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(-) Description

Title :  CRYSTAL STRUCTURE OF THE RIESKE PROTEIN FROM THERMUS THERMOPHILUS
 
Authors :  L. M. Hunsicker-Wang, A. Heine, Y. Chen, E. P. Luna, T. Todaro, Y. M. Zhang, P. A. Williams, D. E. Mcree, J. Hirst, C. D. Stout, J. A. Fee
Date :  12 Feb 03  (Deposition) - 24 Jun 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.31
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Beta Barrel, Iron Sulfur Cluster, Electron Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. M. Hunsicker-Wang, A. Heine, Y. Chen, E. P. Luna, T. Todaro, Y. M. Zhang, P. A. Williams, D. E. Mcree, J. Hirst, C. D. Stout, J. A. Fee
High Resolution Structure Of The Soluble, Respiratory-Type Rieske Protein From Thermus Thermophilus: Analysis And Comparison
Biochemistry V. 42 7303 2003
PubMed-ID: 12809486  |  Reference-DOI: 10.1021/BI0342719
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RIESKE IRON-SULFUR PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET17B
    Expression System Strain: DH10
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 274

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
1FES2Ligand/IonFE2/S2 (INORGANIC) CLUSTER
2MG3Ligand/IonMAGNESIUM ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1FES1Ligand/IonFE2/S2 (INORGANIC) CLUSTER
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1FES1Ligand/IonFE2/S2 (INORGANIC) CLUSTER
2MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:1182 , HOH A:1218 , HOH A:1262 , HOH A:1266 , HOH A:1278 , HOH A:1279BINDING SITE FOR RESIDUE MG A 1
2AC2SOFTWAREHIS A:162 , HOH A:1116 , HOH A:1227 , HOH A:1259 , HOH A:1273 , HOH A:1280BINDING SITE FOR RESIDUE MG A 2
3AC3SOFTWAREHOH A:1201 , HOH A:1220 , HOH A:1230 , HOH A:1234 , HOH A:1282 , HOH A:1283BINDING SITE FOR RESIDUE MG A 3
4AC4SOFTWARECYS A:132 , HIS A:134 , LEU A:135 , CYS A:137 , CYS A:151 , HIS A:154 , GLY A:156BINDING SITE FOR RESIDUE FES A 211
5AC5SOFTWARECYS B:132 , HIS B:134 , LEU B:135 , GLY B:136 , CYS B:137 , CYS B:151 , HIS B:154 , GLY B:156BINDING SITE FOR RESIDUE FES B 211

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:137 -A:153
2B:137 -B:153

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1NYK)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1NYK)

(-) 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:156
 aligned with O52396_THETH | O52396 from UniProtKB/TrEMBL  Length:210

    Alignment length:156
                                    55        65        75        85        95       105       115       125       135       145       155       165       175       185       195      
         O52396_THETH    46 TPEKEPLKPGDILVYAQGGGEPKPIRLEELKPGDPFVLAYPMDPKTKVVKSGEAKNTLLVARFDPEELAPEVAQHAAEGVVAYSAVCTHLGCIVSQWVADEEAALCPCHGGVYDLRHGAQVIAGPPPKPVPQLPVRVEDGVLVAAGEFLGPVGVQA 201
               SCOP domains d1nyka_ A: Soluble Rieske protein                                                                                                                            SCOP domains
               CATH domains 1nykA00 A:46-201 'Rieske'-like iron-sulphur domains                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhh......eeee..........hhhhh......eeeeee..........hhhh.eeeee.hhhhhhhhhhh.....eeeee...........eee....eee......eee.hhh..eee........ee.eeee..eeee............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1nyk A  46 TPEKEPLKPGDILVYAQGGGEPKPIRLEELKPGDPFVLAYPMDPKTKVVKSGEAKNTLLVARFDPEELAPEVAQHAAEGVVAYSAVCTHLGCIVSQWVADEEAALCPCHGGVYDLRHGAQVIAGPPPRPVPQLPVRVEDGVLVAAGEFLGPVGVQA 201
                                    55        65        75        85        95       105       115       125       135       145       155       165       175       185       195      


Chain A from PDB  Type:PROTEIN  Length:156
 aligned with Q5SGZ9_THET8 | Q5SGZ9 from UniProtKB/TrEMBL  Length:210

    Alignment length:156
                                    55        65        75        85        95       105       115       125       135       145       155       165       175       185       195      
         Q5SGZ9_THET8    46 TPEKEPLKPGDILVYAQGGGEPKPIRLEELKPGDPFVLAYPMDPKTKVVKSGEAKNTLLVARFDPEELAPEVAQHAAEGVVAYSAVCTHLGCIVSQWVADEEAALCPCHGGVYDLRHGAQVIAGPPPRPVPQLPVRVEDGVLVAAGEFLGPVGVQA 201
               SCOP domains d1nyka_ A: Soluble Rieske protein                                                                                                                            SCOP domains
               CATH domains 1nykA00 A:46-201 'Rieske'-like iron-sulphur domains                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhh......eeee..........hhhhh......eeeeee..........hhhh.eeeee.hhhhhhhhhhh.....eeeee...........eee....eee......eee.hhh..eee........ee.eeee..eeee............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1nyk A  46 TPEKEPLKPGDILVYAQGGGEPKPIRLEELKPGDPFVLAYPMDPKTKVVKSGEAKNTLLVARFDPEELAPEVAQHAAEGVVAYSAVCTHLGCIVSQWVADEEAALCPCHGGVYDLRHGAQVIAGPPPRPVPQLPVRVEDGVLVAAGEFLGPVGVQA 201
                                    55        65        75        85        95       105       115       125       135       145       155       165       175       185       195      


