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(-) Description

Title :  CRYSTAL STRUCTURE OF STAPHYLOCOCCUS AUREUS HYPOTHETICAL PROTEIN SA1388
 
Authors :  K. S. Singh, X. Zhang, H. Zhang
Date :  20 Nov 06  (Deposition) - 09 Jan 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (3x)
Keywords :  Hypothetical Protein Sa1388, Selenomethionine Sad, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Singh Saikatendu, X. Zhang, L. Kinch, M. Leybourne, N. V. Grishin, H. Zhang
Structure Of A Conserved Hypothetical Protein Sa1388 From S Aureus Reveals A Capped Hexameric Toroid With Two Pii Domai Lids And A Dinuclear Metal Center.
Bmc Struct. Biol. V. 6 27 2006
PubMed-ID: 17187687  |  Reference-DOI: 10.1186/1472-6807-6-27

(-) Compounds

Molecule 1 - UPF0135 PROTEIN SA1388
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: P-PROEX
    Gene: SA1388
    Organism Scientific: STAPHYLOCOCCUS AUREUS SUBSP. AUREUS
    Organism Taxid: 158879
    Strain: N315

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (3x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1ZN4Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:64 , ASP A:102 , GLU A:329 , ZN A:402 , HOH A:604BINDING SITE FOR RESIDUE ZN A 401
2AC2SOFTWAREHIS A:65 , HIS A:326 , GLU A:329 , ZN A:401 , HOH A:604 , HOH B:660BINDING SITE FOR RESIDUE ZN A 402
3AC3SOFTWAREHOH A:579 , HIS B:65 , HIS B:326 , GLU B:329 , ZN B:402 , HOH B:615BINDING SITE FOR RESIDUE ZN B 401
4AC4SOFTWAREHIS B:64 , ASP B:102 , GLU B:329 , ZN B:401 , HOH B:615BINDING SITE FOR RESIDUE ZN B 402

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2NYD)

(-) Sequences/Alignments

Asymmetric 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:300
 aligned with GCH1L_STAAM | P67272 from UniProtKB/Swiss-Prot  Length:366

    Alignment length:368
                              1                                                                                                                                                                                                                                                                                                                                                                             
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358        
          GCH1L_STAAM     - --MKIADLMTLLDHHVPFSTAESWDNVGLLIGDGDVEVTGVLTALDCTLEVVNEAIEKGYNTIISHHPLIFKGVTSLKANGYGLIIRKLIQHDINLIAMHTNLDVNPYGVNMMLAKAMGLKNISIINNQQDVYYKVQTYIPKDNVGPFKDKLSENGLAQEGNYEYCFFESEGRGQFKPVGEANPTIGQIDKIEDVDEVKIEFMIDAYQKSRAEQLIKQYHPYETPVFDFIEIKQTSLYGLGVMAEVDNQMTLEDFAADIKSKLNIPSVRFVGESNQKIKRIAIIGGSGIGYEYQAVQQGADVFVTGDIKHHDALDAKIHGVNLIDINHYSEYVMKEGLKTLLMNWFNIEKINIDVEASTINTDPFQYI 366
               SCOP domains d2nyda_ A: automated matches                                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhh......eeee.........eeee...hhhhhhhhhhhh..eeee...............hhhhhhhhhhhh..eeee.hhhhhh...hhhhhhhhhh..eeeee..eeeeeeeeee---------------------------------------------------------------.eee..hhhhhhhhhhh.-----....eeeeeeeeeeee..eeeeeeeeeehhhhhhhhhhhh.....eee.....eeeeeee.......hhhhhhhh...eeee...hhhhhhhhhhh...eee.hhhhhhhhhhhhhhhhhhhhhhh.....eee........eee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2nyd A  -1 DPMKIADLMTLLDHHVPFSTAESWDNVGLLIGDEDVEVTGVLTALDCTLEVVNEAIEKGYNTIISHHPLIFKGVTSLKANGYGLIIRKLIQHDINLIAMHTNLDVNPYGVNMMLAKVMGLKNISIINNQQDVYYKVQ---------------------------------------------------------------EFMIDAYQKSRAEQLIKQ-----TPVFDFIEIKQTSLYGLGVMAEVDNQMTLEDFAADIKSKLNIPSVRFVGESNQKIKRIAIIGGSGIGYEYQAVQQGADVFVTGDIKHHDALDAKIHGVNLIDINHYSEYVMKEGLKTLLMNWFNIEKINIDVEASTINTDPFQYI 366
                                     8        18        28        38        48        58        68        78        88        98       108       118       128      |  -         -         -         -         -         -         -|      208       | -   |   228       238       248       258       268       278       288       298       308       318       328       338       348       358        
                                                                                                                                                                  135                                                             199              216   222                                                                                                                                                


