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(-) Description

Title :  CRYSTAL STRUCTURE OF PROTEINACEOUS RNASE P 1 (PRORP1) FROM A. THALIANA WITH MN
 
Authors :  M. Koutmos, M. J. Howard, C. A. Fierke
Date :  11 Jul 12  (Deposition) - 26 Sep 12  (Release) - 14 Nov 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym./Biol. Unit :  A
Keywords :  Metallonuclease, Prorp, Ribonuclease, Pin, Trna Processing, Rnase P, Nyn Domain, Ppr Domain, Chloroplasts, Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. J. Howard, W. H. Lim, C. A. Fierke, M. Koutmos
Mitochondrial Ribonuclease P Structure Provides Insight Int The Evolution Of Catalytic Strategies For Precursor-Trna 5' Processing.
Proc. Natl. Acad. Sci. Usa V. 109 16149 2012
PubMed-ID: 22991464  |  Reference-DOI: 10.1073/PNAS.1209062109

(-) Compounds

Molecule 1 - PENTATRICOPEPTIDE REPEAT-CONTAINING PROTEIN AT2G32230, MITOCHONDRIAL
    Chains: A
    EC Number: 3.1.26.5
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PETM-11
    Expression System Strain: ROSETTA(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 77-572
    Gene: AT2G32230, F22D22.2
    Organism Common: MOUSE-EAR CRESS,THALE-CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
1ACA1Ligand/Ion6-AMINOHEXANOIC ACID
2MN2Ligand/IonMANGANESE (II) ION
3ZN1Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:344 , CYS A:347 , HIS A:548 , CYS A:565BINDING SITE FOR RESIDUE ZN A 1001
2AC2SOFTWAREASP A:475 , MN A:1003 , ACA A:1004 , HOH A:1218 , HOH A:1414 , HOH A:1423BINDING SITE FOR RESIDUE MN A 1002
3AC3SOFTWAREASP A:475 , ASP A:493 , ASP A:497 , MN A:1002 , ACA A:1004BINDING SITE FOR RESIDUE MN A 1003
4AC4SOFTWAREASN A:402 , VAL A:406 , ASP A:493 , MN A:1002 , MN A:1003 , HOH A:1172 , HOH A:1218 , HOH A:1423BINDING SITE FOR RESIDUE ACA A 1004

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4G24)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Cys A:107 -Ser A:108
2Gly A:392 -Pro A:393
3Gly A:445 -Pro A:446

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4G24)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4G24)

(-) Exons   (0, 0)

(no "Exon" information available for 4G24)

(-) 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:476
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh....hhhhhhhhhhhhhhh....hhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh.............eeeeee....................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeehhhhhhh.....hhhhhhhhhhhhhhhh......eeeeehhhhh.....hhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhh.eee......hhhhhh...hhhhhhhhhheeeeeee...eeeee.........ee.....eeee............eeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4g24 A  95 SPEALLKQKLDMCSKKGDVLEALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPGLSRGFDIFKQMIVDKVVPNEATFTNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPALFGFCRKGDADKAYEVDAHMVESEVVPEEPELAALLKVSMDTKNADKVYKTLQRLRDLVRQVSKSTFDMIEEWFKSEVATKTGVKKWDVKKIRDAVVSGGGGWHGQGWLGTGKWNVKRTEMDENGVCKCCKEKLVCIDINPVETETFAASLTRLACEREVKANFNQFQEWLERHGPFDAVIDGANMGLVNQRSFSFFQLNNTVQRCQQISPSKRLPLVILHKSRVNGGPATYPKNRALLEKWKNAGALYATPPGSNDDWYWLYAAVSCKCLLVTNDEMRDHLFQLLGNSFFPRWKEKHQVRISVTREDGLKLNMPPPYSIVIQESEDGTWHVPMSVEDDLQTSRQWLCAKRSK 570
                                   104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564
   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  (0, 0)

(no "SCOP Domain" information available for 4G24)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4G24)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4G24)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Cys A:107 - Ser A:108   [ RasMol ]  
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 Related Entries

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

UniProtKB/Swiss-Prot
        PRRP1_ARATH | Q66GI4: 4g23 4g25 4g26

(-) Related Entries Specified in the PDB File

4g23 4g25 4g26