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(-) Description

Title :  CRYSTAL STRUCTURE OF THE PYROCOCCUS FURIOSUS FERREDOXIN D14C VARIANT CONTAINING THE HETEROMETALLIC [AGFE3S4] CLUSTER
 
Authors :  I. N. Jakab-Simon, H. E. M. Christensen, L. T. Haahr
Date :  30 Jan 12  (Deposition) - 16 Jan 13  (Release) - 06 Mar 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Ferredoxin, Pyrococcus Furiosus, Iron-Sulfur Protein, Electron Transport, Heterometallic, [Agfe3S4] Cluster, Silver, Artificial Metalloprotein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Martic, I. N. Jakab-Simon, L. T. Haahr, W. R. Hagen, H. E. Christense
Heterometallic [Agfe(3)S (4)] Ferredoxin Variants: Synthesis, Characterization, And The First Crystal Structur Of An Engineered Heterometallic Iron-Sulfur Protein.
J. Biol. Inorg. Chem. V. 18 261 2013
PubMed-ID: 23296387  |  Reference-DOI: 10.1007/S00775-012-0971-3

(-) Compounds

Molecule 1 - FERREDOXIN
    Chains: B, A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET3A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: FDXA, FERREDOXIN, PF1909
    Mutation: YES
    Organism Scientific: PYROCOCCUS FURIOSUS
    Organism Taxid: 186497
    Strain: DSM3638

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
10KA2Ligand/IonSILVER/IRON/SULFUR CLUSTER
2NCO4Ligand/IonCOBALT HEXAMMINE(III)

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL B:6 , CYS B:11 , ILE B:12 , CYS B:14 , ALA B:15 , ILE B:16 , CYS B:17 , ALA B:33 , CYS B:56 , VAL B:58 , ILE B:61 , HOH B:249BINDING SITE FOR RESIDUE 0KA B 101
2AC2SOFTWARESER A:19 , LEU A:20 , CYS A:48 , GLU B:41 , ASP B:42 , GLU B:43BINDING SITE FOR RESIDUE NCO B 102
3AC3SOFTWAREASP A:42 , GLU A:44 , HOH A:217 , LEU B:20 , CYS B:48 , GLU B:51BINDING SITE FOR RESIDUE NCO A 101
4AC4SOFTWARECYS A:11 , ILE A:12 , CYS A:14 , ALA A:15 , CYS A:17 , ALA A:33 , CYS A:56 , ILE A:61BINDING SITE FOR RESIDUE 0KA A 102
5AC5SOFTWAREASP A:9 , GLU A:26 , MET A:27 , ASN A:28 , ASP A:29 , HOH A:218 , GLU B:54 , ALA B:55 , CYS B:56 , PRO B:57 , SER B:59 , HOH B:210 , HOH B:252BINDING SITE FOR RESIDUE NCO A 103
6AC6SOFTWAREMET A:53 , GLU A:54 , ALA A:55 , CYS A:56 , PRO A:57 , SER A:59 , ASP B:7BINDING SITE FOR RESIDUE NCO A 104

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:21 -A:48
2B:21 -B:48

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4DHV)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4DHV)

(-) PROSITE Motifs  (1, 4)

Asymmetric/Biological Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
14FE4S_FER_2PS51379 4Fe-4S ferredoxin-type iron-sulfur binding domain profile.FER_PYRFU3-31
 
36-67
 		  4A:2-30
B:2-30
A:35-66
B:35-66

(-) Exons   (0, 0)

(no "Exon" information available for 4DHV)

(-) Sequences/Alignments

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:66
 aligned with FER_PYRFU | P29603 from UniProtKB/Swiss-Prot  Length:67

    Alignment length:66
                                    11        21        31        41        51        61      
             FER_PYRFU    2 AWKVSVDQDTCIGDAICASLCPDVFEMNDEGKAQPKVEVIEDEELYNCAKEAMEACPVSAITIEEA 67
               SCOP domains d4dhva_ A: Fe3S4-ferredoxin PF1909                                 SCOP domains
               CATH domains ------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee........hhhhhhh...eee.....eee......hhhhhhhhhhhhhhh....eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -4FE4S_FER_2  PDB: A:2-30     ----4FE4S_FER_2  PDB: A:35-66        PROSITE
                 Transcript ------------------------------------------------------------------ Transcript
                  4dhv A  1 AWKVSVDQDTCIGCAICASLCPDVFEMNDEGKAQPKVEVIEDEELYNCAKEAMEACPVSAITIEEA 66
                                    10        20        30        40        50        60      


Chain B from PDB  Type:PROTEIN  Length:66
 aligned with FER_PYRFU | P29603 from UniProtKB/Swiss-Prot  Length:67

    Alignment length:66
                                    11        21        31        41        51        61      
             FER_PYRFU    2 AWKVSVDQDTCIGDAICASLCPDVFEMNDEGKAQPKVEVIEDEELYNCAKEAMEACPVSAITIEEA 67
               SCOP domains d4dhvb_ B: Fe3S4-ferredoxin PF1909                                 SCOP domains
               CATH domains ------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee........hhhhhhh...eee.....eee...ee.hhhhhhhhhhhhhhh....eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -4FE4S_FER_2  PDB: B:2-30     ----4FE4S_FER_2  PDB: B:35-66        PROSITE
                 Transcript ------------------------------------------------------------------ Transcript
                  4dhv B  1 AWKVSVDQDTCIGCAICASLCPDVFEMNDEGKAQPKVEVIEDEELYNCAKEAMEACPVSAITIEEA 66
                                    10        20        30        40        50        60
   Legend:   → Mismatch (orange background)
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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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4DHV)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4DHV)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (FER_PYRFU | P29603)
molecular function
    GO:0051538    3 iron, 4 sulfur cluster binding    Interacting selectively and non-covalently with a 3 iron, 4 sulfur (3Fe-4S) cluster; this cluster consists of three iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands. It is essentially a 4Fe-4S cluster with one iron missing.
    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:0005506    iron ion binding    Interacting selectively and non-covalently with iron (Fe) ions.
    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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  4dhv
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 Related Entries

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

UniProtKB/Swiss-Prot
        FER_PYRFU | P29603: 1siz 1sj1 2z8q 3pni

(-) Related Entries Specified in the PDB File

1sj1 PF FD WT
2z8q PF FD D14C MUTANT WITH [FE4S4] CLUSTER
3pni PF FD D14C MUTANT WITH [FE3S4] CLUSTER