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(-) Description

Title :  CRYSTAL STRUCTURE OF THE COVALENT PUTIDAREDOXIN REDUCTASE-PUTIDAREDOXIN COMPLEX
 
Authors :  I. F. Sevrioukova
Date :  07 Jan 10  (Deposition) - 23 Feb 10  (Release) - 19 May 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Covalently Linked Protein-Protein Complex, Fad, Flavoprotein, Oxidoreductase, 2Fe-2S, Electron Transport, Iron-Sulfur, Metal- Binding, Oxidoreductase-Electron Transport Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  I. F. Sevrioukova, T. L. Poulos, I. Y. Churbanova
Crystal Structure Of The Putidaredoxin Reductase X Putidaredoxin Electron Transfer Complex.
J. Biol. Chem. V. 285 13616 2010
PubMed-ID: 20179327  |  Reference-DOI: 10.1074/JBC.M110.104968

(-) Compounds

Molecule 1 - PUTIDAREDOXIN REDUCTASE
    ChainsA, B
    EC Number1.18.1.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET-PDR
    Expression System StrainBL21(DE3)
    Expression System Taxid562
    Expression System Vector TypePET
    GeneCAMA
    Organism ScientificPSEUDOMONAS PUTIDA
    Organism Taxid303
 
Molecule 2 - PUTIDAREDOXIN
    ChainsC, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET-PDR
    Expression System StrainBL21(DE3)
    Expression System Taxid562
    Expression System Vector TypePET
    GeneCAMA, CAMB
    MutationYES
    Organism ScientificPSEUDOMONAS PUTIDA
    Organism Taxid303
    SynonymPDX

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)A C 
Biological Unit 2 (1x) B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2FES2Ligand/IonFE2/S2 (INORGANIC) CLUSTER
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2FES1Ligand/IonFE2/S2 (INORGANIC) CLUSTER
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2FES1Ligand/IonFE2/S2 (INORGANIC) CLUSTER

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:1 , GLY A:11 , GLY A:13 , LEU A:14 , ALA A:15 , GLY A:36 , ASP A:37 , LEU A:45 , PRO A:46 , SER A:49 , LYS A:50 , THR A:81 , GLN A:82 , VAL A:83 , ALA A:109 , THR A:110 , GLY A:111 , GLY A:112 , ARG A:134 , ILE A:160 , ASP A:284 , GLU A:300 , SER A:301 , VAL A:302 , PRO A:303 , PHE A:329 , TRP A:330 , HOH A:438 , HOH A:439 , HOH A:471 , HOH A:475BINDING SITE FOR RESIDUE FAD A 449
2AC2SOFTWAREVAL B:10 , GLY B:11 , GLY B:13 , LEU B:14 , ALA B:15 , GLY B:36 , ASP B:37 , LEU B:45 , PRO B:46 , SER B:49 , LYS B:50 , THR B:81 , VAL B:83 , ALA B:109 , THR B:110 , GLY B:111 , GLY B:112 , LEU B:133 , ARG B:134 , ILE B:160 , ASN B:251 , LEU B:254 , GLY B:283 , ASP B:284 , GLU B:300 , SER B:301 , VAL B:302 , PRO B:303 , PHE B:329 , TRP B:330 , HOH B:438 , HOH B:443BINDING SITE FOR RESIDUE FAD B 449
3AC3SOFTWAREGLY C:37 , CYS C:39 , GLY C:41 , ALA C:43 , SER C:44 , CYS C:45 , ALA C:46 , CYS C:48 , CYS C:86BINDING SITE FOR RESIDUE FES C 107
4AC4SOFTWAREGLY D:37 , CYS D:39 , GLY D:40 , GLY D:41 , ALA D:43 , SER D:44 , CYS D:45 , CYS D:48 , LEU D:84 , CYS D:86BINDING SITE FOR RESIDUE FES D 107

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1D:48 -D:86

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3LB8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3LB8)

(-) PROSITE Motifs  (2, 4)

Asymmetric Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
12FE2S_FER_2PS51085 2Fe-2S ferredoxin-type iron-sulfur binding domain profile.PUTX_PSEPU2-106
 
  2C:1-104
D:1-103
2ADXPS00814 Adrenodoxin family, iron-sulfur binding region signature.PUTX_PSEPU40-50
 
  2C:39-49
D:39-49
Biological Unit 1 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
12FE2S_FER_2PS51085 2Fe-2S ferredoxin-type iron-sulfur binding domain profile.PUTX_PSEPU2-106
 
  1C:1-104
-
2ADXPS00814 Adrenodoxin family, iron-sulfur binding region signature.PUTX_PSEPU40-50
 
  1C:39-49
-
Biological Unit 2 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
12FE2S_FER_2PS51085 2Fe-2S ferredoxin-type iron-sulfur binding domain profile.PUTX_PSEPU2-106
 
  1-
D:1-103
2ADXPS00814 Adrenodoxin family, iron-sulfur binding region signature.PUTX_PSEPU40-50
 
