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(-) Description

Title :  CRYSTAL STRUCTURE ANALYSIS OF THE K2 CLEAVED ADHESIN DOMAIN OF LYS-GINGIPAIN (KGP)
 
Authors :  N. Li, C. A. Collyer, N. Hunter
Date :  09 Nov 09  (Deposition) - 31 Mar 10  (Release) - 26 May 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Beta Jelly Roll Barrel, Cleaved Adhesin Family, Lys-Gingipain, Hemagglutination Domain, Cell Invasion (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Li, P. Yun, M. A. Nadkarni, N. B. Ghadikolaee, K. -A. Nguyen, M. Lee, N. Hunter, C. A. Collyer
Structure Determination And Analysis Of A Haemolytic Gingipain Adhesin Domain From Porphyromonas Gingivalis
Mol. Microbiol. V. 76 861 2010
PubMed-ID: 20233299  |  Reference-DOI: 10.1111/J.1365-2958.2010.07123.X

(-) Compounds

Molecule 1 - LYSINE SPECIFIC CYSTEINE PROTEASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET32
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: K2 CLEAVED ADHESIN DOMAIN, RESIDUES 1157-1334
    Gene: KGP
    Organism Scientific: PORPHYROMONAS GINGIVALIS
    Organism Taxid: 242619
    Strain: W83

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 8)

Asymmetric Unit (4, 8)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION
2GOL1Ligand/IonGLYCEROL
3NO32Ligand/IonNITRATE ION
4SO41Ligand/IonSULFATE ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2GOL-1Ligand/IonGLYCEROL
3NO31Ligand/IonNITRATE ION
4SO41Ligand/IonSULFATE ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2GOL1Ligand/IonGLYCEROL
3NO31Ligand/IonNITRATE ION
4SO4-1Ligand/IonSULFATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:3 , ASP A:1179 , ASP A:1181 , ASP A:1183 , GLN A:1185 , ASN A:1221BINDING SITE FOR RESIDUE CA A 2011
2AC2SOFTWAREHOH A:8 , THR A:1162 , GLU A:1164 , GLY A:1202 , ASN A:1205 , ASP A:1326BINDING SITE FOR RESIDUE CA A 2012
3AC3SOFTWAREHOH A:52 , HOH A:172 , HOH A:259 , HOH A:288 , GLU A:1161 , THR A:1162 , PHE A:1163 , GLU A:1164 , SER A:1165 , ASN B:1218BINDING SITE FOR RESIDUE SO4 A 2022
4AC4SOFTWAREHOH A:304 , GLY A:1184 , GLN A:1185 , GLY A:1186 , LEU A:1188 , ARG A:1299 , THR A:1300BINDING SITE FOR RESIDUE NO3 A 2021
5AC5SOFTWAREHOH B:58 , TRP B:1197 , LEU B:1198 , THR B:1199 , ALA B:1239 , VAL B:1240 , GLN B:1293 , SER B:1294 , TRP B:1296 , TYR B:1322BINDING SITE FOR RESIDUE GOL B 2001
6AC6SOFTWAREHOH B:116 , ASP B:1179 , ASP B:1181 , ASP B:1183 , GLN B:1185 , ASN B:1221BINDING SITE FOR RESIDUE CA B 2011
7AC7SOFTWAREHOH B:2 , THR B:1162 , GLU B:1164 , GLY B:1202 , ASN B:1205 , ASP B:1326BINDING SITE FOR RESIDUE CA B 2012
8AC8SOFTWAREHOH B:121 , HOH B:237 , GLY B:1184 , GLN B:1185 , GLY B:1186 , LEU B:1188 , GLU B:1298 , ARG B:1299 , THR B:1300BINDING SITE FOR RESIDUE NO3 B 2021

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3KM5)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3KM5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3KM5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3KM5)

(-) Exons   (0, 0)

(no "Exon" information available for 3KM5)

