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(-) Description

Title :  CRYSTAL STRUCTURE ANALYSIS OF THE K3 CLEAVED ADHESIN DOMAIN OF LYS-GINGIPAIN (KGP) FROM PORPHYROMONAS GINGIVALIS W83
 
Authors :  N. Li, C. A. Collyer, N. Hunter
Date :  05 Mar 10  (Deposition) - 23 Mar 11  (Release) - 18 Sep 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.56
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Beta Jelly Roll Barrel, Cleaved Adhesin Family, Lys-Gingipain, Hemagglutination Domain, Carbohydrate Binding, Protease, Cell Invasion (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Li, P. Yun, C. M. Jeffries, D. Langley, R. Gamsjaeger, W. B. Church, N. Hunter, C. A. Collyer
The Modular Structure Of Haemagglutinin/Adhesin Regions In Gingipains Of Porphyromonas Gingivalis.
Mol. Microbiol. V. 81 1358 2011
PubMed-ID: 21812842  |  Reference-DOI: 10.1111/J.1365-2958.2011.07768.X
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - LYSINE SPECIFIC CYSTEINE PROTEASE
    Chains: A, B, C, D
    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: K3 CLEAVED ADHESIN DOMAIN, RESIDUES 1427-1602
    Gene: KGP
    Organism Common: BACTEROIDES GINGIVALIS
    Organism Scientific: PORPHYROMONAS GINGIVALIS
    Organism Taxid: 242619
    Strain: W83

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 17)

Asymmetric Unit (2, 17)
No.NameCountTypeFull Name
1CA8Ligand/IonCALCIUM ION
2NA9Ligand/IonSODIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2NA-1Ligand/IonSODIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2NA-1Ligand/IonSODIUM ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2NA-1Ligand/IonSODIUM ION
Biological Unit 4 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2NA-1Ligand/IonSODIUM ION

(-) Sites  (17, 17)

Asymmetric Unit (17, 17)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHOH A:211 , ASP A:1446 , ASP A:1448 , ASP A:1450 , ASN A:1452 , ASN A:1490BINDING SITE FOR RESIDUE CA A 2001
02AC2SOFTWAREHOH A:10 , ASP A:1433 , GLU A:1435 , SER A:1470 , ILE A:1472 , ASP A:1595BINDING SITE FOR RESIDUE CA A 2002
03AC3SOFTWAREHOH A:576 , HOH A:691 , HOH A:692 , HOH A:693 , HOH A:695 , ASN A:1431BINDING SITE FOR RESIDUE NA A 2003
04AC4SOFTWAREHOH A:163 , HOH A:366 , HOH A:460 , HOH A:604 , HOH A:682 , ASN A:1530 , HOH D:327BINDING SITE FOR RESIDUE NA A 2004
05AC5SOFTWAREHOH A:259 , HOH A:713 , HOH A:822 , HOH A:823 , ALA A:1440 , TRP A:1442BINDING SITE FOR RESIDUE NA A 2005
06AC6SOFTWAREHOH B:18 , ASP B:1446 , ASP B:1448 , ASP B:1450 , ASN B:1452 , ASN B:1490BINDING SITE FOR RESIDUE CA B 2001
07AC7SOFTWAREHOH B:477 , ASP B:1433 , GLU B:1435 , SER B:1470 , ILE B:1472 , ASP B:1595BINDING SITE FOR RESIDUE CA B 2002
08AC8SOFTWAREHOH B:518 , HOH B:686 , HOH B:687 , HOH B:688 , HOH B:689 , HOH B:690 , ASN B:1431BINDING SITE FOR RESIDUE NA B 2003
09AC9SOFTWAREHOH B:294 , HOH B:321 , HOH B:455 , HOH B:683 , HOH B:685 , ASN B:1530 , HOH C:684BINDING SITE FOR RESIDUE NA B 2004
10BC1SOFTWAREHOH B:485 , HOH B:497 , HOH B:824 , HOH B:825 , ALA B:1440 , TRP B:1442BINDING SITE FOR RESIDUE NA B 2005
11BC2SOFTWAREHOH C:100 , ASP C:1446 , ASP C:1448 , ASP C:1450 , ASN C:1452 , ASN C:1490BINDING SITE FOR RESIDUE CA C 2001
12BC3SOFTWAREHOH C:36 , ASP C:1433 , GLU C:1435 , SER C:1470 , ILE C:1472 , ASP C:1595BINDING SITE FOR RESIDUE CA C 2002
13BC4SOFTWAREHOH C:513 , HOH C:514 , HOH C:515 , HOH C:516 , HOH C:517 , ASN C:1431 , SER D:1498BINDING SITE FOR RESIDUE NA C 2003
14BC5SOFTWAREHOH B:611 , HOH C:154 , HOH C:387 , HOH C:498 , HOH C:781 , GLU C:1483BINDING SITE FOR RESIDUE NA C 2004
15BC6SOFTWAREHOH D:28 , ASP D:1446 , ASP D:1448 , ASP D:1450 , ASN D:1452 , ASN D:1490BINDING SITE FOR RESIDUE CA D 2001
16BC7SOFTWAREHOH D:285 , ASP D:1433 , GLU D:1435 , SER D:1470 , ILE D:1472 , ASP D:1595BINDING SITE FOR RESIDUE CA D 2002
17BC8SOFTWAREHOH A:505 , HOH A:820 , HOH D:271 , HOH D:705 , HOH D:709 , GLU D:1483BINDING SITE FOR RESIDUE NA D 2003

