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(-) Description

Title :  LOW TEMPERATURE STRUCTURE OF P22 TAILSPIKE PROTEIN FRAGMENT (109-666), MUTANT V125L
 
Authors :  M. Becker, J. J. Mueller, U. Heinemann, R. Seckler
Date :  05 Nov 07  (Deposition) - 16 Dec 08  (Release) - 16 Dec 08  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Keywords :  P22 Tailspike Protein, Salmonella Bacteriophage P22, Protein Folding, Protein Stability, Right-Handed Parallel Beta-Helix, Hydrolase, Late Protein, Endoglycosidase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Becker, J. J. Mueller, T. Weikl, U. Heinemann, R. Seckler
Side-Chain Stacking And Beta-Helix Stability In P22 Tailspike Protein
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - P22 TAILSPIKE PROTEIN, MUTANT V125L
    Chains: A
    EC Number: 3.2.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: P125LDN
    Expression System Strain: JM83
    Expression System Taxid: 562
    Expression System Vector: PASK31
    Fragment: RESIDUES 110-667
    Mutation: YES
    Organism Scientific: BACTERIOPHAGE P22
    Organism Taxid: 10754
    Other Details: THE PROTEIN IS LACKING THE N-TERMINAL HEAD- BINDING DOMAIN
    Synonym: P22 TAILSPIKE PROTEIN, WILD TYPE, 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  (3, 9)

Asymmetric Unit (3, 9)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2GOL7Ligand/IonGLYCEROL
3SO41Ligand/IonSULFATE ION
Biological Unit 1 (2, 24)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2GOL21Ligand/IonGLYCEROL
3SO43Ligand/IonSULFATE ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:170 , ALA A:171 , LYS A:186 , PHE A:194 , HOH A:2094 , HOH A:2781 , HOH A:2782 , HOH A:2783BINDING SITE FOR RESIDUE GOL A1667
2AC2SOFTWAREGLU A:359 , LYS A:363 , HOH A:2784 , HOH A:2785BINDING SITE FOR RESIDUE GOL A1668
3AC3SOFTWAREASN A:547 , SER A:557 , ALA A:559 , LYS A:561 , HOH A:2651 , HOH A:2786BINDING SITE FOR RESIDUE GOL A1669
4AC4SOFTWAREGLY A:154 , ASP A:176 , HIS A:468 , SER A:493 , GLY A:494 , ASN A:520 , HOH A:2787 , HOH A:2788 , HOH A:2789BINDING SITE FOR RESIDUE GOL A1670
5AC5SOFTWARELYS A:172 , GLU A:196 , LYS A:228 , HOH A:2039 , HOH A:2237BINDING SITE FOR RESIDUE GOL A1671
6AC6SOFTWARETHR A:307 , TRP A:365 , HOH A:2396 , HOH A:2791BINDING SITE FOR RESIDUE GOL A1672
7AC7SOFTWARETRP A:315 , ASN A:340 , TYR A:377 , ASP A:411 , TYR A:412 , HOH A:2519 , HOH A:2792 , HOH A:2793BINDING SITE FOR RESIDUE GOL A1673
8AC8SOFTWARETHR A:235 , VAL A:236 , LYS A:302 , HOH A:2170 , HOH A:2248 , HOH A:2794 , HOH A:2795BINDING SITE FOR RESIDUE SO4 A1674
9AC9SOFTWARELEU A:663 , HOH A:2774BINDING SITE FOR RESIDUE CA A1675

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2VFO)

(-) 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:555
 aligned with FIBER_BPP22 | P12528 from UniProtKB/Swiss-Prot  Length:667

