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(-) Description

Title :  PORPHYROMONAS GINGIVALIS GINGIPAIN K (KGP) CATALYTIC AND IMMUNOGLOBULIN SUPERFAMILY-LIKE DOMAINS
 
Authors :  I. De Diego, F. Veillard, M. N. Sztukowska, T. Guevara, B. Potempa, A. P J. A. Huntington, J. Potempa, F. X. Gomis-Ruth
Date :  12 Sep 14  (Deposition) - 08 Oct 14  (Release) - 10 Dec 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym./Biol. Unit :  A
Keywords :  Alpha/Beta-Hydrolase, Cysteine Peptidase, Lysine-Containing Substrates, Extracellular, Secreted, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. De Diego, F. Veillard, M. N. Sztukowska, T. Guevara, B. Potempa, A. Pomowski, J. A. Huntington, J. Potempa, F. X. Gomis-Ruth
Structure And Mechanism Of Cysteine Peptidase Gingipain K (Kgp), A Major Virulence Factor Of Porphyromonas Gingivalis In Periodontitis.
J. Biol. Chem. V. 289 32291 2014
PubMed-ID: 25266723  |  Reference-DOI: 10.1074/JBC.M114.602052

(-) Compounds

Molecule 1 - LYS-GINGIPAIN W83
    Chains: A
    EC Number: 3.4.22.47
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 229-683
    Gene: KGP, PRTK, PRTP
    Organism Scientific: PORPHYROMONAS GINGIVALIS
    Organism Taxid: 837
    Synonym: LYSINE SPECIFIC CYSTEINE PROTEASE, LYSINE-SPECIFIC CYSTEINE PROTEINASE, PORPHYPAIN, PRTK48, LYS-GINGIPAIN CATALYTIC SUBUNIT, 39 KDA ADHESIN, PRTK39, 15 KDA ADHESIN, PRTK15, 44 KDA ADHESIN, PRTK44

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (8, 17)

Asymmetric/Biological Unit (8, 17)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2AZI3Ligand/IonAZIDE ION
3CA2Ligand/IonCALCIUM ION
4CKC1Ligand/Ion(3S)-3,7-DIAMINOHEPTAN-2-ONE
5GOL4Ligand/IonGLYCEROL
6HIS1Mod. Amino AcidHISTIDINE
7NA3Ligand/IonSODIUM ION
8NI1Ligand/IonNICKEL (II) ION

(-) Sites  (17, 17)

Asymmetric Unit (17, 17)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:313 , PHE A:482 , GLU A:491 , HOH A:816 , HOH A:850 , HOH A:853BINDING SITE FOR RESIDUE CA A 701
02AC2SOFTWAREASP A:337 , ASP A:339 , PHE A:341 , GLU A:343 , HOH A:836 , HOH A:874BINDING SITE FOR RESIDUE CA A 702
03AC3SOFTWARETYR A:402 , VAL A:521 , THR A:536 , SER A:537 , ASP A:542 , HOH A:1275BINDING SITE FOR RESIDUE NA A 703
04AC4SOFTWAREALA A:543 , THR A:544 , LEU A:546 , SER A:549 , TYR A:550 , ASN A:551BINDING SITE FOR RESIDUE NA A 704
05AC5SOFTWAREGLU A:355 , GLU A:379 , HIS A:707 , ACT A:708BINDING SITE FOR RESIDUE NI A 705
06AC6SOFTWARETHR A:415 , GLU A:498 , HOH A:891 , HOH A:904 , HOH A:1060 , HOH A:1204BINDING SITE FOR RESIDUE NA A 706
07AC7SOFTWAREGLU A:355 , GLU A:379 , NI A:705 , ACT A:708 , HOH A:992BINDING SITE FOR RESIDUE HIS A 707
08AC8SOFTWAREGLU A:355 , GLU A:379 , LYS A:497 , NI A:705 , HIS A:707 , HOH A:1313 , HOH A:1315BINDING SITE FOR RESIDUE ACT A 708
09AC9SOFTWAREGLU A:356 , ARG A:495 , HOH A:881 , HOH A:1066 , HOH A:1134BINDING SITE FOR RESIDUE ACT A 709
10BC1SOFTWAREHIS A:234 , ASP A:339 , TYR A:389 , SER A:390 , AZI A:712 , HOH A:1221 , HOH A:1251BINDING SITE FOR RESIDUE AZI A 710
11BC2SOFTWAREHIS A:234 , GLY A:235 , LEU A:237 , TRP A:558 , HOH A:1327BINDING SITE FOR RESIDUE AZI A 711
12BC3SOFTWAREASP A:233 , HIS A:234 , ASP A:388 , AZI A:710 , HOH A:1001 , HOH A:1221BINDING SITE FOR RESIDUE AZI A 712
13BC4SOFTWARELYS A:288 , GLU A:320 , TYR A:332 , HOH A:1097BINDING SITE FOR RESIDUE GOL A 713
14BC5SOFTWARETYR A:418 , ASN A:419 , TYR A:420 , GOL A:716BINDING SITE FOR RESIDUE GOL A 714
15BC6SOFTWARETYR A:420 , LEU A:421 , LYS A:422 , PRO A:424 , HOH A:1076 , HOH A:1140BINDING SITE FOR RESIDUE GOL A 715
16BC7SOFTWAREASP A:416 , VAL A:417 , TYR A:418 , LYS A:466 , GOL A:714 , HOH A:904 , HOH A:1162 , HOH A:1317BINDING SITE FOR RESIDUE GOL A 716
17BC8SOFTWAREASP A:229 , THR A:232 , THR A:442 , ALA A:443 , HIS A:444 , GLY A:445 , ASN A:475 , CYS A:477 , SER A:511 , TRP A:513 , ASP A:516 , HOH A:929 , HOH A:1045 , HOH A:1142BINDING SITE FOR RESIDUE CKC A 717