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3M1H)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Pro A:1459 -Pro A:1460
2Pro B:1459 -Pro B:1460
3Pro C:1459 -Pro C:1460
4Pro D:1459 -Pro D:1460

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3M1H)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3M1H)

(-) Exons   (0, 0)

(no "Exon" information available for 3M1H)

(-) 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:174
 aligned with KGP83_PORGN | Q51817 from UniProtKB/Swiss-Prot  Length:1732

    Alignment length:176
                                  1436      1446      1456      1466      1476      1486      1496      1506      1516      1526      1536      1546      1556      1566      1576      1586      1596      
         KGP83_PORGN   1427 AEVLNEDFENGIPASWKTIDADGDGNNWTTTPPPGGSSFAGHNSAICVSSASHINFEGPQNPDNYLVTPELSLPGGGTLTFWVCAQDANYASEHYAVYASSTGNDASNFANALLEEVLTAKTVVTAPEAIRGTRAQGTWYQKTVQLPAGTKYVAFRHFGCTDFFWINLDDVVITSG 1602
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..........eeee...........................eeee.ee...ee...eeeee.........eeeeeeeee........eeeeeee....hhhhh....eeee.......--.............eeeeeee.....eeeeeee......eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3m1h A 1427 AEVLNEDFENGIPASWKTIDADGDGNNWTTTPPPGGSSFAGHNSAICVSSASYINFEGPQNPDNYLVTPELSLPGGGTLTFWVCAQDANYASEHYAVYASSTGNDASNFANALLEEVLTAKTVV--PEAIRGTRAQGTWYQKTVQLPAGTKYVAFRHFGCTDFFWINLDDVVITSG 1602
                                  1436      1446      1456      1466      1476      1486      1496      1506      1516      1526      1536      1546   |  1556      1566      1576      1586      1596      
                                                                                                                                                    1550  |                                                 
                                                                                                                                                       1553                                                 


Chain B from PDB  Type:PROTEIN  Length:175
 aligned with KGP83_PORGN | Q51817 from UniProtKB/Swiss-Prot  Length:1732

