Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit - manually
(-)Asym./Biol. Unit
collapse expand < >
Image Asym./Biol. Unit - manually
Asym./Biol. Unit - manually  (Jmol Viewer)
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF ESCHERICHIA COLI SIGNAL PEPTIDE PEPTIDASE (SPPA), NATIVE CRYSTALS
 
Authors :  M. Paetzel
Date :  20 Nov 07  (Deposition) - 18 Dec 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.55
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Protease, Bacterial, Hydrolase, Inner Membrane, Membrane, Transmembrane, Ser/Lys Protease (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. C. Kim, D. C. Oliver, M. Paetzel
Crystal Structure Of A Bacterial Signal Peptide Peptidase.
J. Mol. Biol. V. 376 352 2008
PubMed-ID: 18164727  |  Reference-DOI: 10.1016/J.JMB.2007.11.080
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEASE 4
    Chains: A, B, C, D
    EC Number: 3.4.21.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET28
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: SPPA
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: PROTEASE IV, ENDOPEPTIDASE IV, SIGNAL PEPTIDE PEPTIDASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3BF0)

(-) Sites  (0, 0)

(no "Site" information available for 3BF0)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3BF0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3BF0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (6, 24)

Asymmetric/Biological Unit (6, 24)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_SPPA_ECOLI_001 *V151ISPPA_ECOLI  ---  ---A/B/C/DV151I
2UniProtVAR_SPPA_ECOLI_002 *G186SSPPA_ECOLI  ---  ---A/B/C/DG186S
3UniProtVAR_SPPA_ECOLI_003 *E252HSPPA_ECOLI  ---  ---A/B/C/DE252H
4UniProtVAR_SPPA_ECOLI_004 *E252KSPPA_ECOLI  ---  ---A/B/C/DE252K
5UniProtVAR_SPPA_ECOLI_005 *E252QSPPA_ECOLI  ---  ---A/B/C/DE252Q
6UniProtVAR_SPPA_ECOLI_006 *A294TSPPA_ECOLI  ---  ---A/B/C/DA294T
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3BF0)

(-) Exons   (0, 0)

(no "Exon" information available for 3BF0)

(-) Sequences/Alignments

Asymmetric/Biological 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:474
 aligned with SPPA_ECOLI | P08395 from UniProtKB/Swiss-Prot  Length:618

