-110,P:239-317  [code=3.50.50.60, no name defined]                  2yvjP03 P:318-406  [code=3.30.390.30, no name defined]                                    CATH domains
           Pfam domains (1) ---------------------------------------------------------------------------------------------------------------------------------------------Pyr_redox-2yvjP01 P:147-223                                                  --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ---------------------------------------------------------------------------------------------------------------------------------------------Pyr_redox-2yvjP02 P:147-223                                                  --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
           Pfam domains (3) ---Pyr_redox_2-2yvjP03 P:9-279                                                                                                                                                                                                                                                    ------------------------------------------------------------------------------------------------------------------------------- Pfam domains (3)
           Pfam domains (4) ---Pyr_redox_2-2yvjP04 P:9-279                                                                                                                                                                                                                                                    ------------------------------------------------------------------------------------------------------------------------------- Pfam domains (4)
         Sec.struct. author ....eeee..hhhhhhhhhhhhhhh....eeeee........hhhhhhhhhh..hhhhhh.........eeee...eeeee....eeee....eee..eeee...eee..hhhhh...........hhhhhhhhh........eee..hhhhhhhhhhhhhhh....eee..........hhhhhhhhhhhhhh.....ee........................ee....eee.hhhhhhhh......ee...........eee....eeeee....eee...hhhhhhhhhhhhhhhhhh..........eeeeee..eeeeeee.....eeeeeee......eeeeeeee..eeeeeeee.hhhhhhhhhhhhhhh...hhhhhhh...hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yvj P   6 LKAPVVVLGAGLASVSFVAELRQAGYQGLITVVGDEAERPYDRPPLSKDFMAHGDAEKIRLDCKRAPEVEWLLGVTAQSFDPQAHTVALSDGRTLPYGTLVLATGAAPRALPTLQGATMPVHTLRTLEDARRIQAGLRPQSRLLIVGGGVIGLELAATARTAGVHVSLVETQPRLMSRAAPATLADFVARYHAAQGVDLRFERSVTGSVDGVVLLDDGTRIAADMVVVGIGVLANDALARAAGLACDDGIFVDAYGRTTCPDVYALGDVTRQRNPLSGRFERIETWSNAQNQGIAVARHLVDPTAPGYAELPWYWSDQGALRIQVAGLASGDEEIVRGEVSLDAPKFTLIELQKGRIVGATCVNNARDFAPLRRLLAVGAKPDRAALADPATDLRKLAAAV 406
                                    15        25        35        45        55        65        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       365       375       385       395       405

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/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Enolase-like; domain 1 (252)

Homologous Superfamily: [code=3.30.390.30, no name defined] (99)

Pseudomonas sp.. Organism_taxid: 306. Strain: strain kks102. (3)

1a	2yvjA03	A:318-406
1b	2yvjP03	P:318-406

Architecture: 3-Layer(bba) Sandwich (528)

Topology: FAD/NAD(P)-binding domain (373)

Homologous Superfamily: [code=3.50.50.60, no name defined] (373)

Pseudomonas sp.. Organism_taxid: 306. Strain: strain kks102. (3)

2a	2yvjA01	A:5-110,A:239-317
2b	2yvjP01	P:6-110,P:239-317
2c	2yvjA02	A:114-236
2d	2yvjP02	P:114-236

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: ISP-domain (54)

Family: Rieske (53)

Pseudomonas sp. (strain KKS102) (1)

Rieske-2yvjB01

B:2-96

Clan: NADP_Rossmann (1239)

Family: Pyr_redox (62)

Pseudomonas sp. (strain KKS102) (3)

2a	Pyr_redox-2yvjP01	P:147-223
2b	Pyr_redox-2yvjP02	P:147-223

Family: Pyr_redox_2 (69)

Pseudomonas sp. (strain KKS102) (3)

3a	Pyr_redox_2-2yvjP03	P:9-279
3b	Pyr_redox_2-2yvjP04	P:9-279

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,P (Q52437_PSES1 | Q52437)

molecular function
	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:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	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.
biological process
	GO:0045454	cell redox homeostasis	Any process that maintains the redox environment of a cell or compartment within a cell.
	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:0005623	cell	The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope.

Chain B (BPHA3_PSES1 | Q52440)

molecular function
	GO:0051537	2 iron, 2 sulfur cluster binding	Interacting selectively and non-covalently with a 2 iron, 2 sulfur (2Fe-2S) cluster; this cluster consists of two iron atoms, with two inorganic sulfur atoms found between the irons and acting as bridging ligands.
	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.
biological process
	GO:0019439	aromatic compound catabolic process	The chemical reactions and pathways resulting in the breakdown of aromatic compounds, any substance containing an aromatic carbon ring.
	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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Ala A:8 - Pro A:9	[ RasMol ]
		Ala P:8 - Pro P:9	[ RasMol ]
		Pro B:80 - Pro B:81	[ RasMol ]
		Ser P:209 - Val P:210	[ RasMol ]

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	2yvj
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	BPHA3_PSES1 \| Q52440
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	Q52437_PSES1 \| Q52437
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	1.18.1.2
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	BPHA3_PSES1 \| Q52440	:	2e4p 2e4q
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	Q52437_PSES1 \| Q52437	:	1d7y 1f3p 2gqw 2gr0 2gr1 2gr2 2gr3 2yvf 2yvg

(no "Related Entries Specified in the PDB File" available for 2YVJ)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 5)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

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SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (0, 0)

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SCOP Domains (3, 7)

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