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(-) Description

Title :  CRYSTAL STRUCTURE OF THE TYPE-I SIGNAL PEPTIDASE FROM STAPHYLOCOCCUS AUREUS (SPSB) IN COMPLEX WITH A SUBSTRATE PEPTIDE (PEP2).
 
Authors :  P. G. Young, Y. T. Ting, E. N. Baker
Date :  05 Nov 14  (Deposition) - 23 Sep 15  (Release) - 17 Feb 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,D
Keywords :  Spsb Type-I Signal Peptidase, Peptide Complex, Cell Secretion, Mbp Fusion, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. T. Ting, P. W. R. Harris, G. Batot, M. A. Brimble, E. N. Baker, P. G. Young
Peptide Binding To A Bacterial Signal Peptidase Visualized By Peptide Tethering And Carrier-Driven Crystallization
Iucrj V. 3 10 2016
PubMed: search  |  Reference-DOI: 10.1107/S2052252515019971

(-) Compounds

Molecule 1 - MALTOSE-BINDING PERIPLASMIC PROTEIN,SIGNAL PEPTIDASE IB
    Chains: A
    EC Number: 3.4.21.89
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMBP-PPROEXHTA
    Expression System Strain: K12
    Expression System Taxid: 83333
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 33-393, UNP RESIDUES 26-175
    Gene: MALE, Z5632, ECS5017, SPSB, SACOL0969
    Mutation: YES
    Organism Taxid: 83334, 93062
    Strain: COL
    Synonym: MBP,MMBP,MALTODEXTRIN-BINDING PROTEIN,SPASE IB,LEADER PEPTIDASE IB
 
Molecule 2 - SUBSTRATE PEPTIDE (PEP2)
    Chains: D
    Engineered: YES
    Organism Scientific: STAPHYLOCOCCUS AUREUS
    Organism Taxid: 1280
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1MAL1Ligand/IonMALTOSE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:18 , ASP A:20 , LYS A:21 , TRP A:68 , ALA A:69 , ASP A:71 , ARG A:72 , GLU A:117 , GLU A:159 , PRO A:160 , TYR A:161 , TRP A:346 , ARG A:350 , HOH A:803 , HOH A:848 , HOH A:890 , HOH A:1018binding site for residue MAL A 601

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4WVI)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Asp A:389 -Pro A:390

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4WVI)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4WVI)

(-) Exons   (0, 0)

(no "Exon" information available for 4WVI)

(-) 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:521
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee.....hhhhhhhhhhhhhhhhh..eeee...hhhhhhhhhh......eeeee..hhhhhhhh........hhhhhh..hhhhhhhhee..ee..eeeeee..eeeee.........hhhhhhhhhhhhhh...eee.....hhhhhhhhhhhh..eeeeee..eeeeeeee..hhhhhhhhhhhhhhhhh.......hhhhhhhhhhh..eeeeeehhhhhhhhhhhh..eeee............eeeeeeeee.....hhhhhhhhhhhh..hhhhhhhhhhhh...ee.hhhhhhhhh.hhhhhhhhhhhhhhee.....hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.eeeeeee............eeeeee...........eeeee.....eeeeeeee.....eeee..eeee..eee.hhhhhhhhh..........ee.hhh.............eeeee........hhhhhh.ee...eeeee........... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wvi A  10 HHMLVIWINGDKGYNGLAQVGKKFEKDTGIKVTVEHPYKLEEKFPQVAATGGPDIIFWAHDRFGGYACSGLLAEITPDKAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPALDGELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYENGKYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSKVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPLGAVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDEALKDAQTNAGAIVTPYTIKGESMDPTLKDGERVAVNIVGYKTGLEKGNVVVFHANKNDDYVKRVIGVPGDKVEYKNDTLYVNGKKQDEPYLNYNLKHKQGDYITGTFQVKDLPNANPKSNVIPKGKYLVLGDNREVSKDSRAFGLIDEDQIVGKVSFRFWSHPQFE 532
                                    19        29        39        49        59||      70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400      |411       421       431       441       451       461       471       481       491       501       511       521       531 
                                                                             60|                                                                                                                                                                                                                                                                                                                                                      407|                                                                                                                           
                                                                              62                                                                                                                                                                                                                                                                                                                                                       409                                                                                                                           


Chain D from PDB  Type:PROTEIN  Length:11
                                           
               SCOP domains ----------- SCOP domains
               CATH domains ----------- CATH domains
               Pfam domains ----------- Pfam domains
         Sec.struct. author .......eee. Sec.struct. author
                 SAPs(SNPs) ----------- SAPs(SNPs)
                    PROSITE ----------- PROSITE
                 Transcript ----------- Transcript
                 4wvi D 189 GGGGAVPTAKA 199
                                   198
   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 4WVI)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4WVI)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4WVI)

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)

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    Asp A:389 - Pro A:390   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        LEP_STAAC | Q5HHB9: 4wvg 4wvh 4wvj
        MALE_ECO57 | P0AEY0: 1a7l 1anf 1dmb 1ez9 1ezo 1ezp 1fqa 1fqb 1fqc 1fqd 1hsj 1iud 1jvx 1jvy 1jw4 1jw5 1lax 1lls 1mdp 1mdq 1mg1 1mh3 1mh4 1mpb 1mpc 1mpd 1n3w 1n3x 1nl5 1nmu 1omp 1peb 1r6z 1svx 1t0k 1y4c 1ytv 1ziu 1zjl 1zkb 1zmg 2v93 3io4 3io6 3mbp 3osq 3osr 3vd8 4feb 4mbp 4my2 4wgi 4wrn 4wth 4wvg 4wvh 4wvj 4xa2 4xai 4xaj 4xhs 4ys9 5bmy 5c7r 5cl1 5dfm 5e24 5e7u 5edu 5fio 5ii4 5jj4 5jon 5jtq 5jtr 5k94 5ldf 5lof 5t03 5t05 5t0a 5ttd

(-) Related Entries Specified in the PDB File

4wvg 4wvh 4wvj