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(-) Description

Title :  CRYSTAL STRUCTURE OF THE SIALIC ACID BINDING PERIPLASMIC PROTEIN SIAP
 
Authors :  M. Fischer, R. E. Hubbard
Date :  05 Nov 09  (Deposition) - 26 Jan 11  (Release) - 26 Jan 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.37
Chains :  Asym./Biol. Unit :  A
Keywords :  Transport Protein, Sugar Transport, Trap Transporter (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Fischer, R. E. Hubbard
Crystal Structure Of The Sialic Acid Binding Periplasmic Protein Siap.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - SIALIC ACID-BINDING PERIPLASMIC PROTEIN SIAP
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PAH16
    Expression System Strain: BL21(DE3) PLYSS
    Expression System Taxid: 469008
    Expression System Vector: PET21B
    Mutation: YES
    Organism Scientific: HAEMOPHILUS INFLUENZAE
    Organism Taxid: 727
    Synonym: N-ACETYLNEURAMINIC-BINDING PROTEIN, NEU5AC-BINDING PROTEIN, EXTRACYTOPLASMIC SOLUTE RECEPTOR PROTEIN SIAP

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1NGE1Ligand/Ion3,5-DIDEOXY-5-[(HYDROXYACETYL)AMINO]-D-GLYCERO-BETA-D-GALACTO-NON-2-ULOPYRANOSONIC ACID

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:10 , ASP A:49 , PHE A:65 , ALA A:66 , GLU A:67 , ARG A:70 , ARG A:127 , ARG A:147 , PHE A:170 , ASN A:187 , GLN A:214 , HOH A:2046 , HOH A:2047 , HOH A:2130 , HOH A:2178 , HOH A:2546 , HOH A:2547 , HOH A:2548BINDING SITE FOR RESIDUE NGE A1309

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2WX9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2WX9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2WX9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2WX9)

(-) Exons   (0, 0)

(no "Exon" information available for 2WX9)

(-) Sequences/Alignments

Asymmetric/Biological 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:308
 aligned with SIAP_HAEIN | P44542 from UniProtKB/Swiss-Prot  Length:329

    Alignment length:308
                                                                                                                                                                                                                                                                                                                                           329  
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323     |  
           SIAP_HAEIN    24 ADYDLKFGMNAGTSSNEYKAAEMFAKEVKEKSQGKIEISLYPSSQLGDDRAMLKQLKDGSLDFTFAESARFQLFYPEAAVFALPYVISNYNVAQKALFDTEFGKDLIKKMDKDLGVTLLSQAYNGTRQTTSNRAINSIADMKGLKLRVPNAATNLAYAKYVGASPTPMAFSEVYLALQTNAVDGQENPLAAVQAQKFYEVQKFLAMTNHILNDQLYLVSNETYKELPEDLQKVVKDAAENAAKYHTKLFVDGEKDLVTFFEKQGVKITHPDLVPFKESMKPYYAEFVKQTGQKGESALKQIEAINP--   -
               SCOP domains d2wx9a_ A: automated matches                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------SBP_bac_7-2wx9A01 A:7-290                                                                                                                                                                                                                                                                   ------------------ Pfam domains
         Sec.struct. author ..eeeeee......hhhhhhhhhhhhhhhhhh...eeeeee......hhhhhhhhhhh....eeeehhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhheeeeeeeeeeeeeeee.....hhhhhh..eeee..hhhhhhhhhhhh.eeee.hhhhhhhhhhh....eeeeehhhhhhhhhhhh..eee.....eeeeeeeeehhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wx9 A   1 ADYDLKFGMNNGTSSNEYKAAEMFAKEVKEKSQGKIEISLYPSSQLGDDRAMLKQLKDGSLDFTFAESARFQLFYPEAAVFALPYVISNYNVAQKALFDTEFGKDLIKKMDKDLGVTLLSQAYNGTRQTTSNRAINSIADMKGLKLRVPNAATNLAYAKYVGASPTPMAFSEVYLALQTNAVDGQENPLAAVQAQKFYEVQKFLAMTNHILNDQLYLVSNETYKELPEDLQKVVKDAAENAAKYHTKLFVDGEKDLVTFFEKQGVKITHPDLVPFKESMKPYYAEFVKQTGQKGESALKQIEAINPHH 308
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300
   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)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2WX9)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: PBP (391)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (SIAP_HAEIN | P44542)
biological process
    GO:0008643    carbohydrate transport    The directed movement of carbohydrate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Carbohydrates are any of a group of organic compounds based of the general formula Cx(H2O)y.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0030288    outer membrane-bounded periplasmic space    The region between the inner (cytoplasmic or plasma) membrane and outer membrane of organisms with two membranes such as Gram negative bacteria. These periplasmic spaces are relatively thick and contain a thin peptidoglycan layer (PGL), also referred to as a thin cell wall.
    GO:0042597    periplasmic space    The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

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 Related Entries

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

UniProtKB/Swiss-Prot
        SIAP_HAEIN | P44542: 2cex 2cey 2v4c 2wyk 2wyp 2xa5 2xwi 2xwk 2xwo 2xwv 2xxk 3b50

(-) Related Entries Specified in the PDB File

2cex STRUCTURE OF A SIALIC ACID BINDING PROTEIN (SIAP) IN THE PRESENCE OF THE SIALIC ACID ACID ANALOGUE NEU5AC2EN
2cey APO STRUCTURE OF SIAP
2v4c STRUCTURE OF SIALIC ACID BINDING PROTEIN (SIAP) IN THE PRESENCE OF KDN
2wyk SIAP IN COMPLEX WITH NEU5GC
2wyp TO BE CONFIRMED
2xa5 STRUCTURE OF SUBSTRATE BINDING PROTEIN SIAP (A11N) IN COMPLEX WITH NEU5AC
2xwi SIAP R147K MUTANT IN COMPLEX WITH NEU5AC
2xwk SIAP R147A MUTANT IN COMPLEX WITH NEU5AC
2xwo SIAP R147E MUTANT IN COMPLEX WITH SIALYLAMIDE
2xwv SIAP COMPLEX
2xxk SIAP COMPLEX