Chain B from PDB  Type:PROTEIN  Length:156
 aligned with O52396_THETH | O52396 from UniProtKB/TrEMBL  Length:210

    Alignment length:156
                                    55        65        75        85        95       105       115       125       135       145       155       165       175       185       195      
         O52396_THETH    46 TPEKEPLKPGDILVYAQGGGEPKPIRLEELKPGDPFVLAYPMDPKTKVVKSGEAKNTLLVARFDPEELAPEVAQHAAEGVVAYSAVCTHLGCIVSQWVADEEAALCPCHGGVYDLRHGAQVIAGPPPKPVPQLPVRVEDGVLVAAGEFLGPVGVQA 201
               SCOP domains d1nykb_ B: Soluble Rieske protein                                                                                                                            SCOP domains
               CATH domains 1nykB00 B:46-201 'Rieske'-like iron-sulphur domains                                                                                                          CATH domains
           Pfam domains (1) -------------------------------------------Rieske-1nykB01 B:89-185                                                                          ---------------- Pfam domains (1)
           Pfam domains (2) -------------------------------------------Rieske-1nykB02 B:89-185                                                                          ---------------- Pfam domains (2)
         Sec.struct. author hhhhh......eeee..........hhhhh......eeeeee..........hhhh.eeeee.hhhhhhhhhhh.....eeeee...........eee....eee......eee.hhh..eee........ee.eeee..eeee............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1nyk B  46 TPEKEPLKPGDILVYAQGGGEPKPIRLEELKPGDPFVLAYPMDPKTKVVKSGEAKNTLLVARFDPEELAPEVAQHAAEGVVAYSAVCTHLGCIVSQWVADEEAALCPCHGGVYDLRHGAQVIAGPPPRPVPQLPVRVEDGVLVAAGEFLGPVGVQA 201
                                    55        65        75        85        95       105       115       125       135       145       155       165       175       185       195      


Chain B from PDB  Type:PROTEIN  Length:156
 aligned with Q5SGZ9_THET8 | Q5SGZ9 from UniProtKB/TrEMBL  Length:210

    Alignment length:156
                                    55        65        75        85        95       105       115       125       135       145       155       165       175       185       195      
         Q5SGZ9_THET8    46 TPEKEPLKPGDILVYAQGGGEPKPIRLEELKPGDPFVLAYPMDPKTKVVKSGEAKNTLLVARFDPEELAPEVAQHAAEGVVAYSAVCTHLGCIVSQWVADEEAALCPCHGGVYDLRHGAQVIAGPPPRPVPQLPVRVEDGVLVAAGEFLGPVGVQA 201
               SCOP domains d1nykb_ B: Soluble Rieske protein                                                                                                                            SCOP domains
               CATH domains 1nykB00 B:46-201 'Rieske'-like iron-sulphur domains                                                                                                          CATH domains
           Pfam domains (1) -------------------------------------------Rieske-1nykB01 B:89-185                                                                          ---------------- Pfam domains (1)
           Pfam domains (2) -------------------------------------------Rieske-1nykB02 B:89-185                                                                          ---------------- Pfam domains (2)
         Sec.struct. author hhhhh......eeee..........hhhhh......eeeeee..........hhhh.eeeee.hhhhhhhhhhh.....eeeee...........eee....eee......eee.hhh..eee........ee.eeee..eeee............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1nyk B  46 TPEKEPLKPGDILVYAQGGGEPKPIRLEELKPGDPFVLAYPMDPKTKVVKSGEAKNTLLVARFDPEELAPEVAQHAAEGVVAYSAVCTHLGCIVSQWVADEEAALCPCHGGVYDLRHGAQVIAGPPPRPVPQLPVRVEDGVLVAAGEFLGPVGVQA 201
                                    55        65        75        85        95       105       115       125       135       145       155       165       175       185       195
   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: All beta proteins (24004)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: ISP-domain (54)

(-) Gene Ontology  (8, 16)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q5SGZ9_THET8 | Q5SGZ9)
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.
    GO:0016679    oxidoreductase activity, acting on diphenols and related substances as donors    Catalysis of an oxidation-reduction (redox) reaction in which a diphenol or related substance acts as a hydrogen or electron donor and reduces a hydrogen or electron acceptor.
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.
cellular component
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

Chain A,B   (O52396_THETH | O52396)
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.
    GO:0016679    oxidoreductase activity, acting on diphenols and related substances as donors    Catalysis of an oxidation-reduction (redox) reaction in which a diphenol or related substance acts as a hydrogen or electron donor and reduces a hydrogen or electron acceptor.
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.
cellular component
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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 Related Entries

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