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(-) Description

Title :  CRYSTAL STRUCTURE HP-NAP FROM STRAIN YS39 IN APO FORM
 
Authors :  O. Tsuruta, H. Yokoyama, S. Fujii
Date :  03 Aug 11  (Deposition) - 08 Feb 12  (Release) - 25 Apr 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (12x)
Keywords :  Dodecamer, Four-Helix Bundle, Metal Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  O. Tsuruta, H. Yokoyama, S. Fujii
A New Crystal Lattice Structure Of Helicobacter Pylori Neutrophil-Activating Protein (Hp-Nap)
Acta Crystallogr. , Sect. F V. 68 134 2012
PubMed-ID: 22297984  |  Reference-DOI: 10.1107/S1744309111052675

(-) Compounds

Molecule 1 - NEUTROPHIL-ACTIVATING PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-15B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: NAPA
    Organism Scientific: HELICOBACTER PYLORI
    Organism Taxid: 210
    Strain: YS39
    Synonym: BACTERIOFERRITIN, HP-NAP, NEUTROPHIL-ACTIVATING PROTEIN A, NAP A

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (12x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
Biological Unit 1 (1, 12)
No.NameCountTypeFull Name
1EDO12Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:43 , GLY A:46 , PHE A:47 , MET A:50 , TYR A:99 , HOH A:358BINDING SITE FOR RESIDUE EDO A 201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3T9J)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3T9J)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3T9J)

(-) Exons   (0, 0)

(no "Exon" information available for 3T9J)

(-) 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    
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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:144
 aligned with G1UIZ3_HELPX | G1UIZ3 from UniProtKB/TrEMBL  Length:144

    Alignment length:144
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140    
         G1UIZ3_HELPX     1 MKTFEILKHLQADAIVLFMKVHNFHWNVKGTDFFNVHKATEEIYEGFADMFDDLAERIAQLGHHPLVTLSEALKLTRVKEETKTSFHSKDIFKEILEDYKHLEKEFKELSNTAEKEGDKVTVTYADDQLAKLQKSIWMLQAHLA 144
               SCOP domains d3t9ja_ A: Dodecameric ferritin homolog                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3t9j A   1 MKTFEILKHLQADAIVLFMKVHNFHWNVKGTDFFNVHKATEEIYEGFADMFDDLAERIAQLGHHPLVTLSEALKLTRVKEETKTSFHSKDIFKEILEDYKHLEKEFKELSNTAEKEGDKVTVTYADDQLAKLQKSIWMLQAHLA 144
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140
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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: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3T9J)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3T9J)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A   (G1UIZ3_HELPX | G1UIZ3)
molecular function
    GO:0008199    ferric iron binding    Interacting selectively and non-covalently with ferric iron, Fe(III).
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016722    oxidoreductase activity, oxidizing metal ions    Catalysis of an oxidation-reduction in which the oxidation state of metal ion is altered.
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: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.
    GO:0006950    response to stress    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 a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).
cellular component
    GO:0005623    cell    The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope.

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 Related Entries

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

UniProtKB/TrEMBL
        G1UIZ3_HELPX | G1UIZ3: 3ta8 4evb 4evc

(-) Related Entries Specified in the PDB File

3ta8