    Alignment length:175
                                  1436      1446      1456      1466      1476      1486      1496      1506      1516      1526      1536      1546      1556      1566      1576      1586      1596     
         KGP83_PORGN   1427 AEVLNEDFENGIPASWKTIDADGDGNNWTTTPPPGGSSFAGHNSAICVSSASHINFEGPQNPDNYLVTPELSLPGGGTLTFWVCAQDANYASEHYAVYASSTGNDASNFANALLEEVLTAKTVVTAPEAIRGTRAQGTWYQKTVQLPAGTKYVAFRHFGCTDFFWINLDDVVITS 1601
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..........eeee...........................eeee.ee...ee....eeee.........eeeeeeeee........eeeeeee....hhhhh..eeeeee......................eeeeeee.....eeeeee.......eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3m1h B 1427 AEVLNEDFENGIPASWKTIDADGDGNNWTTTPPPGGSSFAGHNSAICVSSASYINFEGPQNPDNYLVTPELSLPGGGTLTFWVCAQDANYASEHYAVYASSTGNDASNFANALLEEVLTAKTVVTAPEAIRGTRAQGTWYQKTVQLPAGTKYVAFRHFGCTDFFWINLDDVVITS 1601
                                  1436      1446      1456      1466      1476      1486      1496      1506      1516      1526      1536      1546      1556      1566      1576      1586      1596     


Chain C from PDB  Type:PROTEIN  Length:170
 aligned with KGP83_PORGN | Q51817 from UniProtKB/Swiss-Prot  Length:1732

    Alignment length:178
                                  1434      1444      1454      1464      1474      1484      1494      1504      1514      1524      1534      1544      1554      1564      1574      1584      1594        
         KGP83_PORGN   1425 KRAEVLNEDFENGIPASWKTIDADGDGNNWTTTPPPGGSSFAGHNSAICVSSASHINFEGPQNPDNYLVTPELSLPGGGTLTFWVCAQDANYASEHYAVYASSTGNDASNFANALLEEVLTAKTVVTAPEAIRGTRAQGTWYQKTVQLPAGTKYVAFRHFGCTDFFWINLDDVVITSG 1602
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee..........eeee...........................eeee.ee...ee...eeeee.........eeeeeeeee........eeeeeee....hhhhh....eeee..--------............eeeeeee.....eeeeeee......eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3m1h C 1425 GSAEVLNEDFENGIPASWKTIDADGDGNNWTTTPPPGGSSFAGHNSAICVSSASYINFEGPQNPDNYLVTPELSLPGGGTLTFWVCAQDANYASEHYAVYASSTGNDASNFANALLEEVLT--------EAIRGTRAQGTWYQKTVQLPAGTKYVAFRHFGCTDFFWINLDDVVITSG 1602
                                  1434      1444      1454      1464      1474      1484      1494      1504      1514      1524      1534      1544|     1554      1564      1574      1584      1594        
                                                                                                                                                 1545     1554                                                


Chain D from PDB  Type:PROTEIN  Length:176
 aligned with KGP83_PORGN | Q51817 from UniProtKB/Swiss-Prot  Length:1732

    Alignment length:176
                                  1436      1446      1456      1466      1476      1486      1496      1506      1516      1526      1536      1546      1556      1566      1576      1586      1596      
         KGP83_PORGN   1427 AEVLNEDFENGIPASWKTIDADGDGNNWTTTPPPGGSSFAGHNSAICVSSASHINFEGPQNPDNYLVTPELSLPGGGTLTFWVCAQDANYASEHYAVYASSTGNDASNFANALLEEVLTAKTVVTAPEAIRGTRAQGTWYQKTVQLPAGTKYVAFRHFGCTDFFWINLDDVVITSG 1602
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..........eeee...........................eeee.ee...ee...eeeee.........eeeeeeeee........eeeeeee....hhhhh....eeee......................eeeeeee.....eeeeeee......eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3m1h D 1427 AEVLNEDFENGIPASWKTIDADGDGNNWTTTPPPGGSSFAGHNSAICVSSASYINFEGPQNPDNYLVTPELSLPGGGTLTFWVCAQDANYASEHYAVYASSTGNDASNFANALLEEVLTAKTVVTAPEAIRGTRAQGTWYQKTVQLPAGTKYVAFRHFGCTDFFWINLDDVVITSG 1602
                                  1436      1446      1456      1466      1476      1486      1496      1506      1516      1526      1536      1546      1556      1566      1576      1586      1596
   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 3M1H)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3M1H)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3M1H)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (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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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

3km5 K2 CLEAVED ADHESIN DOMAIN OF LYS-GINGIPAIN