    Alignment length:494
                                    65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545    
           SPPA_ECOLI    56 RGALLLDISGVIVDKPDSSQRFSKLSRQLLGASSDRLQENSLFDIVNTIRQAKDDRNITGIVMDLKNFAGGDQPSMQYIGKALKEFRDSGKPVYAVGENYSQGQYYLASFANKIWLSPQGVVDLHGFATNGLYYKSLLDKLKVSTHVFRVGTYKSAVEPFIRDDMSPAAREADSRWIGELWQNYLNTVAANRQIPAEQVFPGAQGLLEGLTKTGGDTAKYALENKLVDALASSAEIEKALTKEFGWSKTDKNYRAISYYDYALKTPADTGDSIGVVFANGAIMDGEETQGNVGGDTTAAQIRDARLDPKVKAIVLRVNSPGGSVTASEVIRAELAAARAAGKPVVVSMGGMAASGGYWISTPANYIVANPSTLTGSIGIFGVITTVENSLDSIGVHTDGVSTSPLADVSITRALPPEAQLMMQLSIENGYKRFITLVADARHSTPEQIDKIAQGHVWTGQDAKANGLVDSLGDFDDAVAKAAELAKVKQWHLEY 549
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3bf0A01 A:56-178                    ,A:221-318 2-enoyl-CoA Hydratase; Chain A, domain 1                                    ----------3bf0A02 A:189-220,A:433-498     3bf0A01 A:56-178,A:221-318 2-enoyl-CoA Hydratase; Chain A, domain 1                               3bf0A03 A:319-432,A:499-549 2-enoyl-CoA Hydratase; Chain A, domain 1                                              3bf0A02 A:189-220,A:433-498 peptide peptidase (sppa) like domain  3bf0A03 A:319-432,A:499-549                         CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eeeee...--------------------..eeehhhhhhhhhhhhhh.....eeee..eeee.hhhhhhhhhhhhhhhhhh...eeeee..eehhhhhhhh...eeee.....ee.......eeehhhhhhhh..eeeeeee...hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh...hhhhhhhhh....ee.hhhhhhhhhhhhhh.........eee..............eeeeeeeeeeee........eehhhhhhhhhhhhhh..eeeeeeeeeeeeehhhhhhhhhhhhhhhhhh...eeeeeeeeeehhhhhh.....eeee....eee...eeeeeeehhhhhhhh..eee....hhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhh.....eeehhhhhhh....ee.hhhhhhhhhhhhh....eeee. Sec.struct. author
             SAPs(SNPs) (1) -----------------------------------------------------------------------------------------------I----------------------------------S-----------------------------------------------------------------H-----------------------------------------T--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------K--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (2)
             SAPs(SNPs) (3) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Q--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (3)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bf0 A  56 RGALLLDISGVIVDKP--------------------LQENSLFDIVNTIRQAKDDRNITGIVMDLKNFAGGDQPSMQYIGKALKEFRDSGKPVYAVGENYSQGQYYLASFANKIWLSPQGVVDLHGFATNGLYYKSLLDKLKVSTHVFRVGTYKSAVEPFIRDDMSPAAREADSRWIGELWQNYLNTVAANRQIPAEQVFPGAQGLLEGLTKTGGDTAKYALENKLVDALASSAEIEKALTKEFGWSKTDKNYRAISYYDYALKTPADTGDSIGVVFANGAIMDGEETQGNVGGDTTAAQIRDARLDPKVKAIVLRVNSPGGSVTASEVIRAELAAARAAGKPVVVSMGGMAASGGYWISTPANYIVANPSTLTGSIGIFGVITTVENSLDSIGVHTDGVSTSPLADVSITRALPPEAQLMMQLSIENGYKRFITLVADARHSTPEQIDKIAQGHVWTGQDAKANGLVDSLGDFDDAVAKAAELAKVKQWHLEY 549
                                    65     |   -         -      | 95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545    
                                          71                   92                                                                                                                                                                                                                                                                                                                                                                                                                                                                         


Chain B from PDB  Type:PROTEIN  Length:474
 aligned with SPPA_ECOLI | P08395 from UniProtKB/Swiss-Prot  Length:618

