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(-) Description

Title :  P22 TAILSPIKE COMPLEXED WITH S.PARATYPHI O ANTIGEN OCTASACCHARIDE
 
Authors :  D. Andres, U. Gohlke, U. Heinemann, R. Seckler, S. Barbirz
Date :  18 Aug 11  (Deposition) - 29 Aug 12  (Release) - 13 Aug 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Keywords :  Viral Adhesion Protein, Receptor, Endoglycosidase, Carbohydrate, Cell Receptor, Recognition, Binding Protein Lipopolysaccharide, Beta Helix, Host Recognition, Bacteriophage P22 Baseplate, Hydrolase, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Andres, U. Gohlke, N. K. Broeker, S. Schulze, W. Rabsch, U. Heinemann, S. Barbirz, R. Seckler
An Essential Serotype Recognition Pocket On Phage P22 Tailspike Protein Forces Salmonella Enterica Serovar Paratyphi A O-Antigen Fragments To Bind As Nonsolution Conformers.
Glycobiology V. 23 486 2013
PubMed-ID: 23292517  |  Reference-DOI: 10.1093/GLYCOB/CWS224
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BIFUNCTIONAL TAIL PROTEIN
    Chains: A
    EC Number: 3.2.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PTSF1
    Expression System Strain: BL21DE3
    Expression System Taxid: 469008
    Fragment: UNP RESIDUES 109-657
    Gene: 9, PHAGE P22 GENE 9
    Organism Scientific: ENTEROBACTERIA PHAGE P22
    Organism Taxid: 10754
    Synonym: LATE PROTEIN GP9, TAILSPIKE-PROTEIN, TSP, ENDORHAMNOSIDASE, ENDO-1,3-ALPHA-L-RHAMNOSIDASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (3x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 11)

Asymmetric Unit (5, 11)
No.NameCountTypeFull Name
1GLA2Ligand/IonALPHA D-GALACTOSE
2GOL3Ligand/IonGLYCEROL
3MAN2Ligand/IonALPHA-D-MANNOSE
4PZU2Ligand/Ion3,6-DIDEOXY-ALPHA-D-RIBO-HEXOPYRANOSE
5RAM2Ligand/IonALPHA-L-RHAMNOSE
Biological Unit 1 (5, 33)
No.NameCountTypeFull Name
1GLA6Ligand/IonALPHA D-GALACTOSE
2GOL9Ligand/IonGLYCEROL
3MAN6Ligand/IonALPHA-D-MANNOSE
4PZU6Ligand/Ion3,6-DIDEOXY-ALPHA-D-RIBO-HEXOPYRANOSE
5RAM6Ligand/IonALPHA-L-RHAMNOSE

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:285 , PRO A:404 , LEU A:419 , MAN A:702 , HOH A:1469 , HOH A:1520 , HOH A:1524BINDING SITE FOR RESIDUE GLA A 701
02AC2SOFTWAREASP A:303 , GLA A:701 , PZU A:703 , RAM A:704 , HOH A:1458 , HOH A:1459 , HOH A:1496 , HOH A:1524 , HOH A:1528BINDING SITE FOR RESIDUE MAN A 702
03AC3SOFTWAREPRO A:404 , MAN A:702 , GLA A:705 , HOH A:1467BINDING SITE FOR RESIDUE RAM A 704
04AC4SOFTWAREGLU A:359 , LYS A:363 , TRP A:365 , RAM A:704 , MAN A:706 , HOH A:928 , HOH A:1448 , HOH A:1456 , HOH A:1458 , HOH A:1459 , HOH A:1482BINDING SITE FOR RESIDUE GLA A 705
05AC5SOFTWARELYS A:363 , GLN A:366 , THR A:400 , ASN A:403 , GLA A:705 , PZU A:707 , RAM A:708 , HOH A:1452 , HOH A:1456BINDING SITE FOR RESIDUE MAN A 706
06AC6SOFTWARESER A:237 , GLU A:359 , LYS A:363 , GLN A:366 , TRP A:391 , ASP A:395 , MET A:402 , MAN A:706 , HOH A:1067 , HOH A:1196BINDING SITE FOR RESIDUE RAM A 708
07AC7SOFTWAREARG A:285 , GLU A:309 , LEU A:311 , MAN A:702 , HOH A:1447 , HOH A:1468BINDING SITE FOR RESIDUE PZU A 703
08AC8SOFTWAREVAL A:236 , MET A:402 , ASN A:403 , MAN A:706 , HOH A:1144 , HOH A:1270 , HOH A:1341 , HOH A:1456 , HOH A:1478BINDING SITE FOR RESIDUE PZU A 707
09AC9SOFTWARESER A:557 , ALA A:559 , LYS A:561 , HOH A:1107 , HOH A:1204 , HOH A:1491BINDING SITE FOR RESIDUE GOL A 801
10BC1SOFTWARETRP A:315 , ASN A:340 , TYR A:377 , ASP A:411 , HOH A:1291 , HOH A:1374BINDING SITE FOR RESIDUE GOL A 802
11BC2SOFTWARELYS A:170 , ALA A:171 , PHE A:194 , HOH A:1017 , HOH A:1066 , HOH A:1085BINDING SITE FOR RESIDUE GOL A 803

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3TH0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3TH0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3TH0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3TH0)

(-) Exons   (0, 0)

(no "Exon" information available for 3TH0)

