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(-) Description

Title :  STRUCTURE OF A SIALIC ACID BINDING PROTEIN (SIAP) IN THE PRESENCE OF THE SIALIC ACID ACID ANALOGUE NEU5AC2EN
 
Authors :  A. Muller, E. Severi, C. Mulligan, A. G. Watts, D. J. Kelly, K. S. Wilson, A. J. Wilkinson, G. H. Thomas
Date :  10 Feb 06  (Deposition) - 15 May 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Esr, Periplasmic Binding Protein, Tripartite Atp-Independent Periplasmic (Trap)Transport, Virulence Factor, Transport, Periplasmic (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Muller, E. Severi, C. Mulligan, A. G. Watts, D. J. Kelly, K. S. Wilson A. J. Wilkinson, G. H. Thomas
Conservation Of Structure And Mechanism In Primary And Secondary Transporters Exemplified By Siap, A Sialic Acid Binding Virulence Factor From Haemophilus Influenzae
J. Biol. Chem. V. 281 22212 2006
PubMed-ID: 16702222  |  Reference-DOI: 10.1074/JBC.M603463200

(-) Compounds

Molecule 1 - PROTEIN HI0146
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: HAEMOPHILUS INFLUENZAE
    Organism Taxid: 727
    Synonym: SIAP

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 10)

Asymmetric Unit (3, 10)
No.NameCountTypeFull Name
1DAN1Ligand/Ion2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID
2GOL3Ligand/IonGLYCEROL
3ZN6Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1DAN-1Ligand/Ion2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID
2GOL-1Ligand/IonGLYCEROL
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1DAN1Ligand/Ion2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID
2GOL2Ligand/IonGLYCEROL
3ZN-1Ligand/IonZINC ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1DAN-1Ligand/Ion2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID
2GOL-1Ligand/IonGLYCEROL
3ZN-1Ligand/IonZINC ION
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1DAN-1Ligand/Ion2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID
2GOL1Ligand/IonGLYCEROL
3ZN-1Ligand/IonZINC ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:2 , ASP A:4 , HOH A:2088BINDING SITE FOR RESIDUE ZN A1306
02AC2SOFTWAREHIS A:269 , HIS B:269 , HOH B:2145 , HOH B:2146BINDING SITE FOR RESIDUE ZN B1310
03AC3SOFTWAREASP B:2 , ASP B:4 , HOH B:2147BINDING SITE FOR RESIDUE ZN B1311
04AC4SOFTWAREHIS C:269 , HOH C:2096 , HOH C:2097 , HIS D:269BINDING SITE FOR RESIDUE ZN C1306
05AC5SOFTWAREASP C:2 , ASP C:4BINDING SITE FOR RESIDUE ZN C1307
06AC6SOFTWAREASP D:2 , ASP D:4 , HOH D:2122BINDING SITE FOR RESIDUE ZN D1307
07AC7SOFTWAREASN B:10 , ASP B:49 , PHE B:65 , GLU B:67 , ARG B:127 , ARG B:147 , ALA B:151 , PHE B:170 , ASN B:187 , GLN B:214 , HOH B:2011 , HOH B:2038 , HOH B:2140 , HOH B:2141 , HOH B:2142 , HOH B:2144BINDING SITE FOR RESIDUE DAN B1307
08AC8SOFTWARESER B:137 , ILE B:138 , ASP B:271 , PRO B:274 , HOH B:2079BINDING SITE FOR RESIDUE GOL B1308
09AC9SOFTWARELYS B:159BINDING SITE FOR RESIDUE GOL B1309
10BC1SOFTWARELEU B:40 , TYR B:41 , GLN B:45 , HOH B:2026 , THR D:100 , GLU D:101 , GLN D:300BINDING SITE FOR RESIDUE GOL D1306

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2CEX)

(-) 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:304
 aligned with SIAP_HAEIN | P44542 from UniProtKB/Swiss-Prot  Length:329

