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(-) Description

Title :  STRUCTURE OF A DOMAIN FROM THE TYPE IV PILUS BIOGENESIS LIPOPROTEIN PILP, FROM PSEUDOMONAS AERUGINOSA
 
Authors :  J. P. Derrick, J. Berry
Date :  11 Jan 11  (Deposition) - 18 Jan 12  (Release) - 18 Jan 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (2x)
Keywords :  Biosynthetic Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Berry, J. P. Derrick
Structure Of A Domain From The Type Iv Pilus Biogenesis Lipoprotein Pilp, From Pseudomonas Aeruginosa
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PILP PROTEIN
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector: PET15B
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 83-171
    Organism Scientific: PSEUDOMONAS AERUGINOSA PAO1
    Organism Taxid: 208964
    Synonym: PILP, TYPE 4 FIMBRIAL BIOGENESIS PROTEIN PILP

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (2x): ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 12)

Asymmetric Unit (2, 12)
No.NameCountTypeFull Name
1ACT6Ligand/IonACETATE ION
2ZN6Ligand/IonZINC ION
Biological Unit 1 (1, 12)
No.NameCountTypeFull Name
1ACT12Ligand/IonACETATE ION
2ZN-1Ligand/IonZINC ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:125 , ACT A:1176 , HOH A:2084 , GLU C:103BINDING SITE FOR RESIDUE ZN A1172
02AC2SOFTWAREASN A:110 , ARG A:126 , HOH A:2085BINDING SITE FOR RESIDUE ACT A1173
03AC3SOFTWAREARG A:126 , ACT C:1174BINDING SITE FOR RESIDUE ACT A1174
04AC4SOFTWAREGLU A:163 , HOH A:2086 , HOH A:2087 , GLU D:163BINDING SITE FOR RESIDUE ZN A1175
05AC5SOFTWAREHIS A:125 , ARG A:126 , ZN A:1172 , HOH A:2089 , GLU C:103 , VAL C:105BINDING SITE FOR RESIDUE ACT A1176
06AC6SOFTWAREGLU B:103 , HIS C:125 , HOH C:2076 , HOH C:2077BINDING SITE FOR RESIDUE ZN C1172
07AC7SOFTWAREHIS B:125 , HOH B:2068BINDING SITE FOR RESIDUE ZN B1172
08AC8SOFTWAREGLU B:163 , HOH B:2069 , HIS C:81 , GLU C:163BINDING SITE FOR RESIDUE ZN B1173
09AC9SOFTWAREVAL A:105 , ASN C:110 , ARG C:126BINDING SITE FOR RESIDUE ACT C1173
10BC1SOFTWAREACT A:1174 , ARG C:126 , HOH C:2037BINDING SITE FOR RESIDUE ACT C1174
11BC2SOFTWAREVAL B:105 , ASN D:110 , ARG D:126BINDING SITE FOR RESIDUE ACT D1171
12BC3SOFTWAREGLU A:103 , HIS D:125 , HOH D:2061 , HOH D:2062 , HOH D:2063BINDING SITE FOR RESIDUE ZN D1172

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Y4Y)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2Y4Y)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Y4Y)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2Y4Y)

(-) Exons   (0, 0)

(no "Exon" information available for 2Y4Y)

(-) 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:82
 aligned with G3XCX7_PSEAE | G3XCX7 from UniProtKB/TrEMBL  Length:174

    Alignment length:89
                                    92       102       112       122       132       142       152       162         
         G3XCX7_PSEAE    83 IKPDETRVKQFLEGFNIETFEMVGTLSNAQGTFALVKGAGGVHRVRVGDYLGRNDGKVVGISEGKIDVIEIVPDGEGNWLERPRSLTLK 171
               SCOP domains ----------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhheeeeeeee..eeeeeeee..eeeee....ee....eeeeee.--.eeeeeee.-----.eeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------- Transcript
                 2y4y A  83 IKPDETRVKQFLEGFNIETFEMVGTLSNAQGTFALVKGAGGVHRVRVGDYLGRNDGKVVGIS--KIDVIEIVP-----WLERPRSLTLK 171
                                    92       102       112       122       132       142 |  |  152  |    162         
                                                                                       144  |     155   161          
                                                                                          147                        


