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(-) Description

Title :  CRYSTAL STRUCTURE AT 1.5 ANGSTROMS RESOLUTION OF THE WILD TYPE THIOREDOXIN-LIKE [2FE-2S] FERREDOXIN FROM AQUIFEX AEOLICUS
 
Authors :  A. P. Yeh, X. I. Ambroggio, S. L. A. Andrade, O. Einsle, C. Chatelet, J. Meyer, D. C. Rees
Date :  22 Jun 02  (Deposition) - 18 Sep 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A (1x),B (1x)
Keywords :  Ferredoxin, Thioredoxin-Like Fold, [2Fe-2S] Cluster, Electron Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. P. Yeh, X. I. Ambroggio, S. L. A. Andrade, O. Einsle, C. Chatelet, J. Meyer, D. C. Rees
High-Resolution Crystal Structures Of The Wild Type And Cys-55-->Ser And Cys-59-->Ser Variants Of The Thioredoxin-Like [2Fe-2S] Ferredoxin From Aquifex Aeolicus
J. Biol. Chem. V. 277 34499 2002
PubMed-ID: 12089152  |  Reference-DOI: 10.1074/JBC.M205096200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - [2FE-2S] FERREDOXIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PT7-7
    Expression System Strain: K38
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: FDX4
    Organism Scientific: AQUIFEX AEOLICUS
    Organism Taxid: 63363
    Synonym: AAFD4

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (1x): A (1x)B (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric Unit (3, 7)
No.NameCountTypeFull Name
1FES2Ligand/IonFE2/S2 (INORGANIC) CLUSTER
2SO41Ligand/IonSULFATE ION
3ZN4Ligand/IonZINC ION
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1FES2Ligand/IonFE2/S2 (INORGANIC) CLUSTER
2SO41Ligand/IonSULFATE ION
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1FES1Ligand/IonFE2/S2 (INORGANIC) CLUSTER
2SO4-1Ligand/IonSULFATE ION
3ZN-1Ligand/IonZINC ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:83 , ASP B:83BINDING SITE FOR RESIDUE ZN A 301
2AC2SOFTWAREHIS A:17 , HOH A:385 , HOH A:386 , GLU B:97BINDING SITE FOR RESIDUE ZN A 302
3AC3SOFTWAREALA A:1 , ASP A:12BINDING SITE FOR RESIDUE ZN A 303
4AC4SOFTWAREGLU A:97 , HOH A:373 , HIS B:17BINDING SITE FOR RESIDUE ZN A 304
5AC5SOFTWAREPRO B:52 , THR B:53BINDING SITE FOR RESIDUE SO4 B 401
6AC6SOFTWARECYS A:9 , GLN A:11 , ARG A:13 , CYS A:22 , CYS A:55 , MET A:56 , ASN A:57 , ALA A:58 , CYS A:59BINDING SITE FOR RESIDUE FES A 201
7AC7SOFTWARECYS B:9 , GLN B:11 , ARG B:13 , CYS B:22 , CYS B:55 , MET B:56 , ASN B:57 , ALA B:58 , CYS B:59BINDING SITE FOR RESIDUE FES B 202

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1M2A)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Gly A:62 -Pro A:63
2Tyr A:68 -Pro A:69
3Gly B:62 -Pro B:63
4Tyr B:68 -Pro B:69

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1M2A)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1M2A)

(-) Exons   (0, 0)

(no "Exon" information available for 1M2A)

(-) 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:103
 aligned with FER2_AQUAE | O66511 from UniProtKB/Swiss-Prot  Length:111

    Alignment length:103
                                    11        21        31        41        51        61        71        81        91       101   
           FER2_AQUAE     2 AEFKHVFVCVQDRPPGHPQGSCAQRGSREVFQAFMEKIQTDPQLFMTTVITPTGCMNACMMGPVVVVYPDGVWYGQVKPEDVDEIVEKHLKGGEPVERLVISK 104
               SCOP domains d1m2aa_ A: Thioredoxin-like 2Fe-2S ferredoxin                                                           SCOP domains
               CATH domains 1m2aA00 A:1-103 Glutaredoxin                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee................hhhhhhhhhhhhhh.hhhhhh.eeeeee....hhhhh..eeee...eee...hhhhhhhhhhhh......hhh.eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                 1m2a A   1 AEFKHVFVCVQDRPPGHPQGSCAQRGSREVFQAFMEKIQTDPQLFMTTVITPTGCMNACMMGPVVVVYPDGVWYGQVKPEDVDEIVEKHLKGGEPVERLVISK 103
                                    10        20        30        40        50        60        70        80        90       100   


Chain B from PDB  Type:PROTEIN  Length:101
 aligned with FER2_AQUAE | O66511 from UniProtKB/Swiss-Prot  Length:111

    Alignment length:101
                                    13        23        33        43        53        63        73        83        93       103 
           FER2_AQUAE     4 FKHVFVCVQDRPPGHPQGSCAQRGSREVFQAFMEKIQTDPQLFMTTVITPTGCMNACMMGPVVVVYPDGVWYGQVKPEDVDEIVEKHLKGGEPVERLVISK 104
               SCOP domains d1m2ab_ B: Thioredoxin-like 2Fe-2S ferredoxin                                                         SCOP domains
               CATH domains 1m2aB00 B:3-103 Glutaredoxin                                                                          CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee................hhhhhhhhhhhhhhhhhhhhh.eeeeee....hhhhh..eeee...eee...hhhhhhhhhhhh......hhh.eee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------- Transcript
                 1m2a B   3 FKHVFVCVQDRPPGHPQGSCAQRGSREVFQAFMEKIQTDPQLFMTTVITPTGCMNACMMGPVVVVYPDGVWYGQVKPEDVDEIVEKHLKGGEPVERLVISK 103
                                    12        22        32        42        52        62        72        82        92       102
   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
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1M2A)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (FER2_AQUAE | O66511)
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: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:0010181    FMN binding    Interacting selectively and non-covalently with flavin mono nucleotide. Flavin mono nucleotide (FMN) is the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes.
    GO:0051287    NAD binding    Interacting selectively and non-covalently with nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NAD+, or the reduced form, NADH.
    GO:0003954    NADH dehydrogenase activity    Catalysis of the reaction: NADH + H+ + acceptor = NAD+ + reduced acceptor.
    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:0009060    aerobic respiration    The enzymatic release of energy from inorganic and organic compounds (especially carbohydrates and fats) which requires oxygen as the terminal electron acceptor.
    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
        FER2_AQUAE | O66511: 1f37 1m2b 1m2d

(-) Related Entries Specified in the PDB File

1f37 1F37 IS THE SAME WILD TYPE PROTEIN, BUT ITS CRYSTAL STRUCTURE WAS DETERMINED USING A DIFFERENT CRYSTAL FORM AND AT THE LOWER RESOLUTION OF 2.3 ANGSTROMS
1m2b STRUCTURE AT 1.25 ANGSTROMS RESOLUTION OF CYS55SER VARIANT OF AQUIFEX AEOLICUS [2FE-2S] FERREDOXIN
1m2d STRUCTURE AT 1.05 ANGSTROMS RESOLUTION OF CYS59SER VARIANT OF AQUIFEX AEOLICUS [2FE-2S] FERREDOXIN