    Alignment length:304
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324    
           SIAP_HAEIN    25 DYDLKFGMNAGTSSNEYKAAEMFAKEVKEKSQGKIEISLYPSSQLGDDRAMLKQLKDGSLDFTFAESARFQLFYPEAAVFALPYVISNYNVAQKALFDTEFGKDLIKKMDKDLGVTLLSQAYNGTRQTTSNRAINSIADMKGLKLRVPNAATNLAYAKYVGASPTPMAFSEVYLALQTNAVDGQENPLAAVQAQKFYEVQKFLAMTNHILNDQLYLVSNETYKELPEDLQKVVKDAAENAAKYHTKLFVDGEKDLVTFFEKQGVKITHPDLVPFKESMKPYYAEFVKQTGQKGESALKQIEAIN 328
               SCOP domains d2cexa_ A: Sialic acid-binding protein SiaP                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee......hhhhhhhhhhhhhhhhhh...eeeeee......hhhhhhhhhhh....eeee.hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeeeeeeeeee.....hhhhhh..eeee..hhhhhhhhhhh..eeee.hhhhhhhhhhh....eeeeehhhhhhhhhhhh..eee.....eeeeeeeeehhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2cex A   2 DYDLKFGMNAGTSSNEYKAAEMFAKEVKEKSQGKIEISLYPSSQLGDDRAMLKQLKDGSLDFTFAESARFQLFYPEAAVFALPYVISNYNVAQKALFDTEFGKDLIKKMDKDLGVTLLSQAYNGTRQTTSNRAINSIADMKGLKLRVPNAATNLAYAKYVGASPTPMAFSEVYLALQTNAVDGQENPLAAVQAQKFYEVQKFLAMTNHILNDQLYLVSNETYKELPEDLQKVVKDAAENAAKYHTKLFVDGEKDLVTFFEKQGVKITHPDLVPFKESMKPYYAEFVKQTGQKGESALKQIEAIN 305
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301    


Chain B from PDB  Type:PROTEIN  Length:305
 aligned with SIAP_HAEIN | P44542 from UniProtKB/Swiss-Prot  Length:329

    Alignment length:305
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324     
           SIAP_HAEIN    25 DYDLKFGMNAGTSSNEYKAAEMFAKEVKEKSQGKIEISLYPSSQLGDDRAMLKQLKDGSLDFTFAESARFQLFYPEAAVFALPYVISNYNVAQKALFDTEFGKDLIKKMDKDLGVTLLSQAYNGTRQTTSNRAINSIADMKGLKLRVPNAATNLAYAKYVGASPTPMAFSEVYLALQTNAVDGQENPLAAVQAQKFYEVQKFLAMTNHILNDQLYLVSNETYKELPEDLQKVVKDAAENAAKYHTKLFVDGEKDLVTFFEKQGVKITHPDLVPFKESMKPYYAEFVKQTGQKGESALKQIEAINP 329
               SCOP domains d2cexb_ B: Sialic acid-binding protein SiaP                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee......hhhhhhhhhhhhhhhhhh...eeeeee......hhhhhhhhhhh....eeeehhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeeeeeeeeee.....hhhhhh..eeee..hhhhhhhhhhhh.eeee.hhhhhhhhhhh....eeeeehhhhhhh.......eeeeeeeeeeeeeeeeehhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2cex B   2 DYDLKFGMNAGTSSNEYKAAEMFAKEVKEKSQGKIEISLYPSSQLGDDRAMLKQLKDGSLDFTFAESARFQLFYPEAAVFALPYVISNYNVAQKALFDTEFGKDLIKKMDKDLGVTLLSQAYNGTRQTTSNRAINSIADMKGLKLRVPNAATNLAYAKYVGASPTPMAFSEVYLALQTNAVDGQENPLAAVQAQKFYEVQKFLAMTNHILNDQLYLVSNETYKELPEDLQKVVKDAAENAAKYHTKLFVDGEKDLVTFFEKQGVKITHPDLVPFKESMKPYYAEFVKQTGQKGESALKQIEAINP 306
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301     


Chain C from PDB  Type:PROTEIN  Length:300
 aligned with SIAP_HAEIN | P44542 from UniProtKB/Swiss-Prot  Length:329

