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(-) Description

Title :  CRYSTAL STRUCTURE ANALYSIS OF IRON REGULATORY PROTEIN 1 IN COMPLEX WITH TRANSFERRIN RECEPTOR IRE B RNA
 
Authors :  K. Volz, A. I. Selezneva, W. E. Walden
Date :  28 Jun 11  (Deposition) - 23 Nov 11  (Release) - 24 Dec 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.99
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Rna Binding, Iron Sulfur Cluster Binding, Phosphorylation, Lyase-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. E. Walden, A. Selezneva, K. Volz
Accommodating Variety In Iron-Responsive Elements: Crystal Structure Of Transferrin Receptor 1 B Ire Bound To Iron Regulatory Protein 1.
Febs Lett. V. 586 32 2012
PubMed-ID: 22119729  |  Reference-DOI: 10.1016/J.FEBSLET.2011.11.018
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CYTOPLASMIC ACONITATE HYDRATASE
    Chains: A
    EC Number: 4.2.1.3
    Engineered: YES
    Expression System: SACCHAROMYCES CEREVISIAE
    Expression System Strain: BJ5465
    Expression System Taxid: 4932
    Expression System Vector Type: PLASMID
    Gene: ACO1, FRP, IREB1, IREBP, IRP1
    Mutation: YES
    Organism Common: RABBIT
    Organism Scientific: ORYCTOLAGUS CUNICULUS
    Organism Taxid: 9986
    Synonym: IRON REGULATORY PROTEIN 1, IRP1, ACONITASE, CITRATE HYDRO- LYASE, FERRITIN REPRESSOR PROTEIN, IRON-RESPONSIVE ELEMENT-BINDING PROTEIN 1, IRE-BP 1
 
Molecule 2 - TRANSFERRIN RECEPTOR IRON REGULATORY ELEMENT B RNA
    Chains: B
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3SN2)

(-) Sites  (0, 0)

(no "Site" information available for 3SN2)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3SN2)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gly A:372 -Pro A:373

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3SN2)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ACONITASE_1PS00450 Aconitase family signature 1.ACOC_RABIT429-445  1A:429-445
2ACONITASE_2PS01244 Aconitase family signature 2.ACOC_RABIT495-508  1A:495-499

(-) Exons   (0, 0)

(no "Exon" information available for 3SN2)

(-) 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:848
 aligned with ACOC_RABIT | Q01059 from UniProtKB/Swiss-Prot  Length:889