Chain A from PDB  Type:PROTEIN  Length:300
 aligned with GCH1L_STAAN | P67273 from UniProtKB/Swiss-Prot  Length:366

    Alignment length:368
                              1                                                                                                                                                                                                                                                                                                                                                                             
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358        
          GCH1L_STAAN     - --MKIADLMTLLDHHVPFSTAESWDNVGLLIGDGDVEVTGVLTALDCTLEVVNEAIEKGYNTIISHHPLIFKGVTSLKANGYGLIIRKLIQHDINLIAMHTNLDVNPYGVNMMLAKAMGLKNISIINNQQDVYYKVQTYIPKDNVGPFKDKLSENGLAQEGNYEYCFFESEGRGQFKPVGEANPTIGQIDKIEDVDEVKIEFMIDAYQKSRAEQLIKQYHPYETPVFDFIEIKQTSLYGLGVMAEVDNQMTLEDFAADIKSKLNIPSVRFVGESNQKIKRIAIIGGSGIGYEYQAVQQGADVFVTGDIKHHDALDAKIHGVNLIDINHYSEYVMKEGLKTLLMNWFNIEKINIDVEASTINTDPFQYI 366
               SCOP domains d2nyda_ A: automated matches                                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhh......eeee.........eeee...hhhhhhhhhhhh..eeee...............hhhhhhhhhhhh..eeee.hhhhhh...hhhhhhhhhh..eeeee..eeeeeeeeee---------------------------------------------------------------.eee..hhhhhhhhhhh.-----....eeeeeeeeeeee..eeeeeeeeeehhhhhhhhhhhh.....eee.....eeeeeee.......hhhhhhhh...eeee...hhhhhhhhhhh...eee.hhhhhhhhhhhhhhhhhhhhhhh.....eee........eee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2nyd A  -1 DPMKIADLMTLLDHHVPFSTAESWDNVGLLIGDEDVEVTGVLTALDCTLEVVNEAIEKGYNTIISHHPLIFKGVTSLKANGYGLIIRKLIQHDINLIAMHTNLDVNPYGVNMMLAKVMGLKNISIINNQQDVYYKVQ---------------------------------------------------------------EFMIDAYQKSRAEQLIKQ-----TPVFDFIEIKQTSLYGLGVMAEVDNQMTLEDFAADIKSKLNIPSVRFVGESNQKIKRIAIIGGSGIGYEYQAVQQGADVFVTGDIKHHDALDAKIHGVNLIDINHYSEYVMKEGLKTLLMNWFNIEKINIDVEASTINTDPFQYI 366
                                     8        18        28        38        48        58        68        78        88        98       108       118       128      |  -         -         -         -         -         -         -|      208       | -   |   228       238       248       258       268       278       288       298       308       318       328       338       348       358        
                                                                                                                                                                  135                                                             199              216   222                                                                                                                                                


Chain B from PDB  Type:PROTEIN  Length:348
 aligned with GCH1L_STAAM | P67272 from UniProtKB/Swiss-Prot  Length:366