(-) 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:179
 aligned with HAGA1_PORGI | P59915 from UniProtKB/Swiss-Prot  Length:2164

    Alignment length:180
                                  1143      1153      1163      1173      1183      1193      1203      1213      1223      1233      1243      1253      1263      1273      1283      1293      1303      1313
         HAGA1_PORGI   1134 GKRADFTETFESSTHGEAPAEWTTIDADGDGQGWLCLSSGQLDWLTAHGGTNVVASFSWNGMALNPDNYLISKDVTGATKVKYYYAVNDGFPGDHYAVMISKTGTNAGDFTVVFEETPNGINKGGARFGLSTEANGAKPQSVWIERTVDLPAGTKYVAFRHYNCSDLNYILLDDIQFTMG 1313
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .-...eee..............eeee........eeee.............eeeeee.........eeeee........eeeeeeee........eeeeee....hhh.eeeeeee...........................eeeeee......eeeeeee......eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                3km5 A 1155 G-SADFTETFESSTHGEAPAEWTTIDADGDGQGWLCLSSGQLDWLTAHGGSNVVSSFSWNGMALNPDNYLISKDVTGATKVKYYYAVNDGFPGDHYAVMISKTGTNAGDFTVVFEETPNGINKGGARFGLSTEANGAKPQSVWIERTVDLPAGTKYVAFRHYNCSDLNYILLDDIQFTMG 1333
                            | |   1163      1173      1183      1193      1203      1213      1223      1233      1243      1253      1263      1273      1283      1293      1303      1313      1323      1333
                            | |                                                                                                                                                                                 
                         1155 |                                                                                                                                                                                 
                           1156                                                                                                                                                                                 


Chain A from PDB  Type:PROTEIN  Length:179
 aligned with KGP83_PORGN | Q51817 from UniProtKB/Swiss-Prot  Length:1732

    Alignment length:180
                                  1163      1173      1183      1193      1203      1213      1223      1233      1243      1253      1263      1273      1283      1293      1303      1313      1323      1333
         KGP83_PORGN   1154 GKRADFTETFESSTHGEAPAEWTTIDADGDGQGWLCLSSGQLDWLTAHGGSNVVSSFSWNGMALNPDNYLISKDVTGATKVKYYYAVNDGFPGDHYAVMISKTGTNAGDFTVVFEETPNGINKGGARFGLSTEANGAKPQSVWIERTVDLPAGTKYVAFRHYNCSDLNYILLDDIQFTMG 1333
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .-...eee..............eeee........eeee.............eeeeee.........eeeee........eeeeeeee........eeeeee....hhh.eeeeeee...........................eeeeee......eeeeeee......eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                3km5 A 1155 G-SADFTETFESSTHGEAPAEWTTIDADGDGQGWLCLSSGQLDWLTAHGGSNVVSSFSWNGMALNPDNYLISKDVTGATKVKYYYAVNDGFPGDHYAVMISKTGTNAGDFTVVFEETPNGINKGGARFGLSTEANGAKPQSVWIERTVDLPAGTKYVAFRHYNCSDLNYILLDDIQFTMG 1333
                            | |   1163      1173      1183      1193      1203      1213      1223      1233      1243      1253      1263      1273      1283      1293      1303      1313      1323      1333
                         1155 |                                                                                                                                                                                 
                           1156                                                                                                                                                                                 


Chain B from PDB  Type:PROTEIN  Length:173
 aligned with HAGA1_PORGI | P59915 from UniProtKB/Swiss-Prot  Length:2164