    Alignment length:494
                                    65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545    
           SPPA_ECOLI    56 RGALLLDISGVIVDKPDSSQRFSKLSRQLLGASSDRLQENSLFDIVNTIRQAKDDRNITGIVMDLKNFAGGDQPSMQYIGKALKEFRDSGKPVYAVGENYSQGQYYLASFANKIWLSPQGVVDLHGFATNGLYYKSLLDKLKVSTHVFRVGTYKSAVEPFIRDDMSPAAREADSRWIGELWQNYLNTVAANRQIPAEQVFPGAQGLLEGLTKTGGDTAKYALENKLVDALASSAEIEKALTKEFGWSKTDKNYRAISYYDYALKTPADTGDSIGVVFANGAIMDGEETQGNVGGDTTAAQIRDARLDPKVKAIVLRVNSPGGSVTASEVIRAELAAARAAGKPVVVSMGGMAASGGYWISTPANYIVANPSTLTGSIGIFGVITTVENSLDSIGVHTDGVSTSPLADVSITRALPPEAQLMMQLSIENGYKRFITLVADARHSTPEQIDKIAQGHVWTGQDAKANGLVDSLGDFDDAVAKAAELAKVKQWHLEY 549
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3bf0B01 B:56-178,                    B:221-318 2-enoyl-CoA Hydratase; Chain A, domain 1                                    ----------3bf0B02 B:189-220,B:433-498     3bf0B01 B:56-178,B:221-318 2-enoyl-CoA Hydratase; Chain A, domain 1                               3bf0B03 B:319-432,B:499-549 2-enoyl-CoA Hydratase; Chain A, domain 1                                              3bf0B02 B:189-220,B:433-498 peptide peptidase (sppa) like domain  3bf0B03 B:319-432,B:499-549                         CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eeee....--------------------.eeehhhhhhhhhhhhh......eeee...eee.hhhhhhhhhhhhhhhhhh...eeeee..eehhhhhhhh...eeee.....ee.......eeehhhhhhhh..eeeeeee...hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh.hhhhhhhhh.....hhhhhhhhh....ee.hhhhhhhhhhhhh.ee....ee.eee..............eeeeeeee.eee.......eeehhhhhhhhhhhhhh..eeeeeeeeee...hhhhhhhhhhhhhhhhhh...eeeeeeeeeehhhhhh.....eeee....eee...eeeeeeehhhhhhhh..eee....hhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh...eeehhhhhhh....ee.hhhhhhhhhhhhhh...eeee. Sec.struct. author
             SAPs(SNPs) (1) -----------------------------------------------------------------------------------------------I----------------------------------S-----------------------------------------------------------------H-----------------------------------------T--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------K--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (2)
             SAPs(SNPs) (3) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Q--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (3)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bf0 B  56 RGALLLDISGVIVDKPD--------------------QENSLFDIVNTIRQAKDDRNITGIVMDLKNFAGGDQPSMQYIGKALKEFRDSGKPVYAVGENYSQGQYYLASFANKIWLSPQGVVDLHGFATNGLYYKSLLDKLKVSTHVFRVGTYKSAVEPFIRDDMSPAAREADSRWIGELWQNYLNTVAANRQIPAEQVFPGAQGLLEGLTKTGGDTAKYALENKLVDALASSAEIEKALTKEFGWSKTDKNYRAISYYDYALKTPADTGDSIGVVFANGAIMDGEETQGNVGGDTTAAQIRDARLDPKVKAIVLRVNSPGGSVTASEVIRAELAAARAAGKPVVVSMGGMAASGGYWISTPANYIVANPSTLTGSIGIFGVITTVENSLDSIGVHTDGVSTSPLADVSITRALPPEAQLMMQLSIENGYKRFITLVADARHSTPEQIDKIAQGHVWTGQDAKANGLVDSLGDFDDAVAKAAELAKVKQWHLEY 549
                                    65      |  -         -       |95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545    
                                           72                   93                                                                                                                                                                                                                                                                                                                                                                                                                                                                        


Chain C from PDB  Type:PROTEIN  Length:478
 aligned with SPPA_ECOLI | P08395 from UniProtKB/Swiss-Prot  Length:618

