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(-) Description

Title :  CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN FERREDOXIN AND FERREDOXIN-NADP+ REDUCTASE
 
Authors :  G. Kurisu, M. Kusunoki, T. Hase
Date :  08 May 00  (Deposition) - 07 Feb 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.59
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C  (1x)
Keywords :  Oxidoreductase/Electron Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Kurisu, M. Kusunoki, E. Katoh, T. Yamazaki, K. Teshima, Y. Onda, Y. Kimata-Ariga, T. Hase
Structure Of The Electron Transfer Complex Between Ferredoxin And Ferredoxin-Nadp(+) Reductase.
Nat. Struct. Biol. V. 8 117 2001
PubMed-ID: 11175898  |  Reference-DOI: 10.1038/84097
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - FERREDOXIN-NADP+ REDUCTASE
    Chains: A, C
    EC Number: 1.18.1.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE60
    Expression System Taxid: 562
    Organism Scientific: ZEA MAYS
    Organism Taxid: 4577
    Synonym: FNR
 
Molecule 2 - FERREDOXIN I
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: ZEA MAYS
    Organism Taxid: 4577
    Synonym: FD

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): AB 
Biological Unit 2 (1x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2FES1Ligand/IonFE2/S2 (INORGANIC) CLUSTER
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2FES1Ligand/IonFE2/S2 (INORGANIC) CLUSTER
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2FES-1Ligand/IonFE2/S2 (INORGANIC) CLUSTER

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:93 , LEU A:94 , TYR A:95 , SER A:96 , CYS A:114 , VAL A:115 , LYS A:116 , LEU A:118 , TYR A:120 , GLY A:130 , VAL A:131 , CYS A:132 , SER A:133 , THR A:172 , TYR A:314 , HOH A:334 , HOH A:351 , SER B:38 , GLU B:94 , THR C:121 , FAD C:321BINDING SITE FOR RESIDUE FAD A 320
2AC2SOFTWARESER B:38 , CYS B:39 , ARG B:40 , GLY B:42 , SER B:43 , CYS B:44 , CYS B:47 , CYS B:77BINDING SITE FOR RESIDUE FES B 99
3AC3SOFTWAREFAD A:320 , ARG C:93 , LEU C:94 , TYR C:95 , SER C:96 , CYS C:114 , LYS C:116 , LEU C:118 , TYR C:120 , GLY C:130 , VAL C:131 , CYS C:132 , SER C:133 , THR C:172 , GLU C:312 , TYR C:314 , HOH C:348 , HOH C:351BINDING SITE FOR RESIDUE FAD C 321

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gly A:149 -Pro A:150
2Gly C:149 -Pro C:150

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

Asymmetric Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
12FE2S_FER_2PS51085 2Fe-2S ferredoxin-type iron-sulfur binding domain profile.FER1_MAIZE55-145  1B:3-93
22FE2S_FER_1PS00197 2Fe-2S ferredoxin-type iron-sulfur binding region signature.FER1_MAIZE91-99  1B:39-47
Biological Unit 1 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
12FE2S_FER_2PS51085 2Fe-2S ferredoxin-type iron-sulfur binding domain profile.FER1_MAIZE55-145  1B:3-93
22FE2S_FER_1PS00197 2Fe-2S ferredoxin-type iron-sulfur binding region signature.FER1_MAIZE91-99  1B:39-47
Biological Unit 2 (, 0)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
12FE2S_FER_2PS51085 2Fe-2S ferredoxin-type iron-sulfur binding domain profile.FER1_MAIZE55-145  0-
22FE2S_FER_1PS00197 2Fe-2S ferredoxin-type iron-sulfur binding region signature.FER1_MAIZE91-99  0-

(-) Exons   (0, 0)

(no "Exon" information available for 1GAQ)

(-) Sequences/Alignments

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:296
 aligned with Q9SLP6_MAIZE | Q9SLP6 from UniProtKB/TrEMBL  Length:355

    Alignment length:296
                                    69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349      
         Q9SLP6_MAIZE    60 ESKKQEEGVVTNLYKPKEPYVGRCLLNTKITGDDAPGETWHMVFSTEGKIPYREGQSIGVIADGVDKNGKPHKVRLYSIASSAIGDFGDSKTVSLCVKRLIYTNDAGEIVKGVCSNFLCDLQPGDNVQITGPVGKEMLMPKDPNATIIMLATGTGIAPFRSFLWKMFFEKHDDYKFNGLGWLFLGVPTSSSLLYKEEFGKMKERAPENFRVDYAVSREQTNAAGERMYIQTRMAEYKEELWELLKKDNTYVYMCGLKGMEKGIDDIMVSLAEKDGIDWFDYKKQLKRGDQWNVEVY 355
               SCOP domains d1gaqa1 A:19-156 Ferredoxin reductase (flavodoxin reductase) N-terminal domain                                                            d1gaqa2 A:157-314 Ferredoxin reductase (flavodoxin reductase)                                                                                                  SCOP domains
               CATH domains 1gaqA01 A:19-151 Translation factors                                                                                                 1gaqA02 A:152-314 Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module                                                                               CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...................eeeeeeeeee.........eeeeeee...........eeeee.............eeee.............eeeeeee..eee.....eeehhhhhhhhh.....eeeeeeee............eeeeeee...hhhhhhhhhhhh...........eeeeeeee.hhhhh.hhhhhhhhhhhh...eeeeeee............hhhhhhhhhhhhhhh......eeeeeeee.hhhhhhhhhhhhhhh....hhhhhhhhhhhhh.eeeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1gaq A  19 ESKKQEEGVVTNLYKPKEPYVGRCLLNTKITGDDAPGETWHMVFSTEGKIPYREGQSIGVIADGVDKNGKPHKVRLYSIASSAIGDFGDSKTVSLCVKRLIYTNDAGEIVKGVCSNFLCDLQPGDNVQITGPVGKEMLMPKDPNATIIMLATGTGIAPFRSFLWKMFFEKHDDYKFNGLGWLFLGVPTSSSLLYKEEFGKMKERAPENFRVDYAVSREQTNAAGERMYIQTRMAEYKEELWELLKKDNTYVYMCGLKGMEKGIDDIMVSLAEKDGIDWFDYKKQLKRGDQWNVEVY 314
                                    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       308      