  1-
D:39-49

(-) Exons   (0, 0)

(no "Exon" information available for 3LB8)

(-) 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:419
 aligned with CAMA_PSEPU | P16640 from UniProtKB/Swiss-Prot  Length:422

    Alignment length:419
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411         
           CAMA_PSEPU     2 NANDNVVIVGTGLAGVEVAFGLRASGWEGNIRLVGDATVIPHHLPPLSKAYLAGKATAESLYLRTPDAYAAQNIQLLGGTQVTAINRDRQQVILSDGRALDYDRLVLATGGRPRPLPVASGAVGKANNFRYLRTLEDAECIRRQLIADNRLVVIGGGYIGLEVAATAIKANMHVTLLDTAARVLERVTAPPVSAFYEHLHREAGVDIRTGTQVCGFEMSTDQQKVTAVLCEDGTRLPADLVIAGIGLIPNCELASAAGLQVDNGIVINEHMQTSDPLIMAVGDCARFHSQLYDRWVRIESVPNALEQARKIAAILCGKVPRDEAAPWFWSDQYEIGLKMVGLSEGYDRIIVRGSLAQPDFSVFYLQGDRVLAVDTVNRPVEFNQSKQIITDRLPVEPNLLGDESVPLKEIIAAAKAELS 420
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3lb8A01 A:2-115,A:247-327  [code=3.50.50.60, no name defined]                                                     3lb8A02 A:116-246  [code=3.50.50.60, no name defined]                                                                              3lb8A01 A:2-115,A:247-327  [code=3.50.50.60, no name defined]                    3lb8A03 A:328-420  [code=3.30.390.30, no name defined]                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee..hhhhhhhhhhhhhh....eeeee.........hhhhhh........hhhhh....hhhhhh.eeee....eeeee....eeee....eee..eeee...eee..hhhhhhhhhhh..eee..hhhhhhhhhh......eeeee..hhhhhhhhhhhhhh..eeeee...........hhhhhhhhhhhhhhhh.eee....eeeeee......eeeeee....eee..eeee...eee.hhhhhhh.......eee..........eee....eeeee....eee...hhhhhhhhhhhhhhhhh..........eeeeee..eeeeeee......eeeeee......eeeeeee..eeeeeeee.hhhhhhhhhhhhhh....hhhhhh....hhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lb8 A   2 NANDNVVIVGTGLAGVEVAFGLRASGWEGNIRLVGDATVIPHHLPPLSKAYLAGKATAESLYLRTPDAYAAQNIQLLGGTQVTAINRDRQQVILSDGRALDYDRLVLATGGRPRPLPVASGAVGKANNFRYLRTLEDAECIRRQLIADNRLVVIGGGYIGLEVAATAIKANMHVTLLDTAARVLERVTAPPVSAFYEHLHREAGVDIRTGTQVCGFEMSTDQQKVTAVLCEDGTRLPADLVIAGIGLIPNCELASAAGLQVDNGIVINEHMQTSDPLIMAVGDCARFHSQLYDRWVRIESVPNALEQARKIAAILCGKVPRDEAAPWFWSDQYEIGLKMVGLSEGYDRIIVRGSLAQPDFSVFYLQGDRVLAVDTVNRPVEFNQSKQIITDRLPVEPNLLGDESVPLKEIIAAAKAELS 420
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411         

Chain B from PDB  Type:PROTEIN  Length:417
 aligned with CAMA_PSEPU | P16640 from UniProtKB/Swiss-Prot  Length:422