    Alignment length:496
                                    65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545      
           SPPA_ECOLI    56 RGALLLDISGVIVDKPDSSQRFSKLSRQLLGASSDRLQENSLFDIVNTIRQAKDDRNITGIVMDLKNFAGGDQPSMQYIGKALKEFRDSGKPVYAVGENYSQGQYYLASFANKIWLSPQGVVDLHGFATNGLYYKSLLDKLKVSTHVFRVGTYKSAVEPFIRDDMSPAAREADSRWIGELWQNYLNTVAANRQIPAEQVFPGAQGLLEGLTKTGGDTAKYALENKLVDALASSAEIEKALTKEFGWSKTDKNYRAISYYDYALKTPADTGDSIGVVFANGAIMDGEETQGNVGGDTTAAQIRDARLDPKVKAIVLRVNSPGGSVTASEVIRAELAAARAAGKPVVVSMGGMAASGGYWISTPANYIVANPSTLTGSIGIFGVITTVENSLDSIGVHTDGVSTSPLADVSITRALPPEAQLMMQLSIENGYKRFITLVADARHSTPEQIDKIAQGHVWTGQDAKANGLVDSLGDFDDAVAKAAELAKVKQWHLEYYV 551
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3bf0C01 C:56-178,                  C:221-318 2-enoyl-CoA Hydratase; Chain A, domain 1                                      ----------3bf0C02 C:189-220,C:433-498     3bf0C01 C:56-178,C:221-318 2-enoyl-CoA Hydratase; Chain A, domain 1                               3bf0C03 C:319-432,C:499-551 2-enoyl-CoA Hydratase; Chain A, domain 1                                              3bf0C02 C:189-220,C:433-498 peptide peptidase (sppa) like domain  3bf0C03 C:319-432,C:499-551                           CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...eeee....------------------...eeehhhhhhhhhhhhhh..eeeeeee...eee.hhhhhhhhhhhhhhhhhh...eeeee..eehhhhhhhh...eeee.....ee.......eeehhhhhhhhh.eeeeeee...hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.hhhhhhhhhhhh..hhhhhhhhh....ee.hhhhhhhhhhhhhhee....ee.eee.hhh..........eeeeeeee..ee........eehhhhhhhhhhhhhh..eeeeeeeeee...hhhhhhhhhhhhhhhhhh...eeeeeeeee.hhhhhh.....eeee....eee...eeeeeeehhhhhhhh..eee....hhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhh.....eeehhhhhhh....ee.hhhhhhhhhhhh.....eeee... Sec.struct. author
             SAPs(SNPs) (1) -----------------------------------------------------------------------------------------------I----------------------------------S-----------------------------------------------------------------H-----------------------------------------T----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------K----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (2)
             SAPs(SNPs) (3) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Q----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (3)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bf0 C  56 RGALLLDISGVIVDKPD------------------RLQENSLFDIVNTIRQAKDDRNITGIVMDLKNFAGGDQPSMQYIGKALKEFRDSGKPVYAVGENYSQGQYYLASFANKIWLSPQGVVDLHGFATNGLYYKSLLDKLKVSTHVFRVGTYKSAVEPFIRDDMSPAAREADSRWIGELWQNYLNTVAANRQIPAEQVFPGAQGLLEGLTKTGGDTAKYALENKLVDALASSAEIEKALTKEFGWSKTDKNYRAISYYDYALKTPADTGDSIGVVFANGAIMDGEETQGNVGGDTTAAQIRDARLDPKVKAIVLRVNSPGGSVTASEVIRAELAAARAAGKPVVVSMGGMAASGGYWISTPANYIVANPSTLTGSIGIFGVITTVENSLDSIGVHTDGVSTSPLADVSITRALPPEAQLMMQLSIENGYKRFITLVADARHSTPEQIDKIAQGHVWTGQDAKANGLVDSLGDFDDAVAKAAELAKVKQWHLEYYV 551
                                    65      |  -         -     |  95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545      
                                           72                 91                                                                                                                                                                                                                                                                                                                                                                                                                                                                            


Chain D from PDB  Type:PROTEIN  Length:476
 aligned with SPPA_ECOLI | P08395 from UniProtKB/Swiss-Prot  Length:618