Chain A from PDB  Type:PROTEIN  Length:82
 aligned with Q51354_PSEAI | Q51354 from UniProtKB/TrEMBL  Length:174

    Alignment length:89
                                    92       102       112       122       132       142       152       162         
         Q51354_PSEAI    83 IKPDETRVKQFLEGFNIETFEMVGTLSNAQGTFALVKGAGGVHRVRVGDYLGRNDGKVVGISEGKIDVIEIVPDGEGNWLERPRSLTLK 171
               SCOP domains ----------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhheeeeeeee..eeeeeeee..eeeee....ee....eeeeee.--.eeeeeee.-----.eeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------- Transcript
                 2y4y A  83 IKPDETRVKQFLEGFNIETFEMVGTLSNAQGTFALVKGAGGVHRVRVGDYLGRNDGKVVGIS--KIDVIEIVP-----WLERPRSLTLK 171
                                    92       102       112       122       132       142 |  |  152  |    162         
                                                                                       144  |     155   161          
                                                                                          147                        


Chain B from PDB  Type:PROTEIN  Length:76
 aligned with G3XCX7_PSEAE | G3XCX7 from UniProtKB/TrEMBL  Length:174

    Alignment length:83
                                    98       108       118       128       138       148       158       168   
         G3XCX7_PSEAE    89 RVKQFLEGFNIETFEMVGTLSNAQGTFALVKGAGGVHRVRVGDYLGRNDGKVVGISEGKIDVIEIVPDGEGNWLERPRSLTLK 171
               SCOP domains ----------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhheeeeeeee..eeeeeeee..eeeee....ee....eeeeeee..eeeeeee.-------.eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------- Transcript
                 2y4y B  89 RVKQFLEGFNIETFEMVGTLSNAQGTFALVKGAGGVHRVRVGDYLGRNDGKVVGISEGKIDVIEIV-------LERPRSLTLK 171
                                    98       108       118       128       138       148     |   -   |   168   
                                                                                           154     162         


Chain B from PDB  Type:PROTEIN  Length:76
 aligned with Q51354_PSEAI | Q51354 from UniProtKB/TrEMBL  Length:174

    Alignment length:83
                                    98       108       118       128       138       148       158       168   
         Q51354_PSEAI    89 RVKQFLEGFNIETFEMVGTLSNAQGTFALVKGAGGVHRVRVGDYLGRNDGKVVGISEGKIDVIEIVPDGEGNWLERPRSLTLK 171
               SCOP domains ----------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhheeeeeeee..eeeeeeee..eeeee....ee....eeeeeee..eeeeeee.-------.eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------- Transcript
                 2y4y B  89 RVKQFLEGFNIETFEMVGTLSNAQGTFALVKGAGGVHRVRVGDYLGRNDGKVVGISEGKIDVIEIV-------LERPRSLTLK 171
                                    98       108       118       128       138       148     |   -   |   168   
                                                                                           154     162         


Chain C from PDB  Type:PROTEIN  Length:79
 aligned with G3XCX7_PSEAE | G3XCX7 from UniProtKB/TrEMBL  Length:174

    Alignment length:91
                                    90       100       110       120       130       140       150       160       170 
         G3XCX7_PSEAE    81 KVIKPDETRVKQFLEGFNIETFEMVGTLSNAQGTFALVKGAGGVHRVRVGDYLGRNDGKVVGISEGKIDVIEIVPDGEGNWLERPRSLTLK 171
               SCOP domains ------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..------...hhhhhhhhhhheeeeeeee..eeeeeeee..eeeee....ee....eeeeeee..eeeeeee.------..eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------- Transcript
                 2y4y C  81 HM------RVKQFLEGFNIETFEMVGTLSNAQGTFALVKGAGGVHRVRVGDYLGRNDGKVVGISEGKIDVIEIV------WLERPRSLTLK 171
                             |      90       100       110       120       130       140       150   |     -|      170 
                            82     89                                                              154    161          


Chain C from PDB  Type:PROTEIN  Length:79
 aligned with Q51354_PSEAI | Q51354 from UniProtKB/TrEMBL  Length:174

