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(-) Description

Title :  CRYSTAL STRUCTURE ANALYSIS OF THE K1 CLEAVED ADHESIN DOMAIN OF LYS-GINGIPAIN (KGP) FROM PORPHYROMONAS GINGIVALIS W83
 
Authors :  L. A. Ganuelas, N. Li, N. Hunter, C. A. Collyer
Date :  18 Jan 13  (Deposition) - 25 Sep 13  (Release) - 15 Jan 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.55
Chains :  Asym./Biol. Unit :  A
Keywords :  Beta Sandwich, Cleaved Adhesin Family, Lys-Gingipain, Hemagglutinin Domain, Cell Invasion, Cysteine Protease, Calcium Binding, Membrane Surface, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. A. Ganuelas, N. Li, P. Yun, N. Hunter, C. A. Collyer
The Lysine Gingipain Adhesin Domains From Porphyromonas Gingivalis Interact With Erythrocytes And Albumin: Structures Correlate To Function.
Eur J Microbiol Immunol (Bp) V. 3 152 2013
PubMed-ID: 24265933  |  Reference-DOI: 10.1556/EUJMI.3.2013.3.2

(-) Compounds

Molecule 1 - LYS-GINGIPAIN W83
    Chains: A
    EC Number: 3.4.22.47
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX-5X-3
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: K1 CLEAVED ADHESIN DOMAIN, RESIDUES 982-1154
    Gene: KGP, PRTK, PRTP
    Organism Scientific: PORPHYROMONAS GINGIVALIS
    Organism Taxid: 837
    Strain: W83
    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  (3, 7)

Asymmetric/Biological Unit (3, 7)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2GAI3Ligand/IonGUANIDINE
3GOL2Ligand/IonGLYCEROL

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:1001 , ASP A:1003 , ASP A:1005 , HIS A:1007 , ASN A:1043 , HOH A:1301BINDING SITE FOR RESIDUE CA A 1201
2AC2SOFTWARESER A:988 , GLU A:990 , SER A:1022 , GLY A:1024 , ASP A:1146 , GLU A:1147BINDING SITE FOR RESIDUE CA A 1202
3AC3SOFTWAREPRO A:1053 , ASN A:1054BINDING SITE FOR RESIDUE GAI A 1203
4AC4SOFTWAREASN A:991 , PRO A:994 , TYR A:1069 , ASP A:1139 , MET A:1140 , HOH A:1340BINDING SITE FOR RESIDUE GAI A 1204
5AC5SOFTWARESER A:996 , SER A:1071 , GLN A:1136 , SER A:1137 , THR A:1138 , MET A:1140 , HOH A:1345BINDING SITE FOR RESIDUE GOL A 1205
6AC6SOFTWAREILE A:993 , PRO A:994 , TRP A:997 , THR A:999 , HOH A:1304 , HOH A:1353BINDING SITE FOR RESIDUE GAI A 1206
7AC7SOFTWARELEU A:985 , SER A:986 , GLU A:987 , TRP A:997 , SER A:1071BINDING SITE FOR RESIDUE GOL A 1207

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ala A:1014 -Pro A:1015

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4ITC)

(-) 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:170
                                                                                                                                                                                                           
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..........eeee........eeee..........eeeeee.ee....ee....eeee.........eeeeeeeee........eeeeeee....hhhhh.eeeeeee.................eeeeeee.....eeeeee.......eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4itc A  982 GTTLSESFENGIPASWKTIDADGDGHGWKPGNAPGIAGYNSNGCVYSESFGLGGIGVLTPDNYLITPALDLPNGGKLTFWVCAQDANYASEHYAVYASSTGNDASNFTNALLEETITAKSPKAIRGRIQGTWRQKTVDLPAGTKYVAFRHFQSTDMFYIDLDEVEIKANG 1154
                                   991      1001      1011      1021      1031      1041      1051      1061      1071      1081      1091      1104      1114      1124      1134      1144      1154
                                                                                                                                               1100|                                                  
                                                                                                                                                1104
   Legend:   → Mismatch (orange background)
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  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 4ITC)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        KGP83_PORGN | Q51817: 3km5 3m1h 4rbm 4tkx 5mun

(-) Related Entries Specified in the PDB File

3km5 K2 CLEAVED ADHESIN DOMAIN OF LYS-GINGIPAIN
3m1h K3 CLEAVED ADHESIN DOMAIN OF LYS-GINGIPAIN