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(-) Description

Title :  CRYSTAL STRUCTURE OF PAE0151 FROM PYROBACULUM AEROPHILUM
 
Authors :  R. D. Bunker, E. N. Baker, V. L. Arcus
Date :  15 Dec 05  (Deposition) - 27 Dec 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Pin Domain, Structural Genomics, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. D. Bunker, J. L. Mckenzie, E. N. Baker, V. L. Arcus
Crystal Structure Of Pae0151 From Pyrobaculum Aerophilum, A Pin-Domain (Vapc) Protein From A Toxin-Antitoxin Operon.
Proteins V. 72 510 2008
PubMed-ID: 18398909  |  Reference-DOI: 10.1002/PROT.22048

(-) Compounds

Molecule 1 - CONSERVED HYPOTHETICAL PROTEIN PAE0151
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PPROEX-HTA
    Expression System Strain: BL21(DE3) PRI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: PAE0151
    Gene: PAE0151
    Mutation: YES
    Organism Scientific: PYROBACULUM AEROPHILUM
    Organism Taxid: 178306
    Strain: IM2

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (3, 3)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2CL1Ligand/IonCHLORIDE ION
3MN1Ligand/IonMANGANESE (II) ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CL-1Ligand/IonCHLORIDE ION
3MN-1Ligand/IonMANGANESE (II) ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:118 , HOH A:323 , HOH A:370 , HOH A:377BINDING SITE FOR RESIDUE MN A 132
2AC2SOFTWARELYS A:49 , ARG A:52 , ARG A:53 , HOH A:309BINDING SITE FOR RESIDUE CL A 201
3AC3SOFTWAREASP A:86 , HOH A:380 , HOH A:381BINDING SITE FOR RESIDUE CA A 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2FE1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2FE1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2FE1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2FE1)

(-) Exons   (0, 0)

(no "Exon" information available for 2FE1)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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  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:130
 aligned with VAPC3_PYRAE | Q8ZZP3 from UniProtKB/Swiss-Prot  Length:131

    Alignment length:130
                                    10        20        30        40        50        60        70        80        90       100       110       120       130
          VAPC3_PYRAE     1 MKLVVDASAIAALYVPEERSEQAERAVSQAQELHTLDLAAYEVANDLWKHARRGLLREDEASNMLEELWEFFKALKVHSYAEVLKDAFALALKHGVTVYDAAYVALAEKIGGKLLTLDRQLAEKFPALVT 130
               SCOP domains d2fe1a1 A:1-130 Conserved hypothetical protein PAE0151                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeehhhhhhh.......hhhhhhhhhhh.eeeeehhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh..eeehhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.eee..hhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2fe1 A   1 MELVVDASAIAALYVPEERSEQAERAVSQAQELHTLDLAAYEVANDLWKHARRGLLREDEASNMLEELWEFFKALKVHSYAEVLKDAFALALKHGVTVYDAAYVALAEKIGGKLLTLDRQLAEKFPALVT 130
                                    10        20        30        40        50        60        70        80        90       100       110       120       130
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2FE1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2FE1)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A   (VAPC3_PYRAE | Q8ZZP3)
molecular function
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
    GO:0004540    ribonuclease activity    Catalysis of the hydrolysis of phosphodiester bonds in chains of RNA.
biological process
    GO:0090501    RNA phosphodiester bond hydrolysis    The RNA metabolic process in which the phosphodiester bonds between ribonucleotides are cleaved by hydrolysis.
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.

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