    Alignment length:176
                                  1146      1156      1166      1176      1186      1196      1206      1216      1226      1236      1246      1256      1266      1276      1286      1296      1306      
         HAGA1_PORGI   1137 ADFTETFESSTHGEAPAEWTTIDADGDGQGWLCLSSGQLDWLTAHGGTNVVASFSWNGMALNPDNYLISKDVTGATKVKYYYAVNDGFPGDHYAVMISKTGTNAGDFTVVFEETPNGINKGGARFGLSTEANGAKPQSVWIERTVDLPAGTKYVAFRHYNCSDLNYILLDDIQFTM 1312
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --Cleaved_Adhesin-3km5B01 B:1159-1330                                                                                                                                         -- Pfam domains (1)
           Pfam domains (2) --Cleaved_Adhesin-3km5B02 B:1159-1330                                                                                                                                         -- Pfam domains (2)
         Sec.struct. author ..eee..............eeee........eeee.............eeeeee.........eeeee........eeeeeeee........eeeeee....hhh.eeeeeee.................---.......eeeeee......eeeeeee......eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3km5 B 1157 ADFTETFESSTHGEAPAEWTTIDADGDGQGWLCLSSGQLDWLTAHGGSNVVSSFSWNGMALNPDNYLISKDVTGATKVKYYYAVNDGFPGDHYAVMISKTGTNAGDFTVVFEETPNGINKGGARFGLSTE---AKPQSVWIERTVDLPAGTKYVAFRHYNCSDLNYILLDDIQFTM 1332
                                  1166      1176      1186      1196      1206      1216      1226      1236      1246      1256      1266      1276      1286   |  1296      1306      1316      1326      
                                                                                                                                                          1286   |                                          
                                                                                                                                                              1290                                          


Chain B from PDB  Type:PROTEIN  Length:173
 aligned with KGP83_PORGN | Q51817 from UniProtKB/Swiss-Prot  Length:1732

    Alignment length:176
                                  1166      1176      1186      1196      1206      1216      1226      1236      1246      1256      1266      1276      1286      1296      1306      1316      1326      
         KGP83_PORGN   1157 ADFTETFESSTHGEAPAEWTTIDADGDGQGWLCLSSGQLDWLTAHGGSNVVSSFSWNGMALNPDNYLISKDVTGATKVKYYYAVNDGFPGDHYAVMISKTGTNAGDFTVVFEETPNGINKGGARFGLSTEANGAKPQSVWIERTVDLPAGTKYVAFRHYNCSDLNYILLDDIQFTM 1332
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --Cleaved_Adhesin-3km5B01 B:1159-1330                                                                                                                                         -- Pfam domains (1)
           Pfam domains (2) --Cleaved_Adhesin-3km5B02 B:1159-1330                                                                                                                                         -- Pfam domains (2)
         Sec.struct. author ..eee..............eeee........eeee.............eeeeee.........eeeee........eeeeeeee........eeeeee....hhh.eeeeeee.................---.......eeeeee......eeeeeee......eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3km5 B 1157 ADFTETFESSTHGEAPAEWTTIDADGDGQGWLCLSSGQLDWLTAHGGSNVVSSFSWNGMALNPDNYLISKDVTGATKVKYYYAVNDGFPGDHYAVMISKTGTNAGDFTVVFEETPNGINKGGARFGLSTE---AKPQSVWIERTVDLPAGTKYVAFRHYNCSDLNYILLDDIQFTM 1332
                                  1166      1176      1186      1196      1206      1216      1226      1236      1246      1256      1266      1276      1286   |  1296      1306      1316      1326      
                                                                                                                                                          1286   |                                          
                                                                                                                                                              1290
   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 3KM5)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3KM5)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: GBD (153)

(-) Gene Ontology  (8, 13)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (HAGA1_PORGI | P59915)
molecular function
    GO:0008234    cysteine-type peptidase activity    Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
    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.
biological process
    GO:0009405    pathogenesis    The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.

Chain A,B   (KGP83_PORGN | Q51817)
molecular function
    GO:0004197    cysteine-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
    GO:0008234    cysteine-type peptidase activity    Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
    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.
biological process
    GO:0009405    pathogenesis    The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.

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  KGP83_PORGN | Q51817
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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3KM5)