(-) 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:552
 aligned with FIBER_BPP22 | P12528 from UniProtKB/Swiss-Prot  Length:667

    Alignment length:554
                                   123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663    
          FIBER_BPP22   114 YSIEADKKFKYSVKLSDYPTLQDAASAAVDGLLIDRDYNFYGGETVDFGGKVLTIECKAKFIGDGNLIFTKLGKGSRIAGVFMESTTTPWVIKPWTDDNQWLTDAAAVVATLKQSKTDGYQPTVSDYVKFPGIETLLPPNAKGQNITSTLEIRECIGVEVHRASGLMAGFLFRGCHFCKMVDANNPSGGKDGIITFENLSGDWGKGNYVIGGRTSYGSVSSAQFLRNNGGFERDGGVIGFTSYRAGESGVKTWQGTVGSTTSRNYNLQFRDSVVIYPVWDGFDLGADTDMNPELDRPGDYPITQYPLHQLPLNHLIDNLLVRGALGVGFGMDGKGMYVSNITVEDCAGSGAYLLTHESVFTNIAIIDTNTKDFQANQIYISGACRVNGLRLIGIRSTDGQGLTIDAPNSTVSGITGMVDPSRINVANLAEEGLGNIRANSFGYDSAAIKLRIHKLSKTLDSGALYSHINGGAGSGSAYTQLTAISGSTPDAVSLKVNHKDCRGAEIPFVPDIASDDFIKDSSCFLPYWENNSTSLKALVKKPNGELVRLTLATL 667
               SCOP domains d3th0a_ A: P22 tailspike protein                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhh..eee.hhh.hhhhhhhhh..eeee...ee.....eee......eeee...ee..eeeeee......eee..eee.....ee............hhhhhhhh.ee........hhhhhhhh.hhhhhhhhhhh.....eeeeee.....eee..eeeeeeeeee.....eee..eeeee.....eeee..........eee..eeee.....eeee..........eee..eee......eee...ee..ee......eeeeeeee......eee..............................eeeeeeee......eeeeee..eeeeeeee......eeeeee..eeeeeeee...........eee....eeeeeee.....--.....eeeeeeeeeeee...hhh.eeeeee................eeeeee...........eeeeeee........eeeeeeeee..eeeeeeeee.hhhh..ee........hhhhh....eeeeeeehhhheeeeeee.....eeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3th0 A 113 YSIEADKKFKYSVKLSDYPTLQDAASAAVDGLLIDRDYNFYGGETVDFGGKVLTIECKAKFIGDGNLIFTKLGKGSRIAGVFMESTTTPWVIKPWTDDNQWLTDAAAVVATLKQSKTDGYQPTVSDYVKFPGIETLLPPNAKGQNITSTLEIRECIGVEVHRASGLMAGFLFRGCHFCKMVDANNPSGGKDGIITFENLSGDWGKGNYVIGGRTSYGSVSSAQFLRNNGGFERDGGVIGFTSYRAGESGVKTWQGTVGSTTSRNYNLQFRDSVVIYPVWDGFDLGADTDMNPELDRPGDYPITQYPLHQLPLNHLIDNLLVRGALGVGFGMDGKGMYVSNITVEDCAGSGAYLLTHESVFTNIAIIDTNTKDFQANQIYISGACRVNGLRLIGIRS--GQSLTIDAPNSTVSGITGMVDPSRINVANLAEEGLGNIRANSFGYDSAAIKLRIHKLSKTLDSGALYSHINGGAGSGSAYTQLTAISGSTPDAVSLKVNHKDCRGAEIPFVPDIASDDFIKDSSCFLPYWENNSTSLKALVKKPNGELVRLTLATL 666
                                   122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502     | 512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662    
                                                                                                                                                                                                                                                                                                                                                                                                                                     508  |                                                                                                                                                           
                                                                                                                                                                                                                                                                                                                                                                                                                                        511
   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, 1)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3TH0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3TH0)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A   (FIBER_BPP22 | P12528)
molecular function
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0016798    hydrolase activity, acting on glycosyl bonds    Catalysis of the hydrolysis of any glycosyl bond.
biological process
    GO:0085027    entry into host via enzymatic degradation of host anatomical structure    Penetration by symbiont of a host anatomical structure which provides a barrier to symbiont entry, mediated by symbiont degradative enzymes.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0009405    pathogenesis    The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
    GO:0046718    viral entry into host cell    The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
    GO:0019062    virion attachment to host cell    The process by which a virion protein binds to molecules on the host cellular surface or host cell surface projection.
cellular component
    GO:0019012    virion    The complete fully infectious extracellular virus particle.

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 Related Entries

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

UniProtKB/Swiss-Prot
        FIBER_BPP22 | P12528: 1clw 1lkt 1qa1 1qa2 1qa3 1qq1 1qrb 1qrc 1tsp 1tyu 1tyv 1tyw 1tyx 2vfm 2vfn 2vfo 2vfp 2vfq 2vky 2vnl 2xc1 5gai

(-) Related Entries Specified in the PDB File

1tyu P22 TAILSPIKE WITH S.ENTERITIDIS OCTASACCHARIDE LIGAND
1tyv P22 TAILSPIKE WITHOUT LIGAND
1tyx P22 TAILSPIKE WITH S.TYPHIMURIUM OCTASACCHARIDE LIGAND