    Alignment length:304
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324    
           SIAP_HAEIN    25 DYDLKFGMNAGTSSNEYKAAEMFAKEVKEKSQGKIEISLYPSSQLGDDRAMLKQLKDGSLDFTFAESARFQLFYPEAAVFALPYVISNYNVAQKALFDTEFGKDLIKKMDKDLGVTLLSQAYNGTRQTTSNRAINSIADMKGLKLRVPNAATNLAYAKYVGASPTPMAFSEVYLALQTNAVDGQENPLAAVQAQKFYEVQKFLAMTNHILNDQLYLVSNETYKELPEDLQKVVKDAAENAAKYHTKLFVDGEKDLVTFFEKQGVKITHPDLVPFKESMKPYYAEFVKQTGQKGESALKQIEAIN 328
               SCOP domains d2cexc_ C: Sialic acid-binding     protein SiaP                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee......hhhhhhhhhhhhhh...----..eeee......hhhhhhhhhhh....eeeehhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeeeeeeeeee.....hhhhh...eee...hhhhhhhhhhh..eee..hhhhhhhhhhh....eeeeehhhhhhhhhhhh..eeeeeeeeeeeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee...hhhhhhhhhhhhhhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2cex C   2 DYDLKFGMNAGTSSNEYKAAEMFAKEVKEK----IEISLYPSSQLGDDRAMLKQLKDGSLDFTFAESARFQLFYPEAAVFALPYVISNYNVAQKALFDTEFGKDLIKKMDKDLGVTLLSQAYNGTRQTTSNRAINSIADMKGLKLRVPNAATNLAYAKYVGASPTPMAFSEVYLALQTNAVDGQENPLAAVQAQKFYEVQKFLAMTNHILNDQLYLVSNETYKELPEDLQKVVKDAAENAAKYHTKLFVDGEKDLVTFFEKQGVKITHPDLVPFKESMKPYYAEFVKQTGQKGESALKQIEAIN 305
                                    11        21        31    |   41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301    
                                                        31   36                                                                                                                                                                                                                                                                             


Chain D from PDB  Type:PROTEIN  Length:305
 aligned with SIAP_HAEIN | P44542 from UniProtKB/Swiss-Prot  Length:329

    Alignment length:305
                                    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 ADYDLKFGMNAGTSSNEYKAAEMFAKEVKEKSQGKIEISLYPSSQLGDDRAMLKQLKDGSLDFTFAESARFQLFYPEAAVFALPYVISNYNVAQKALFDTEFGKDLIKKMDKDLGVTLLSQAYNGTRQTTSNRAINSIADMKGLKLRVPNAATNLAYAKYVGASPTPMAFSEVYLALQTNAVDGQENPLAAVQAQKFYEVQKFLAMTNHILNDQLYLVSNETYKELPEDLQKVVKDAAENAAKYHTKLFVDGEKDLVTFFEKQGVKITHPDLVPFKESMKPYYAEFVKQTGQKGESALKQIEAIN 328
               SCOP domains d2cexd_ D: Sialic acid-binding protein SiaP                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee......hhhhhhhhhhhhhhhhhh...eeeeee......hhhhhhhhhhh....eeeehhhhhhh.hhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeeeeeeeeee.............eee...hhhhhhhhhhh..eee..hhhhhhhhhhh....eeeeehhhhhhh.......eeeeeeeeeeeeeeeeehhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2cex D   1 ADYDLKFGMNAGTSSNEYKAAEMFAKEVKEKSQGKIEISLYPSSQLGDDRAMLKQLKDGSLDFTFAESARFQLFYPEAAVFALPYVISNYNVAQKALFDTEFGKDLIKKMDKDLGVTLLSQAYNGTRQTTSNRAINSIADMKGLKLRVPNAATNLAYAKYVGASPTPMAFSEVYLALQTNAVDGQENPLAAVQAQKFYEVQKFLAMTNHILNDQLYLVSNETYKELPEDLQKVVKDAAENAAKYHTKLFVDGEKDLVTFFEKQGVKITHPDLVPFKESMKPYYAEFVKQTGQKGESALKQIEAIN 305
                                    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)
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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, 4)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (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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  2cex
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  SIAP_HAEIN | P44542
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 Related Entries

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

UniProtKB/Swiss-Prot
        SIAP_HAEIN | P44542: 2cey 2v4c 2wx9 2wyk 2wyp 2xa5 2xwi 2xwk 2xwo 2xwv 2xxk 3b50

(-) Related Entries Specified in the PDB File

2cey APO STRUCTURE OF SIAP