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(-) Description

Title :  SOLUTION STRUCTURE OF THE ISDC NEAT DOMAIN BOUND TO ZINC PROTOPORPHYRIN
 
Authors :  V. A. Villareal, R. M. Pilpa, S. A. Robson, E. A. Fadeev, R. T. Clubb
Date :  06 Aug 08  (Deposition) - 19 Aug 08  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (30x)
Keywords :  Neat Domain, Nmr Complex, Heme, Isd, Isdc, Cell Wall, Iron, Metal-Binding, Peptidoglycan-Anchor, Secreted, Transport Protein, Heme-Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. A. Villareal, R. M. Pilpa, S. A. Robson, E. A. Fadeev, R. T. Clubb
The Isdc Protein From Staphylococcus Aureus Uses A Flexible Binding Pocket To Capture Heme.
J. Biol. Chem. V. 283 31591 2008
PubMed-ID: 18715872  |  Reference-DOI: 10.1074/JBC.M801126200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - IRON-REGULATED SURFACE DETERMINANT PROTEIN C
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector: PET15B
    Fragment: NEAT DOMAIN, UNP RESIDUES 25-150
    Gene: ISDC, SIRD, MW1013
    Organism Scientific: STAPHYLOCOCCUS AUREUS (STRAIN MW2)
    Organism Taxid: 196620
    Synonym: STAPHYLOCOCCAL IRON-REGULATED PROTEIN D

 Structural Features

(-) Chains, Units

  
NMR Structure (30x): 

Summary Information (see also Sequences/Alignments below)

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

NMR Structure (1, 1)
No.NameCountTypeFull Name
1ZNH1Ligand/IonPROTOPORPHYRIN IX CONTAINING ZN

(-) Sites  (1, 1)

NMR Structure (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:39 , LYS A:40 , TYR A:41 , ILE A:48 , ALA A:49 , TYR A:52 , PHE A:53 , HIS A:74 , TRP A:77 , ILE A:117 , ILE A:121 , TYR A:132BINDING SITE FOR RESIDUE ZNH A 151

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2K78)

(-) Cis Peptide Bonds  (1, 30)

NMR Structure
No.ModelResidues
11, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30Lys A:55 -Pro A:56

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2K78)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1NEATPS50978 NEAT domain profile.ISDC_STAAW27-150  1A:27-150

(-) Exons   (0, 0)

(no "Exon" information available for 2K78)

(-) Sequences/Alignments

NMR Structure
   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:126
 aligned with ISDC_STAAW | Q7A151 from UniProtKB/Swiss-Prot  Length:227

    Alignment length:126
                                    34        44        54        64        74        84        94       104       114       124       134       144      
           ISDC_STAAW    25 SANAADSGTLNYEVYKYNTNDTSIANDYFNKPAKYIKKNGKLYVQITVNHSHWITGMSIEGHKENIISKNTAKDERTSEFEVSKLNGKIDGKIDVYIDEKVNGKPFKYDHHYNITYKFNGPTDVAG 150
               SCOP domains d2k78a_ A: automated matches                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains NEAT-2k78A01 A:25-146                                                                                                     ---- Pfam domains
         Sec.struct. author ......eeeeeeeeee.......hhhhh....eeeee....eeeeeeee....eeeeee..ee.ee........eeeeeee.......eeeeeeeeeeee....eeeeeeeeeeeeeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --NEAT  PDB: A:27-150 UniProt: 27-150                                                                                          PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2k78 A  25 SANAADSGTLNYEVYKYNTNDTSIANDYFNKPAKYIKKNGKLYVQITVNHSHWITGMSIEGHKENIISKNTAKDERTSEFEVSKLNGKIDGKIDVYIDEKVNGKPFKYDHHYNITYKFNGPTDVAG 150
                                    34        44        54        64        74        84        94       104       114       124       134       144
   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, 1)

NMR Structure
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2K78)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: no clan defined [family: NEAT] (8)

(-) Gene Ontology  (6, 6)

NMR Structure(hide GO term definitions)
Chain A   (ISDC_STAAW | Q7A151)
molecular function
    GO:0030492    hemoglobin binding    Interacting selectively and non-covalently with hemoglobin, an oxygen carrying, conjugated protein containing four heme groups and globin.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0015886    heme transport    The directed movement of heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
cellular component
    GO:0005618    cell wall    The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, most prokaryotic cells and some protozoan parasites, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan; in protozoan parasites such as Giardia species, it's made of carbohydrates and proteins.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0009274    peptidoglycan-based cell wall    A protective structure outside the cytoplasmic membrane composed of peptidoglycan (also known as murein), a molecule made up of a glycan (sugar) backbone of repetitively alternating N-acetylglucosamine and N-acetylmuramic acid with short, attached, cross-linked peptide chains containing unusual amino acids. An example of this component is found in Escherichia coli.

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