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(-) Description

Title :  CRYSTAL STRUCTURE OF NEAT DOMAIN FROM STAPHYLOCOCCUS AUREUS IN COMPLEX WITH HEME
 
Authors :  Y. Tanaka, A. Suenaga, K. Tsumoto
Date :  31 Jul 07  (Deposition) - 29 Jul 08  (Release) - 09 Dec 08  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Igg-Like Fold, Cell Wall, Peptidoglycan-Anchor, Secreted, Heme Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Watanabe, Y. Tanaka, A. Suenaga, M. Kuroda, M. Yao, N. Watanabe, F. Arisaka, T. Ohta, I. Tanaka, K. Tsumoto
Structural Basis For Multimeric Heme Complexation Through A Specific Protein-Heme Interaction: The Case Of The Third Neat Domain Of Isdh From Staphylococcus Aureus
J. Biol. Chem. V. 283 28649 2008
PubMed-ID: 18667422  |  Reference-DOI: 10.1074/JBC.M803383200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - IRON-REGULATED SURFACE DETERMINANT PROTEIN H
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PDBHT3
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: NEAT 3 DOMAIN, RESIDUE 539-664
    Gene: ISDH
    Organism Scientific: STAPHYLOCOCCUS AUREUS
    Organism Taxid: 158878
    Strain: MU50
    Synonym: HAPTOGLOBIN RECEPTOR A, STAPHYLOCOCCUS AUREUS SURFACE PROTEIN I

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:2 , HOH A:33 , HOH A:76 , SER A:563 , VAL A:564 , PHE A:568 , TRP A:594 , VAL A:635 , ILE A:640 , TYR A:642 , TYR A:646 , VAL A:648BINDING SITE FOR RESIDUE HEM A3747

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Z6F)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1His A:571 -Pro A:572

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Z6F)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2Z6F)

(-) Exons   (0, 0)

(no "Exon" information available for 2Z6F)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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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:112
 aligned with ISDH_STAAM | Q931P4 from UniProtKB/Swiss-Prot  Length:891

    Alignment length:112
                                   553       563       573       583       593       603       613       623       633       643       653  
           ISDH_STAAM   544 LTDLQEAHFVVFESEENSESVMDGFVEHPFYTATLNGQKYVVMKTKDDSYWKDLIVEGKRVTTVSKDPKNNSRTLIFPYIPDKAVYNAIVKVVVANIGYEGQYHVRIINQDI 655
               SCOP domains d2z6fa_ A: automated matches                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains NEAT-2z6fA01 A:544-655                                                                                           Pfam domains
         Sec.struct. author .eeeeee.eeeee......hhhhhh....eeeeee..eeeeeee..hhh.eeeeee..ee.eeeeeehhhheeeeeee......eeeeeeeeeehhhheeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------- Transcript
                 2z6f A 544 LTDLQEAHFVVFESEENSESVMDGFVEHPFYTATLNGQKYVVMKTKDDSYWKDLIVEGKRVTTVSKDPKNNSRTLIFPYIPDKAVYNAIVKVVVANIGYEGQYHVRIINQDI 655
                                   553       563       573       583       593       603       613       623       633       643       653
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 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2Z6F)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: no clan defined [family: NEAT] (8)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A   (ISDH_STAAM | Q931P4)
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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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 Related Entries

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

UniProtKB/Swiss-Prot
        ISDH_STAAM | Q931P4: 2e7d 3qug 3quh 3vtm 3vua

(-) Related Entries Specified in the PDB File

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