    Alignment length:888
                                    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       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711       721       731       741       751       761       771       781       791       801       811       821       831       841       851       861       871       881        
           ACOC_RABIT     2 SNPFAYLAEPLDPAQPGKKFFNLNKLDYSRYGRLPFSIRVLLEAAVRNCDKFLVKKEDIENILNWNVTQHMNIEVPFKPARVILQDFTGVPSVVDFAAMRDAVKKLGGDPEKINPICPVDLVIDHSIQVDFNRRADSLQKNQDLEFERNRERFEFLKWGSKAFRNMRIIPPGSGIIHQVNLEYLARVVFDQDGYYYPDSLVGTDSHTTMIDGLGVLGWGVGGIEAEAVMLGQPISMVLPQVIGYRLMGKPHPLVTSTDIVLTITKHLRQVGVVGKFVEFFGLGVAQLSIADRATIANMCPEYGATATFFPVDEVSIKYLVQTGRDESKVKQIRKYLQAVGMFRDYSDPSQDPDFTQVVELDLKTVVPCCSGPKRPQDKVAVSDMKKDFESCLGAKQGFKGFQVAPDHHNDHKTFIYNDSEFTLSHGSVVIAAITSCTNTSNPSVMLGAGLLAKKAVDAGLNVKPYVKTSLSPGSGVVTYYLRESGVMPYLSQLGFDVVGYGCMTCIGNSGPLPEPVVEAITQGDLVAVGVLSGNRNFEGRVHPNTRANYLASPPLVIAYAIAGTIRIDFEKEPLGTNAKGQQVFLRDIWPTREEIQAVERQYVIPGMFTEVYQKIETVNASWNALAAPSDKLYLWNPKSTYIKSPPFFENLTLDLQPPKSIVDAYVLLNLGDSVTTDHISPAGNIARNSPAARYLTNRGLTPREFNSYGSRRGNDAIMARGTFANIRLLNRFLNKQAPQTIHLPSGETLDVFDAAERYQQEGHPLIVLAGKEYGSGSSRDWAAKGPFLLGIKAVLAESYERIHRSNLVGMGVIPLEYLPGENADSLGLTGRERYTIIIPENLTPRMHVQVKLDTGKTFQAVIRFDTDVELTYLHNGGILNYMIRKMAK 889
               SCOP domains d3sn2a1 A:2-630 automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    d3sn2a2 A:631-889 automated matches                                                                                                                                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhh.eee........eee.hhhhhhhhhh..hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh....eeee...eeeee...hhhhhhhhhhhhhhhhhh..hhhhh.....eeee..---------------------...hhhhhhhhhhhhhhh..eeee......hhhhhhhhhh..eeee..eeee.eeeee..hhhhhhhhh.eeee.hhhhhhhhhh...eeee...eeeeeee.......hhhhhhhhhhhhhhhhh....eeeeehhhhhhhhhhhhhhhhhhhhhhh..eee...hhhhhhhhhhh..hhhhhhhhhhhhhhhh......hhhhh....eeeeee......eee.......eee..hhhhhhhhhhhh...........hhhh.eeeee....eeeee...eeeeeee.....hhhhhhhhhhhhhhhhhhhh.......eeeee....hhhhhhhh..hhhhhhhh.....------------..hhhhhhhhhhhh...eeeee....hhhhh.....eeee.hhhhhhhhhhhh...........ee.....eehhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.-------................................eeeeeeeee.....hhhhhh........hhhhhhhhh...hhhhhh.hhhhh.hhhhhhhh.................eeee....eeeehhhhhhhhhhhh..eeee..............hhhhhhhheeeeee...hhhhhhhhhhhh.eeee.................eeee.........eeeeee....eeeeee...hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACONITASE_1      -------------------------------------------------ACONITASE_2   --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3sn2 A   2 SNPFAYLAEPLDPAQPGKKFFNLNKLDYSRYGRLPFSIRVLLEAAVRNCDKFLVKKEDIENILNWNVTQHMNIEVPFKPARVILQDFTGVPSVVDFAAMRDAVKKLGGDPEKINPICPVDLVID---------------------FERNRERFEFLKWGSKAFRNMRIIPPGSGIIHQVNLEYLARVVFDQDGYYYPDSLVGTDSHTTMIDGLGVLGWGVGGIEAEAVMLGQPISMVLPQVIGYRLMGKPHPLVTSTDIVLTITKHLRQVGVVGKFVEFFGPGVAQLSIADRATIANMCPEYGATATFFPVDEVSIKYLVQTGRDESKVKQIRKYLQAVGMFRDYSDPSQDPDFTQVVELDLKTVVPCCSGPKRPQDKVAVSDMKKDFESCLGAKQGFKGFQVAPDHHNDHKTFIYNDSEFTLSHGSVVIAAITSSTNTSNPSVMLGAGLLAKKAVDAGLNVKPYVKTSLSPGSGVVTYYLRESGVMPYLSQLGFDVV------------PLPEPVVEAITQGDLVAVGVLSGNRNFEGRVHPNTRANYLASPPLVIAYAIAGTIRIDFEKEPLGTNAKGQQVFLRDIWPTREEIQAVERQYVIPGMFTEVYQKIETVNAS-------SDKLYLWNPKSTYIKSPPFFENLTLDLQPPKSIVDAYVLLNLGDSVTTDHISPAGNIARNSPAARYLTNRGLTPREFNSYGSRRGNDAIMARGTFANIRLLNRFLNKQAPQTIHLPSGETLDVFDAAERYQQEGHPLIVLAGKEYGSGSSRDWAAKGPFLLGIKAVLAESYERIHRSNLVGMGVIPLEYLPGENADSLGLTGRERYTIIIPENLTPRMHVQVKLDTGKTFQAVIRFDTDVELTYFHNGGILNYMIRKMAK 889
                                    11        21        31        41        51        61        71        81        91       101       111       121   |     -         -     | 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       421       431       441       451       461       471       481       491       | -         -|      521       531       541       551       561       571       581       591       601       611       621|      631       641       651       661       671       681       691       701       711       721       731       741       751       761       771       781       791       801       811       821       831       841       851       861       871       881        
                                                                                                                                                     125                   147                                                                                                                                                                                                                                                                                                                                                             499          512                                                                                                           622     630                                                                                                                                                                                                                                                                   


Chain B from PDB  Type:RNA  Length:29
                                                             
                 3sn2 B   2 GAUUAUCGGAAGCAGUGCCUUCCAUAAUC  30
                                    11        21
   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  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3SN2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3SN2)

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (ACOC_RABIT | Q01059)
molecular function
    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:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0003994    aconitate hydratase activity    Catalysis of the reaction: citrate = isocitrate. The reaction occurs in two steps: (1) citrate = cis-aconitate + H2O, (2) cis-aconitate + H2O = isocitrate. This reaction is the interconversion of citrate and isocitrate via the labile, enzyme-bound intermediate cis-aconitate. Water is removed from one part of the citrate molecule and added back to a different atom to form isocitrate.
    GO:0030350    iron-responsive element binding    Interacting selectively and non-covalently with the iron-responsive element, a regulatory sequence found in the 5'- and 3'-untranslated regions of mRNAs encoding many iron-binding proteins.
    GO:0051536    iron-sulfur cluster binding    Interacting selectively and non-covalently with an iron-sulfur cluster, a combination of iron and sulfur atoms.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0006879    cellular iron ion homeostasis    Any process involved in the maintenance of an internal steady state of iron ions at the level of a cell.
    GO:0006101    citrate metabolic process    The chemical reactions and pathways involving citrate, 2-hydroxy-1,2,3-propanetricarboyxlate. Citrate is widely distributed in nature and is an important intermediate in the TCA cycle and the glyoxylate cycle.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0010040    response to iron(II) ion    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an iron(II) ion stimulus.
    GO:0006099    tricarboxylic acid cycle    A nearly universal metabolic pathway in which the acetyl group of acetyl coenzyme A is effectively oxidized to two CO2 and four pairs of electrons are transferred to coenzymes. The acetyl group combines with oxaloacetate to form citrate, which undergoes successive transformations to isocitrate, 2-oxoglutarate, succinyl-CoA, succinate, fumarate, malate, and oxaloacetate again, thus completing the cycle. In eukaryotes the tricarboxylic acid is confined to the mitochondria. See also glyoxylate cycle.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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  Cis Peptide Bonds
    Gly A:372 - Pro A:373   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        ACOC_RABIT | Q01059: 3snp

(-) Related Entries Specified in the PDB File

2ipy IRP1:FERRITIN H IRE COMPLEX
3snp THE SAME PROTEIN BOUND WITH A DIFFERENT IRE RNA