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(-) Description

Title :  STRUCTURE OF THE E. COLI IVY PROTEIN
 
Authors :  C. Abergel, V. Monchois, D. Byrn, J. C. Lazzaroni, J. M. Claverie
Date :  18 Oct 04  (Deposition) - 02 Nov 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.58
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  B,C  (1x)
Keywords :  Alpha Beta Fold, Dimer, Hydrolase Inhibitor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Abergel, V. Monchois, D. Byrne, S. Chenivesse, F. Lembo, J. C. Lazzaroni, J. M. Claverie
Structure And Evolution Of The Ivy Protein Family, Unexpected Lysozyme Inhibitors In Gram-Negative Bacteria.
Proc. Natl. Acad. Sci. Usa V. 104 6394 2007
PubMed-ID: 17405861  |  Reference-DOI: 10.1073/PNAS.0611019104
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - INHIBITOR OF VERTEBRATE LYSOZYME
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE60
    Expression System Strain: XL1-BLUE
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (2x): A  
Biological Unit 2 (1x):  BC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1XS0)

(-) Sites  (0, 0)

(no "Site" information available for 1XS0)

(-) SS Bonds  (3, 3)

Asymmetric Unit
No.Residues
1A:57 -A:62
2B:57 -B:62
3C:57 -C:62

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1XS0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1XS0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1XS0)

(-) Exons   (0, 0)

(no "Exon" information available for 1XS0)

(-) 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:128
 aligned with IVY_ECO57 | P0AD60 from UniProtKB/Swiss-Prot  Length:157

    Alignment length:128
                                                                                                                                                        157 
                                    40        50        60        70        80        90       100       110       120       130       140       150      | 
            IVY_ECO57    31 DLTISSLAKGETTKAAFNQMVQGHKLPAWVMKGGTYTPAQTVTLGDETYQVMSACKPHDCGSQRIAVMWSEKSNQMTGLFSTIDEKTSQEKLTWLNVNDALSIDGKTVLFAALTGSLENHPDGFNFK-   -
               SCOP domains d1xs0a_ A: Inhibitor of vertebrate lysozyme, Ivy                                                                                 SCOP domains
               CATH domains 1xs0A00 A:3-130 Inhibitor of vertebrate lysozyme, Ivy                                                                            CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhh..hhhhhhhhhh.....hhhhhh.eeeeeeeeeee.eeeeeeeee.......eeeeeee......eeeeeeee......eeeeee......hhhhhhhhhhhhhhhhhhh.....ee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xs0 A   3 DLTISSLAKGETTKAAFNQMVQGHKLPAWVMKGGTYTPAQTVTLGDETYQVMSACKPHDCGSQRIAVMWSEKSNQMTGLFSTIDEKTSQEKLTWLNVNDALSIDGKTVLFAALTGSLENHPDGFNFRS 130
                                    12        22        32        42        52        62        72        82        92       102       112       122        


Chain A from PDB  Type:PROTEIN  Length:128
 aligned with IVY_ECOLI | P0AD59 from UniProtKB/Swiss-Prot  Length:157

    Alignment length:128
                                                                                                                                                        157 
                                    40        50        60        70        80        90       100       110       120       130       140       150      | 
            IVY_ECOLI    31 DLTISSLAKGETTKAAFNQMVQGHKLPAWVMKGGTYTPAQTVTLGDETYQVMSACKPHDCGSQRIAVMWSEKSNQMTGLFSTIDEKTSQEKLTWLNVNDALSIDGKTVLFAALTGSLENHPDGFNFK-   -
               SCOP domains d1xs0a_ A: Inhibitor of vertebrate lysozyme, Ivy                                                                                 SCOP domains
               CATH domains 1xs0A00 A:3-130 Inhibitor of vertebrate lysozyme, Ivy                                                                            CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhh..hhhhhhhhhh.....hhhhhh.eeeeeeeeeee.eeeeeeeee.......eeeeeee......eeeeeeee......eeeeee......hhhhhhhhhhhhhhhhhhh.....ee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xs0 A   3 DLTISSLAKGETTKAAFNQMVQGHKLPAWVMKGGTYTPAQTVTLGDETYQVMSACKPHDCGSQRIAVMWSEKSNQMTGLFSTIDEKTSQEKLTWLNVNDALSIDGKTVLFAALTGSLENHPDGFNFRS 130
                                    12        22        32        42        52        62        72        82        92       102       112       122        