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Thr A:240 -Pro A:241
2Ala A:423 -Pro A:424
3Asp A:452 -Pro A:453

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4RBM)

(-) 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:453
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh.......eeeeeee...hhhhhhhhhhhhhhh.eeeeeee........hhhhhhhhhhhhhhhhhhh.....eeeee........ee......eehhhhhh.........eeeee...hhhhhhhhhhhhhhhhh....hhhhh.eeeeee....hhhhhhhhhhhhhhhhhh.hhhhh..eeeee........hhhhhhh..eeeee..ee..ee....eehhhhhh.......eeeeee............hhhhhhhhh....eeeeeee....hhhhhhhhhhh................hhhhhhhh.....hhhhhhhhhhhhhhhhhhh......hhhhhhhheeeee...............ee..........eeeeee....eeeeee..eeeeeee.....eeeeee.......eeeeeeee......eeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rbm A 229 DVYTDHGDLYNTPVRMLVVAGAKFKEALKPWLTWKAQKGFYLDVHYTDEAEVGTTNASIKAFIHKKYNDGLAASAAPVFLALVGDTDVISGEKGKKTKKVTDLYYSAVDGDYFPEMYTFRMSASSPEELTNIIDKVLMYEKATMPDKSYLEKVLLIAGADYSWNSQVGQPTIKYGMQYYYNQEHGYTDVYNYLKAPYTGCYSHLNTGVSFANYTAHGSETAWADPLLTTSQLKALTNKDKYFLAIGNCCITAQFDYVQPCFGEVITRVKEKGAYAYIGSSPNSYWGEDYYWSVGANAVFGVQPTFEGTSMGSYDATFLEDSYNTVNSIMWAGNLAATHAGNIGNITHIGAHYYWEAYHVLGDGSVMPYRAMPKTNTYTLPASLPQNQASYSIQASAGSYVAISKDGVLYGTGVANASGVATVSMTKQITENGNYDVVITRSNYLPVIKQIQVH 707
                                   238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628       638       648       658       668       678 ||
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             680|
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              707
   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 4RBM)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)

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  KGP83_PORGN | Q51817
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        KGP83_PORGN | Q51817: 3km5 3m1h 4itc 4tkx 5mun

(-) Related Entries Specified in the PDB File

1cvr GINGIPAIN R2 (RGPB) CATALYTIC AND IMMUNOGLOBULIN SUPERFAMILY-LIKE DOMAINS
4ief GINGIPAIN R2 (RGPB) PRO, CATALYTIC AND IMMUNOGLOBULIN SUPERFAMILY-LIKE DOMAINS