    Alignment length:370
                                1                                                                                                                                                                                                                                                                                                                                                                             
                                |    6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366
          GCH1L_STAAM     - ----MKIADLMTLLDHHVPFSTAESWDNVGLLIGDGDVEVTGVLTALDCTLEVVNEAIEKGYNTIISHHPLIFKGVTSLKANGYGLIIRKLIQHDINLIAMHTNLDVNPYGVNMMLAKAMGLKNISIINNQQDVYYKVQTYIPKDNVGPFKDKLSENGLAQEGNYEYCFFESEGRGQFKPVGEANPTIGQIDKIEDVDEVKIEFMIDAYQKSRAEQLIKQYHPYETPVFDFIEIKQTSLYGLGVMAEVDNQMTLEDFAADIKSKLNIPSVRFVGESNQKIKRIAIIGGSGIGYEYQAVQQGADVFVTGDIKHHDALDAKIHGVNLIDINHYSEYVMKEGLKTLLMNWFNIEKINIDVEASTINTDPFQYI 366
               SCOP domains d2nydb_ B: automated matches                                                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhh......eeee.........eeee...hhhhhhhhhhhh..eeee..............hhhhhhhhhhhhh..eeee.hhhhhh...hhhhhhhhhh..eeeee..eeeeeeeeeeeee...hhhhhhhhhhhhh......eeeeeee.----------------------..eeeeeeeeeee..hhhhhhhhhhhhh......eeeeeeeeeeeee..eeeeeeeeeehhhhhhhhhhhh....eeee.....eeeeeee.......hhhhhhhh...eeee...hhhhhhhhhhh...eee.hhhhhhhhhhhhhhhhhhhhhhh.....eee.......eee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2nyd B  -3 AMDPMKIADLMTLLDHHVPFSTAESWDNVGLLIGDEDVEVTGVLTALDCTLEVVNEAIEKGYNTIISHHPLIFKGVTSLKANGYGLIIRKLIQHDINLIAMHTNLDVNPYGVNMMLAKVMGLKNISIINNQQDVYYKVQTYIPKDNVGPFKDKLSENGLAQEGNYEYCFFES----------------------EDVDEVKIEFMIDAYQKSRAEQLIKQYHPYETPVFDFIEIKQTSLYGLGVMAEVDNQMTLEDFAADIKSKLNIPSVRFVGESNQKIKRIAIIGGSGIGYEYQAVQQGADVFVTGDIKHHDALDAKIHGVNLIDINHYSEYVMKEGLKTLLMNWFNIEKINIDVEASTINTDPFQYI 366
                                     6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166 |       -         -    |  196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366
                                                                                                                                                                                                     168                    191                                                                                                                                                                               


Chain B from PDB  Type:PROTEIN  Length:348
 aligned with GCH1L_STAAN | P67273 from UniProtKB/Swiss-Prot  Length:366

    Alignment length:370
                                1                                                                                                                                                                                                                                                                                                                                                                             
                                |    6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366
          GCH1L_STAAN     - ----MKIADLMTLLDHHVPFSTAESWDNVGLLIGDGDVEVTGVLTALDCTLEVVNEAIEKGYNTIISHHPLIFKGVTSLKANGYGLIIRKLIQHDINLIAMHTNLDVNPYGVNMMLAKAMGLKNISIINNQQDVYYKVQTYIPKDNVGPFKDKLSENGLAQEGNYEYCFFESEGRGQFKPVGEANPTIGQIDKIEDVDEVKIEFMIDAYQKSRAEQLIKQYHPYETPVFDFIEIKQTSLYGLGVMAEVDNQMTLEDFAADIKSKLNIPSVRFVGESNQKIKRIAIIGGSGIGYEYQAVQQGADVFVTGDIKHHDALDAKIHGVNLIDINHYSEYVMKEGLKTLLMNWFNIEKINIDVEASTINTDPFQYI 366
               SCOP domains d2nydb_ B: automated matches                                                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhh......eeee.........eeee...hhhhhhhhhhhh..eeee..............hhhhhhhhhhhhh..eeee.hhhhhh...hhhhhhhhhh..eeeee..eeeeeeeeeeeee...hhhhhhhhhhhhh......eeeeeee.----------------------..eeeeeeeeeee..hhhhhhhhhhhhh......eeeeeeeeeeeee..eeeeeeeeeehhhhhhhhhhhh....eeee.....eeeeeee.......hhhhhhhh...eeee...hhhhhhhhhhh...eee.hhhhhhhhhhhhhhhhhhhhhhh.....eee.......eee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2nyd B  -3 AMDPMKIADLMTLLDHHVPFSTAESWDNVGLLIGDEDVEVTGVLTALDCTLEVVNEAIEKGYNTIISHHPLIFKGVTSLKANGYGLIIRKLIQHDINLIAMHTNLDVNPYGVNMMLAKVMGLKNISIINNQQDVYYKVQTYIPKDNVGPFKDKLSENGLAQEGNYEYCFFES----------------------EDVDEVKIEFMIDAYQKSRAEQLIKQYHPYETPVFDFIEIKQTSLYGLGVMAEVDNQMTLEDFAADIKSKLNIPSVRFVGESNQKIKRIAIIGGSGIGYEYQAVQQGADVFVTGDIKHHDALDAKIHGVNLIDINHYSEYVMKEGLKTLLMNWFNIEKINIDVEASTINTDPFQYI 366
                                     6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166 |       -         -    |  196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366
                                                                                                                                                                                                     168                    191
   Legend:   → Mismatch (orange background)
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  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, 2)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (1, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (GCH1L_STAAN | P67273)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

Chain A,B   (GCH1L_STAAM | P67272)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

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  2nyd
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 Related Entries

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

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        GCH1L_STAAM | P67272: 3lnl
        GCH1L_STAAN | P67273: 3lnl

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