Chain B from PDB  Type:PROTEIN  Length:127
 aligned with IVY_ECO57 | P0AD60 from UniProtKB/Swiss-Prot  Length:157

    Alignment length:129
                                    38        48        58        68        78        88        98       108       118       128       138       148         
            IVY_ECO57    29 QDDLTISSLAKGETTKAAFNQMVQGHKLPAWVMKGGTYTPAQTVTLGDETYQVMSACKPHDCGSQRIAVMWSEKSNQMTGLFSTIDEKTSQEKLTWLNVNDALSIDGKTVLFAALTGSLENHPDGFNFK 157
               SCOP domains d1xs0b_ B: Inhibitor of vertebrate lysozyme, Ivy                                                                                  SCOP domains
               CATH domains 1xs0B00 B:1-129 Inhibitor of vertebrate lysozyme, Ivy                                                                             CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhh..hhhhhhhhh.............eeeeeeeeee..eeeeeeeee.......eeeeeee......eeeeeeee...--.eeeeee......hhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xs0 B   1 QDDLTISSLAKGETTKAAFNQMVQGHKLPAWVMKGGTYTPAQTVTLGDETYQVMSACKPHDCGSQRIAVMWSEKSNQMTGLFSTIDEK--QEKLTWLNVNDALSIDGKTVLFAALTGSLENHPDGFNFR 129
                                    10        20        30        40        50        60        70        80       | -|      100       110       120         
                                                                                                                  88 91                                      


Chain B from PDB  Type:PROTEIN  Length:127
 aligned with IVY_ECOLI | P0AD59 from UniProtKB/Swiss-Prot  Length:157

    Alignment length:129
                                    38        48        58        68        78        88        98       108       118       128       138       148         
            IVY_ECOLI    29 QDDLTISSLAKGETTKAAFNQMVQGHKLPAWVMKGGTYTPAQTVTLGDETYQVMSACKPHDCGSQRIAVMWSEKSNQMTGLFSTIDEKTSQEKLTWLNVNDALSIDGKTVLFAALTGSLENHPDGFNFK 157
               SCOP domains d1xs0b_ B: Inhibitor of vertebrate lysozyme, Ivy                                                                                  SCOP domains
               CATH domains 1xs0B00 B:1-129 Inhibitor of vertebrate lysozyme, Ivy                                                                             CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhh..hhhhhhhhh.............eeeeeeeeee..eeeeeeeee.......eeeeeee......eeeeeeee...--.eeeeee......hhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xs0 B   1 QDDLTISSLAKGETTKAAFNQMVQGHKLPAWVMKGGTYTPAQTVTLGDETYQVMSACKPHDCGSQRIAVMWSEKSNQMTGLFSTIDEK--QEKLTWLNVNDALSIDGKTVLFAALTGSLENHPDGFNFR 129
                                    10        20        30        40        50        60        70        80       | -|      100       110       120         
                                                                                                                  88 91                                      


Chain C from PDB  Type:PROTEIN  Length:129
 aligned with IVY_ECO57 | P0AD60 from UniProtKB/Swiss-Prot  Length:157