    Alignment length:417
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       
           CAMA_PSEPU     2 NANDNVVIVGTGLAGVEVAFGLRASGWEGNIRLVGDATVIPHHLPPLSKAYLAGKATAESLYLRTPDAYAAQNIQLLGGTQVTAINRDRQQVILSDGRALDYDRLVLATGGRPRPLPVASGAVGKANNFRYLRTLEDAECIRRQLIADNRLVVIGGGYIGLEVAATAIKANMHVTLLDTAARVLERVTAPPVSAFYEHLHREAGVDIRTGTQVCGFEMSTDQQKVTAVLCEDGTRLPADLVIAGIGLIPNCELASAAGLQVDNGIVINEHMQTSDPLIMAVGDCARFHSQLYDRWVRIESVPNALEQARKIAAILCGKVPRDEAAPWFWSDQYEIGLKMVGLSEGYDRIIVRGSLAQPDFSVFYLQGDRVLAVDTVNRPVEFNQSKQIITDRLPVEPNLLGDESVPLKEIIAAAKAE 418
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3lb8B01 B:2-115,B:247-327  [code=3.50.50.60, no name defined]                                                     3lb8B02 B:116-246  [code=3.50.50.60, no name defined]                                                                              3lb8B01 B:2-115,B:247-327  [code=3.50.50.60, no name defined]                    3lb8B03 B:328-418  [code=3.30.390.30, no name defined]                                      CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee..hhhhhhhhhhhhhh....eeeee.........hhhhhhhhhhh...hhhhh....hhhhhh..eee....eeeee....eeee....eee..eeee...eee..hhhhhhhhhhh..ee...hhhhhhhhhh......eeee...hhhhhhhhhhhhhh..eeee............hhhhhhhhhhhhhhh..ee.......ee..........eee.....eee..eee....eee.hhhhhh........ee...........eee....eeeee....eee...hhhhhhhhhhhhhhhhh..........eee.......eeeee......eeeeeee....eeeeeeee..eeeeeeee.hhhhhhhhhhhhhh..............hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lb8 B   2 NANDNVVIVGTGLAGVEVAFGLRASGWEGNIRLVGDATVIPHHLPPLSKAYLAGKATAESLYLRTPDAYAAQNIQLLGGTQVTAINRDRQQVILSDGRALDYDRLVLATGGRPRPLPVASGAVGKANNFRYLRTLEDAECIRRQLIADNRLVVIGGGYIGLEVAATAIKANMHVTLLDTAARVLERVTAPPVSAFYEHLHREAGVDIRTGTQVCGFEMSTDQQKVTAVLCEDGTRLPADLVIAGIGLIPNCELASAAGLQVDNGIVINEHMQTSDPLIMAVGDCARFHSQLYDRWVRIESVPNALEQARKIAAILCGKVPRDEAAPWFWSDQYEIGLKMVGLSEGYDRIIVRGSLAQPDFSVFYLQGDRVLAVDTVNRPVEFNQSKQIITDRLPVEPNLLGDESVPLKEIIAAAKAE 418
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       

Chain C from PDB  Type:PROTEIN  Length:104
 aligned with PUTX_PSEPU | P00259 from UniProtKB/Swiss-Prot  Length:107

    Alignment length:104
                                    11        21        31        41        51        61        71        81        91       101    
           PUTX_PSEPU     2 SKVVYVSHDGTRRELDVADGVSLMQAAVSNGIYDIVGDCGGSASCATCHVYVNEAFTDKVPAANEREIGMLECVTAELKPNSRLCCQIIMTPELDGIVVDVPDR 105
               SCOP domains d3lb8c_ C: 2Fe-2S ferredoxin                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeehhhhh.eeee.....hhhhhhhhh..................eeeehhhhhh.....hhhhhhhhh.........eee......hhhhh.eeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) 2FE2S_FER_2  PDB: C:1-104 UniProt: 2-106                                                                 PROSITE (1)
                PROSITE (2) --------------------------------------ADX        ------------------------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                 3lb8 C   1 SKVVYVSHDGTRRELDVADGVSLMQAAVSNGIYDIVGDCGGSASCATCHVYVNEAFTDKVPAANEREIGMLESVTAELKPNSRLSCQIIMTPELDGIVVDVPDR 104
                                    10        20        30        40        50        60        70        80        90       100    

Chain D from PDB  Type:PROTEIN  Length:103
 aligned with PUTX_PSEPU | P00259 from UniProtKB/Swiss-Prot  Length:107

    Alignment length:103
                                    11        21        31        41        51        61        71        81        91       101   
           PUTX_PSEPU     2 SKVVYVSHDGTRRELDVADGVSLMQAAVSNGIYDIVGDCGGSASCATCHVYVNEAFTDKVPAANEREIGMLECVTAELKPNSRLCCQIIMTPELDGIVVDVPD 104
               SCOP domains d3lb8d_ D: 2Fe-2S ferredoxin                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee.........hhhhhh...................eee............hhhhhhhh..........eee.hhh............... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) 2FE2S_FER_2  PDB: D:1-103 UniProt: 2-106                                                                PROSITE (1)
                PROSITE (2) --------------------------------------ADX        ------------------------------------------------------ PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                 3lb8 D   1 SKVVYVSHDGTRRELDVADGVSLMQAAVSNGIYDIVGDCGGSASCATCHVYVNEAFTDKVPAANEREIGMLESVTAELKPNSRLSCQIIMTPELDGIVVDVPD 103
                                    10        20        30        40        50        60        70        80        90       100   

   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  (1, 2)

Asymmetric Unit

(-) CATH Domains  (2, 6)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3LB8)

(-) Gene Ontology  (10, 11)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (CAMA_PSEPU | P16640)
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: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:0019383    (+)-camphor catabolic process    The chemical reactions and pathways resulting in the breakdown of (+)-camphor, a bicyclic monoterpene ketone.
    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 C,D   (PUTX_PSEPU | P00259)
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: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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CAMA_PSEPU | P166401q1r 1q1w
        PUTX_PSEPU | P002591gpx 1oqq 1oqr 1pdx 1put 1r7s 1xln 1xlo 1xlp 1xlq 1yji 1yjj 2m56 3w9c 4jws 4jwu 4jx1 5gxg

(-) Related Entries Specified in the PDB File

1oqq PUTIDAREDOXIN
1q1r PUTIDAREDOXIN REDUCTASE