    Alignment length:494
                                    65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545    
           SPPA_ECOLI    56 RGALLLDISGVIVDKPDSSQRFSKLSRQLLGASSDRLQENSLFDIVNTIRQAKDDRNITGIVMDLKNFAGGDQPSMQYIGKALKEFRDSGKPVYAVGENYSQGQYYLASFANKIWLSPQGVVDLHGFATNGLYYKSLLDKLKVSTHVFRVGTYKSAVEPFIRDDMSPAAREADSRWIGELWQNYLNTVAANRQIPAEQVFPGAQGLLEGLTKTGGDTAKYALENKLVDALASSAEIEKALTKEFGWSKTDKNYRAISYYDYALKTPADTGDSIGVVFANGAIMDGEETQGNVGGDTTAAQIRDARLDPKVKAIVLRVNSPGGSVTASEVIRAELAAARAAGKPVVVSMGGMAASGGYWISTPANYIVANPSTLTGSIGIFGVITTVENSLDSIGVHTDGVSTSPLADVSITRALPPEAQLMMQLSIENGYKRFITLVADARHSTPEQIDKIAQGHVWTGQDAKANGLVDSLGDFDDAVAKAAELAKVKQWHLEY 549
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3bf0D01 D:56-178,D                  :221-318 2-enoyl-CoA Hydratase; Chain A, domain 1                                      ----------3bf0D02 D:189-220,D:433-498     3bf0D01 D:56-178,D:221-318 2-enoyl-CoA Hydratase; Chain A, domain 1                               3bf0D03 D:319-432,D:499-549 2-enoyl-CoA Hydratase; Chain A, domain 1                                              3bf0D02 D:189-220,D:433-498 peptide peptidase (sppa) like domain  3bf0D03 D:319-432,D:499-549                         CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...eeee.....------------------.eeeehhhhhhhhhhhhhh..eeeeeee...eee.hhhhhhhhhhhhhhhhhh...eeeee...hhhhhhhhh...eeee..............eeehhhhhhhh..eeeeeee...hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.hhhhhhhhhhh...hhhhhhhhh....ee.hhhhhhhhhhhhhhee....ee.eee..............eeeeeeee..ee........eehhhhhhhhhhhhhh..eeeeeeeeee...hhhhhhhhhhhhhhhhhh...eeeeeeeeeehhhhhh.....eeee....eee...eeeeeeehhhhhhhh..eee....hhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh...eeehhhhhhh....ee.hhhhhhhhhhhhh.....eee. Sec.struct. author
             SAPs(SNPs) (1) -----------------------------------------------------------------------------------------------I----------------------------------S-----------------------------------------------------------------H-----------------------------------------T--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------K--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (2)
             SAPs(SNPs) (3) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Q--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (3)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bf0 D  56 RGALLLDISGVIVDKPDS------------------LQENSLFDIVNTIRQAKDDRNITGIVMDLKNFAGGDQPSMQYIGKALKEFRDSGKPVYAVGENYSQGQYYLASFANKIWLSPQGVVDLHGFATNGLYYKSLLDKLKVSTHVFRVGTYKSAVEPFIRDDMSPAAREADSRWIGELWQNYLNTVAANRQIPAEQVFPGAQGLLEGLTKTGGDTAKYALENKLVDALASSAEIEKALTKEFGWSKTDKNYRAISYYDYALKTPADTGDSIGVVFANGAIMDGEETQGNVGGDTTAAQIRDARLDPKVKAIVLRVNSPGGSVTASEVIRAELAAARAAGKPVVVSMGGMAASGGYWISTPANYIVANPSTLTGSIGIFGVITTVENSLDSIGVHTDGVSTSPLADVSITRALPPEAQLMMQLSIENGYKRFITLVADARHSTPEQIDKIAQGHVWTGQDAKANGLVDSLGDFDDAVAKAAELAKVKQWHLEY 549
                                    65       | -         -      | 95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545    
                                            73                 92
   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 3BF0)

(-) CATH Domains  (2, 12)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Architecture: 3-Layer(aba) Sandwich (12045)
(-)
Architecture: Alpha-Beta Complex (3881)
(-)
Topology: 2-enoyl-CoA Hydratase; Chain A, domain 1 (89)
(-)
Homologous Superfamily: 2-enoyl-CoA Hydratase; Chain A, domain 1 (89)
(-)
Escherichia coli. Organism_taxid: 562. (3)
2a3bf0C01C:56-178,C:221-318
2b3bf0D01D:56-178,D:221-318
2c3bf0A01A:56-178,A:221-318
2d3bf0B01B:56-178,B:221-318
2e3bf0C03C:319-432,C:499-551
2f3bf0A03A:319-432,A:499-549
2g3bf0B03B:319-432,B:499-549
2h3bf0D03D:319-432,D:499-549

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3BF0)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (SPPA_ECOLI | P08395)
molecular function
    GO:0004175    endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain.
    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:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    GO:0008236    serine-type peptidase activity    Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
biological process
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0006465    signal peptide processing    The proteolytic removal of a signal peptide from a protein during or after transport to a specific location in the cell.
cellular component
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0005887    integral component of plasma membrane    The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 3bf0)
 
  Sites
(no "Sites" information available for 3bf0)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3bf0)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3bf0
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  SPPA_ECOLI | P08395
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.4.21.-
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  SPPA_ECOLI | P08395
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        SPPA_ECOLI | P08395: 3bez

(-) Related Entries Specified in the PDB File

3bez