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(-) Description

Title :  CRYSTAL STRUCTURE OF THE ARG SPECIFIC CYSTEINE PROTEINASE GINGIPAIN R (RGPB)
 
Authors :  A. Eichinger, H. -G. Beisel
Date :  24 Aug 99  (Deposition) - 01 Mar 00  (Release) - 16 Oct 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Caspases, Cysteine Proteinase, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Eichinger, H. G. Beisel, U. Jacob, R. Huber, F. J. Medrano, A. Banbula, J. Potempa, J. Travis, W. Bode
Crystal Structure Of Gingipain R: An Arg-Specific Bacterial Cysteine Proteinase With A Caspase-Like Fold.
Embo J. V. 18 5453 1999
PubMed-ID: 10523290  |  Reference-DOI: 10.1093/EMBOJ/18.20.5453

(-) Compounds

Molecule 1 - GINGIPAIN R
    Chains: A
    EC Number: 3.4.22.37
    Engineered: YES
    Organism Scientific: PORPHYROMONAS GINGIVALIS
    Organism Taxid: 837
    Synonym: RGPB

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 9)

Asymmetric/Biological Unit (3, 9)
No.NameCountTypeFull Name
1CA6Ligand/IonCALCIUM ION
2H371Ligand/IonD-PHENYLALANYL-N-[(3S)-6-CARBAMIMIDAMIDO-1-CHLORO-2-OXOHEXAN-3-YL]-L-PHENYLALANINAMIDE
3ZN2Ligand/IonZINC ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:163 , THR A:191 , PRO A:192 , GLY A:210 , HIS A:211 , GLY A:212 , HIS A:221 , VAL A:242 , CYS A:244 , GLN A:282 , TYR A:283 , TRP A:284 , MET A:288 , HOH A:640 , HOH A:724 , HOH A:772BINDING SITE FOR RESIDUE H37 A 501
2AC2SOFTWAREGLU A:161 , HIS A:166 , ASP A:292 , HOH A:717 , HOH A:818 , HOH A:882BINDING SITE FOR RESIDUE CA A 502
3AC3SOFTWAREASP A:78 , PHE A:249 , GLU A:258 , HOH A:632 , HOH A:672 , HOH A:690BINDING SITE FOR RESIDUE CA A 503
4AC4SOFTWAREVAL A:100 , ASP A:103 , TYR A:105 , GLU A:107 , HOH A:716 , HOH A:819BINDING SITE FOR RESIDUE CA A 504
5AC5SOFTWAREGLU A:293 , GLU A:296 , HIS A:302 , HOH A:619BINDING SITE FOR RESIDUE CA A 505
6AC6SOFTWAREHIS A:221 , ASP A:328 , HOH A:646 , HOH A:677BINDING SITE FOR RESIDUE CA A 506
7AC7SOFTWAREGLU A:152 , HIS A:211 , TRP A:284 , LYS A:327 , HOH A:724 , HOH A:920BINDING SITE FOR RESIDUE ZN A 507
8AC8SOFTWAREGLU A:119 , ASP A:387 , GLU A:405 , HOH A:712 , HOH A:922BINDING SITE FOR RESIDUE CA A 508
9AC9SOFTWAREHIS A:130 , ASN A:134 , HOH A:852 , HOH A:921BINDING SITE FOR RESIDUE ZN A 509

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1CVR)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ser A:48 -Pro A:49
2Asp A:187 -Pro A:188

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1CVR)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1CVR)

(-) Exons   (0, 0)

(no "Exon" information available for 1CVR)

(-) 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:432
 aligned with CPG2_PORGI | P95493 from UniProtKB/Swiss-Prot  Length:736

    Alignment length:432
                                   239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659  
           CPG2_PORGI   230 YTPVEEKENGRMIVIVPKKYEEDIEDFVDWKNQRGLRTEVKVAEDIASPVTANAIQQFVKQEYEKEGNDLTYVLLVGDHKDIPAKITPGIKSDQVYGQIVGNDHYNEVFIGRFSCESKEDLKTQIDRTIHYERNITTEDKWLGQALCIASAEGGPSADNGESDIQHENIIANLLTQYGYTKIIKCYDPGVTPKNIIDAFNGGISLANYTGHGSETAWGTSHFGTTHVKQLTNSNQLPFIFDVACVNGDFLYNVPCFAEALMRAQKDGKPTGTVAIIASTINQSWASPMRGQDEMNEILCEKHPNNIKRTFGGVTMNGMFAMVEKYKKDGEKMLDTWTVFGDPSLLVRTLVPTKMQVTAPANISASAQTFEVACDYNGAIATLSDDGDMVGTAIVKDGKAIIKLNESIADETNLTLTVVGYNKVTVIKDVKVE 661
               SCOP domains d1cvra2 A:1-350 Gingipain R (RgpB), N-terminal domain                                                                                                                                                                                                                                                                                                         d1cvra1 A:351-432 Gingipain R (RgpB), C-terminal domain                            SCOP domains
               CATH domains 1cvrA01 A:1-117 Gingipain r; domain 1                                                                                1cvrA02 A:118-348  [code=3.40.50.1460, no name defined]                                                                                                                                                                                -1cvrA03 A:350-432 Immunoglobulins                                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..........eeeeee.hhhhhhhhhhhhhhhhh..eeeeeehhhhh...hhhhhhhhhhhhhhh....eeeeeee........eee..eeehhhhhh..........eeeee...hhhhhhhhhhhhhhhhhh.........eeeeee.......hhhhhhhhhhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhhh..eeeee................hhhhh.......eeeee............hhhhhhhhhee..ee....eeeee......hhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhheeee................ee...eee....eeeeee.....eeeeee..eeeeeee....eeeee.........eeeeeee......eeeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1cvr A   1 YTPVEEKENGRMIVIVAKKYEGDIKDFVDWKNQRGLRTEVKVAEDIASPVTANAIQQFVKQEYEKEGNDLTYVLLVGDHKDIPAKITPGIKSDQVYGQIVGNDHYNEVFIGRFSCESKEDLKTQIDRTIHYERNITTEDKWLGQALCIASAEGGPSADNGESDIQHENVIANLLTQYGYTKIIKCYDPGVTPKNIIDAFNGGISLVNYTGHGSETAWGTSHFGTTHVKQLTNSNQLPFIFDVACVNGDFLFSMPCFAEALMRAQKDGKPTGTVAIIASTIDQYWAPPMRGQDEMNEILCEKHPNNIKRTFGGVTMNGMFAMVEKYKKDGENMLDTWTVFGDPSLLVRTLVPTEMQVTAPANISASAQTFEVACDYNGAIATLSDDGDMVGTAIVKDGKAIIKLNESIADETNLTLTVVGYNKVTVIKDVKVE 432
                                    10        20        30        40        50        60        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       410       420       430
   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  (2, 2)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (3, 3)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1CVR)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CPG2_PORGI | P95493)
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.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CPG2_PORGI | P95493: 4ief 5ag8 5ag9 5hfs

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