    Alignment length:129
                                                                                                                                                        157  
                                    40        50        60        70        80        90       100       110       120       130       140       150      |  
            IVY_ECO57    31 DLTISSLAKGETTKAAFNQMVQGHKLPAWVMKGGTYTPAQTVTLGDETYQVMSACKPHDCGSQRIAVMWSEKSNQMTGLFSTIDEKTSQEKLTWLNVNDALSIDGKTVLFAALTGSLENHPDGFNFK--   -
               SCOP domains d1xs0c_ C: Inhibitor of vertebrate lysozyme, Ivy                                                                                  SCOP domains
               CATH domains 1xs0C00 C:3-131 Inhibitor of vertebrate lysozyme, Ivy                                                                             CATH domains
           Pfam domains (1) ------Ivy-1xs0C01 C:9-124                                                                                                 ------- Pfam domains (1)
           Pfam domains (2) ------Ivy-1xs0C02 C:9-124                                                                                                 ------- Pfam domains (2)
           Pfam domains (3) ------Ivy-1xs0C03 C:9-124                                                                                                 ------- Pfam domains (3)
         Sec.struct. author ..hhhhhhhh..hhhhhhhhh.............eeeeeeeeeee.eeeeeeeee.......eeeeeee......eeeeeeee......eeeeee......hhhhhhhhhhhhhhhhhhh.....ee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xs0 C   3 DLTISSLAKGETTKAAFNQMVQGHKLPAWVMKGGTYTPAQTVTLGDETYQVMSACKPHDCGSQRIAVMWSEKSNQMTGLFSTIDEKTSQEKLTWLNVNDALSIDGKTVLFAALTGSLENHPDGFNFRSH 131
                                    12        22        32        42        52        62        72        82        92       102       112       122         


Chain C from PDB  Type:PROTEIN  Length:129
 aligned with IVY_ECOLI | P0AD59 from UniProtKB/Swiss-Prot  Length:157

    Alignment length:129
                                                                                                                                                        157  
                                    40        50        60        70        80        90       100       110       120       130       140       150      |  
            IVY_ECOLI    31 DLTISSLAKGETTKAAFNQMVQGHKLPAWVMKGGTYTPAQTVTLGDETYQVMSACKPHDCGSQRIAVMWSEKSNQMTGLFSTIDEKTSQEKLTWLNVNDALSIDGKTVLFAALTGSLENHPDGFNFK--   -
               SCOP domains d1xs0c_ C: Inhibitor of vertebrate lysozyme, Ivy                                                                                  SCOP domains
               CATH domains 1xs0C00 C:3-131 Inhibitor of vertebrate lysozyme, Ivy                                                                             CATH domains
           Pfam domains (1) ------Ivy-1xs0C01 C:9-124                                                                                                 ------- Pfam domains (1)
           Pfam domains (2) ------Ivy-1xs0C02 C:9-124                                                                                                 ------- Pfam domains (2)
           Pfam domains (3) ------Ivy-1xs0C03 C:9-124                                                                                                 ------- Pfam domains (3)
         Sec.struct. author ..hhhhhhhh..hhhhhhhhh.............eeeeeeeeeee.eeeeeeeee.......eeeeeee......eeeeeeee......eeeeee......hhhhhhhhhhhhhhhhhhh.....ee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xs0 C   3 DLTISSLAKGETTKAAFNQMVQGHKLPAWVMKGGTYTPAQTVTLGDETYQVMSACKPHDCGSQRIAVMWSEKSNQMTGLFSTIDEKTSQEKLTWLNVNDALSIDGKTVLFAALTGSLENHPDGFNFRSH 131
                                    12        22        32        42        52        62        72        82        92       102       112       122
   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, 3)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 3)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 3)

Asymmetric Unit
(-)
Clan: no clan defined [family: Ivy] (2)

(-) Gene Ontology  (5, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (IVY_ECOLI | P0AD59)
molecular function
    GO:0060241    lysozyme inhibitor activity    Stops, prevents or reduces the activity of a lysozyme, an enzyme that hydrolyses the beta- (1,4) glycosidic bond between N-acetylmuramic acid and N-acetylglucosamine in peptidoglycan.
biological process
    GO:0043086    negative regulation of catalytic activity    Any process that stops or reduces the activity of an enzyme.
    GO:0050790    regulation of catalytic activity    Any process that modulates the activity of an enzyme.
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).

Chain A,B,C   (IVY_ECO57 | P0AD60)
biological process
    GO:0043086    negative regulation of catalytic activity    Any process that stops or reduces the activity of an enzyme.
cellular component
    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)

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        IVY_ECO57 | P0AD60: 1gpq
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(-) Related Entries Specified in the PDB File

1gpq THE E. COLI IVY PROTEIN COMPLEXED WITH LYSOZYME
1hke THE P. AERUGINOSA IVY PROTEIN COMPLEXED WITH LYSOZYME