Chain B from PDB  Type:PROTEIN  Length:98
 aligned with FER1_MAIZE | P27787 from UniProtKB/Swiss-Prot  Length:150

    Alignment length:98
                                    62        72        82        92       102       112       122       132       142        
           FER1_MAIZE    53 ATYNVKLITPEGEVELQVPDDVYILDQAEEDGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSYLDDGQIADGWVLTCHAYPTSDVVIETHKEEELTGA 150
               SCOP domains d1gaqb_ B: 2Fe-2S ferredoxin                                                                       SCOP domains
               CATH domains 1gaqB00 B:1-98  [code=3.10.20.30, no name defined]                                                 CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee...............hhhhhhh...................ee.....ee.........hhhhhh.......ee...eeeee......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --2FE2S_FER_2  PDB: B:3-93 UniProt: 55-145                                                   ----- PROSITE (1)
                PROSITE (2) --------------------------------------2FE2S_FER--------------------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------- Transcript
                 1gaq B   1 ATYNVKLITPEGEVELQVPDDVYILDQAEEDGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSYLDDGQIADGWVLTCHAYPTSDVVIETHKEEELTGA  98
                                    10        20        30        40        50        60        70        80        90        


Chain C from PDB  Type:PROTEIN  Length:296
 aligned with Q9SLP6_MAIZE | Q9SLP6 from UniProtKB/TrEMBL  Length:355

    Alignment length:296
                                    69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349      
         Q9SLP6_MAIZE    60 ESKKQEEGVVTNLYKPKEPYVGRCLLNTKITGDDAPGETWHMVFSTEGKIPYREGQSIGVIADGVDKNGKPHKVRLYSIASSAIGDFGDSKTVSLCVKRLIYTNDAGEIVKGVCSNFLCDLQPGDNVQITGPVGKEMLMPKDPNATIIMLATGTGIAPFRSFLWKMFFEKHDDYKFNGLGWLFLGVPTSSSLLYKEEFGKMKERAPENFRVDYAVSREQTNAAGERMYIQTRMAEYKEELWELLKKDNTYVYMCGLKGMEKGIDDIMVSLAEKDGIDWFDYKKQLKRGDQWNVEVY 355
               SCOP domains d1gaqc1 C:19-156 Ferredoxin reductase (flavodoxin reductase) N-terminal domain                                                            d1gaqc2 C:157-314 Ferredoxin reductase (flavodoxin reductase)                                                                                                  SCOP domains
               CATH domains 1gaqC01 C:19-151 Translation factors                                                                                                 1gaqC02 C:152-314 Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module                                                                               CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...................eeeeeeeeee.........eeeeeee...........eeee..............eeee.............eeeeeee..eee.....eeehhhhhhhh......eeeeeeee............eeeeeee...hhhhhhhhhhhhh..........eeeeeeee.hhhhh.hhhhhhhhhhhh...eeeeeee............hhhhhhhhhhhhhhhhh....eeeeeeee.hhhhhhhhhhhhhhhhh..hhhhhhhhhhh...eeeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1gaq C  19 ESKKQEEGVVTNLYKPKEPYVGRCLLNTKITGDDAPGETWHMVFSTEGKIPYREGQSIGVIADGVDKNGKPHKVRLYSIASSAIGDFGDSKTVSLCVKRLIYTNDAGEIVKGVCSNFLCDLQPGDNVQITGPVGKEMLMPKDPNATIIMLATGTGIAPFRSFLWKMFFEKHDDYKFNGLGWLFLGVPTSSSLLYKEEFGKMKERAPENFRVDYAVSREQTNAAGERMYIQTRMAEYKEELWELLKKDNTYVYMCGLKGMEKGIDDIMVSLAEKDGIDWFDYKKQLKRGDQWNVEVY 314
                                    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       308
   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 '|'

 Classification and Annotation

(-) SCOP Domains  (3, 5)

Asymmetric Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (3, 5)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1GAQ)

(-) Gene Ontology  (10, 11)

Asymmetric Unit(hide GO term definitions)
Chain A,C   (Q9SLP6_MAIZE | Q9SLP6)
molecular function
    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: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.

Chain B   (FER1_MAIZE | P27787)
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: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: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.
biological process
    GO:0022900    electron transport chain    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: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.

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  1gaq
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        FER1_MAIZE | P27787: 3b2f 3w5u 3w5v 5h8y 5h92
UniProtKB/TrEMBL
        Q9SLP6_MAIZE | Q9SLP6: 1gaw 3w5u 3w5v

(-) Related Entries Specified in the PDB File

1gaw FERREDOXIN FREE FERREDOXIN-NADP+ REDUCTASE SOLVED INDEPENDENTLY