    Alignment length:91
                                    90       100       110       120       130       140       150       160       170 
         Q51354_PSEAI    81 KVIKPDETRVKQFLEGFNIETFEMVGTLSNAQGTFALVKGAGGVHRVRVGDYLGRNDGKVVGISEGKIDVIEIVPDGEGNWLERPRSLTLK 171
               SCOP domains ------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..------...hhhhhhhhhhheeeeeeee..eeeeeeee..eeeee....ee....eeeeeee..eeeeeee.------..eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------- Transcript
                 2y4y C  81 HM------RVKQFLEGFNIETFEMVGTLSNAQGTFALVKGAGGVHRVRVGDYLGRNDGKVVGISEGKIDVIEIV------WLERPRSLTLK 171
                             |      90       100       110       120       130       140       150   |     -|      170 
                            82     89                                                              154    161          


Chain D from PDB  Type:PROTEIN  Length:80
 aligned with G3XCX7_PSEAE | G3XCX7 from UniProtKB/TrEMBL  Length:174

    Alignment length:87
                                    93       103       113       123       133       143       153       163       
         G3XCX7_PSEAE    84 KPDETRVKQFLEGFNIETFEMVGTLSNAQGTFALVKGAGGVHRVRVGDYLGRNDGKVVGISEGKIDVIEIVPDGEGNWLERPRSLTL 170
               SCOP domains --------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...--...hhhhhhhhhhheeeeeeee..eeeeeeee..eeeee....ee....eeeeeee..eeeeeeee.-----.eeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------- Transcript
                 2y4y D  84 KPD--RVKQFLEGFNIETFEMVGTLSNAQGTFALVKGAGGVHRVRVGDYLGRNDGKVVGISEGKIDVIEIVP-----WLERPRSLTL 170
                              |  |  93       103       113       123       133       143       153 |     163       
                             86 89                                                               155   161         


Chain D from PDB  Type:PROTEIN  Length:80
 aligned with Q51354_PSEAI | Q51354 from UniProtKB/TrEMBL  Length:174

    Alignment length:87
                                    93       103       113       123       133       143       153       163       
         Q51354_PSEAI    84 KPDETRVKQFLEGFNIETFEMVGTLSNAQGTFALVKGAGGVHRVRVGDYLGRNDGKVVGISEGKIDVIEIVPDGEGNWLERPRSLTL 170
               SCOP domains --------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...--...hhhhhhhhhhheeeeeeee..eeeeeeee..eeeee....ee....eeeeeee..eeeeeeee.-----.eeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------- Transcript
                 2y4y D  84 KPD--RVKQFLEGFNIETFEMVGTLSNAQGTFALVKGAGGVHRVRVGDYLGRNDGKVVGISEGKIDVIEIVP-----WLERPRSLTL 170
                              |  |  93       103       113       123       133       143       153 |     163       
                             86 89                                                               155   161
   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  (0, 0)

(no "SCOP Domain" information available for 2Y4Y)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2Y4Y)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2Y4Y)

(-) Gene Ontology  (3, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q51354_PSEAI | Q51354)
biological process
    GO:0043683    type IV pilus biogenesis    A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a type IV pilus. A type IV pilus is composed of a pilus fiber and approximately ten proteins at its base; type IV pili play a role in cell motility, adherence to substrates, and aggregation.
    GO:0043107    type IV pilus-dependent motility    Any process involved in the controlled movement of a bacterial cell which is dependent on the presence of type IV pili. Includes social gliding motility and twitching motility.

Chain A,B,C,D   (G3XCX7_PSEAE | G3XCX7)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0043683    type IV pilus biogenesis    A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a type IV pilus. A type IV pilus is composed of a pilus fiber and approximately ten proteins at its base; type IV pili play a role in cell motility, adherence to substrates, and aggregation.
    GO:0043107    type IV pilus-dependent motility    Any process involved in the controlled movement of a bacterial cell which is dependent on the presence of type IV pili. Includes social gliding motility and twitching motility.

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 Related Entries

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

UniProtKB/Swiss-Prot
        Q51354_PSEAI | Q51354: 2y4x
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        G3XCX7_PSEAE | G3XCX7: 2y4x
        Q51354_PSEAI | Q51354: 2lc4

(-) Related Entries Specified in the PDB File

2y4x STRUCTURE OF A DOMAIN FROM THE TYPE IV PILUS BIOGENESIS LIPOPROTEIN PILP, FROM PSEUDOMONAS AERUGINOSA PA01