    Alignment length:555
                                   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     
          FIBER_BPP22   113 QYSIEADKKFKYSVKLSDYPTLQDAASAAVDGLLIDRDYNFYGGETVDFGGKVLTIECKAKFIGDGNLIFTKLGKGSRIAGVFMESTTTPWVIKPWTDDNQWLTDAAAVVATLKQSKTDGYQPTVSDYVKFPGIETLLPPNAKGQNITSTLEIRECIGVEVHRASGLMAGFLFRGCHFCKMVDANNPSGGKDGIITFENLSGDWGKGNYVIGGRTSYGSVSSAQFLRNNGGFERDGGVIGFTSYRAGESGVKTWQGTVGSTTSRNYNLQFRDSVVIYPVWDGFDLGADTDMNPELDRPGDYPITQYPLHQLPLNHLIDNLLVRGALGVGFGMDGKGMYVSNITVEDCAGSGAYLLTHESVFTNIAIIDTNTKDFQANQIYISGACRVNGLRLIGIRSTDGQGLTIDAPNSTVSGITGMVDPSRINVANLAEEGLGNIRANSFGYDSAAIKLRIHKLSKTLDSGALYSHINGGAGSGSAYTQLTAISGSTPDAVSLKVNHKDCRGAEIPFVPDIASDDFIKDSSCFLPYWENNSTSLKALVKKPNGELVRLTLATL 667
               SCOP domains d2vfoa_ A: P22 tailspike protein                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 2vfoA00 A:112-666  [code=2.160.20.20, no name defined]                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhh...eeehhh...hhhhhhh...eeee..eee.....eee......eeee..eee..eeeeee......eee..eee....................hhhhh...............hhhhh...hhhh..hhh......eeeeee.....eee..eee.eeeeee.....eee..eeeee.....eeee..........eee..eeee.....eeee..........eee..eee......eee...............eee..eee......eee..............................eee..eee......eeeeee..eee..eee......eeeeee..eee..eee...........eee....eee..ee............eee...eee..ee...hhh......................eeeeee...........eeeeeee........eeeeeeeee..eeeeeeeee.hhh..............hhh.....eeeeeee....eeeeeee.....eeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vfo A 112 QYSIEADKKFKYSLKLSDYPTLQDAASAAVDGLLIDRDYNFYGGETVDFGGKVLTIECKAKFIGDGNLIFTKLGKGSRIAGVFMESTTTPWVIKPWTDDNQWLTDAAAVVATLKQSKTDGYQPTVSDYVKFPGIETLLPPNAKGQNITSTLEIRECIGVEVHRASGLMAGFLFRGCHFCKMVDANNPSGGKDGIITFENLSGDWGKGNYVIGGRTSYGSVSSAQFLRNNGGFERDGGVIGFTSYRAGESGVKTWQGTVGSTTSRNYNLQFRDSVVIYPVWDGFDLGADTDMNPELDRPGDYPITQYPLHQLPLNHLIDNLLVRGALGVGFGMDGKGMYVSNITVEDCAGSGAYLLTHESVFTNIAIIDTNTKDFQANQIYISGACRVNGLRLIGIRSTDGQSLTIDAPNSTVSGITGMVDPSRINVANLAEEGLGNIRANSFGYDSAAIKLRIHKLSKTLDSGALYSHINGGAGSGSAYTQLTAISGSTPDAVSLKVNHKDCRGAEIPFVPDIASDDFIKDSSCFLPYWENNSTSLKALVKKPNGELVRLTLATL 666
                                   121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661
   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)
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  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  (1, 1)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

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

(-) 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 2vfp 2vfq 2vky 2vnl 2xc1 3th0 5gai

(-) Related Entries Specified in the PDB File

1clw TAILSPIKE PROTEIN FROM PHAGE P22, V331A MUTANT
1lkt CRYSTAL STRUCTURE OF THE HEAD-BINDING DOMAIN OF PHAGE P22TAILSPIKE PROTEIN
1qa1 TAILSPIKE PROTEIN, MUTANT V331G
1qa2 TAILSPIKE PROTEIN, MUTANT A334V
1qa3 TAILSPIKE PROTEIN, MUTANT A334I
1qq1 TAILSPIKE PROTEIN, MUTANT E359G
1qrb PLASTICITY AND STERIC STRAIN IN A PARALLEL BETA-HELIX:RATIONAL MUTATIONS IN P22 TAILSPIKE PROTEIN
1qrc TAILSPIKE PROTEIN, MUTANT W391A
1tsp
1tyv STRUCTURE OF TAILSPIKE-PROTEIN
2vfm LOW TEMPERATURE STRUCTURE OF P22 TAILSPIKE PROTEIN FRAGMENT (109-666)
2vfn LOW TEMPERATURE STRUCTURE OF P22 TAILSPIKE PROTEIN FRAGMENT (109-666), MUTANT V125A
2vfp LOW TEMPERATURE STRUCTURE OF P22 TAILSPIKE PROTEIN FRAGMENT (109-666), MUTANT V349L
2vfq LOW TEMPERATURE STRUCTURE OF P22 TAILSPIKE PROTEIN FRAGMENT (109-666), MUTANT V450A