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(-) Description

Title :  CRYSTAL STRUCTURE OF PORPHYROMONAS GINGIVALIS PEPTIDYLARGININE DEIMINASE (PPAD) SUBSTRATE-UNBOUND.
 
Authors :  T. Goulas, D. Mizgalska, I. Garcia-Ferrer, T. Kantyka, T. Guevara, B. Szmigielski, A. Sroka, C. Millan, I. Uson, F. Veillard, B. Potempa, M. Sola, J. Potempa, F. X. Gomis-Ruth
Date :  17 Mar 15  (Deposition) - 15 Jul 15  (Release) - 15 Jul 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Peptidylarginine Deiminase, Citrullination, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Goulas, D. Mizgalska, I. Garcia-Ferrer, T. Kantyka, T. Guevara, B. Szmigielski, A. Sroka, C. Millan, I. Uson, F. Veillard, B. Potempa, P. Mydel, M. Sola, J. Potempa, F. X. Gomis-Ruth
Structure And Mechanism Of A Bacterial Host-Protein Citrullinating Virulence Factor, Porphyromonas Gingivalis Peptidylarginine Deiminase.
Sci Rep V. 5 11969 2015
PubMed-ID: 26132828  |  Reference-DOI: 10.1038/SREP11969

(-) Compounds

Molecule 1 - PEPTIDYLARGININE DEIMINASE
    Chains: A
    EC Number: 3.5.3.-
    Fragment: UNP RESIDUES 44-475
    Organism Scientific: PORPHYROMONAS GINGIVALIS W83
    Organism Taxid: 242619

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 12)

Asymmetric/Biological Unit (4, 12)
No.NameCountTypeFull Name
14GJ3Mod. Amino Acid3-(PYRIDIN-4-YLDISULFANYL)-L-ALANINE
2CSO1Mod. ResidueS-HYDROXYCYSTEINE
3GOL7Ligand/IonGLYCEROL
4NA1Ligand/IonSODIUM ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:147 , PHE A:148 , ASP A:158 , HOH A:818 , HOH A:860binding site for residue NA A 501
2AC2SOFTWAREHIS A:196 , TYR A:199 , GLN A:207 , VAL A:225 , VAL A:226 , GLN A:227 , PRO A:328 , PRO A:455 , ASP A:456 , HOH A:614 , HOH A:618binding site for residue GOL A 502
3AC3SOFTWAREVAL A:226 , GLN A:227 , ASP A:266 , PRO A:455 , HOH A:605 , HOH A:620 , HOH A:641 , HOH A:643 , HOH A:853binding site for residue GOL A 503
4AC4SOFTWAREILE A:149 , LYS A:176 , ASN A:202 , SER A:204 , HOH A:819 , HOH A:857 , HOH A:863binding site for residue GOL A 504
5AC5SOFTWAREPRO A:54 , ARG A:56 , TYR A:138 , THR A:140 , TYR A:363 , HOH A:1026binding site for residue GOL A 505
6AC6SOFTWARELYS A:248 , TRP A:278 , PRO A:450 , ASP A:456 , PRO A:457 , LYS A:459 , HOH A:836 , HOH A:914 , HOH A:915 , HOH A:916 , HOH A:1007binding site for residue GOL A 506
7AC7SOFTWAREVAL A:284 , TYR A:285 , HOH A:631 , HOH A:654 , HOH A:927binding site for residue GOL A 507
8AC8SOFTWAREASP A:228 , ASN A:235 , TRP A:240 , ALA A:263 , LEU A:264 , MET A:267 , HOH A:788binding site for residue GOL A 508

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4YT9)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Gly A:53 -Pro A:54
2Tyr A:71 -Pro A:72
3Gly A:311 -Pro A:312
4Gly A:375 -Pro A:376
5Ser A:393 -Pro A:394
6Tyr A:449 -Pro A:450

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4YT9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4YT9)

(-) Exons   (0, 0)

(no "Exon" information available for 4YT9)

(-) 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:421
                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............ee......eeeeeee.....hhhhhhhhhhhheeeeee.hhhhhhhhhhhhhhhh.hhh.eeeee......hhhhhh.eeeee...eeeeeeeee...hhhhhhhhhhhhhhhh..eeeeeeeehhhhhee....eeeeehhhhhh....hhhhhhhhhhhhhh..eeeee.........hhhh.eeeee..eeeeee......hhhhhhhhhhhhhh.........eeeeee..........eee..eeeeee..hhhhhhhhhhhhhhhh...eeeeee............hhhhheeee....eeeee............eeeeeeee.....eeeeeeeeee......eeee.eeee..eeeee........eeeeeeeeee....eeee........eeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yt9 A  44 AFQETNPPAGPVRAIAEYERSAAVLVRYPFGIPMELIKELAKNDKVITIVASESQKNTVITQYTQSGVNLSNCDFIIAKTDSYWTRDYTGWFAMYDTNKVGLVDFIYNRPRPNDDEFPKYEAQYLGIEMFGMKLKQTGGNYMTDGYGSAVQSHIAYTENSSLSQAQVNQKMKDYLGITHHDVVQDPNGEYINHVDcWGKYLAPNKILIRKVPDNHPQHQALEDMAAYFAAQTCAWGTKYEVYRALATNEQPYTNSLILNNRVFVPVNGPASVDNDALNVYKTAMPGYEIIGVKGASGTPWLGTDALHcRTHEVADKGYLYIKHYPILGEQAGPDYKIEADVVSCANATISPVQCYYRINGSGSFKAADMTMESTGHYTYSFTGLNKNDKVEYYISAADNSGRKETYPFIGEPDPFKFTcMN 464
                                    53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233     | 243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463 
                                                                                                                                                                                                                             239-4GJ                                                                                                         351-4GJ                                                                                                        462-4GJ
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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 4YT9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4YT9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4YT9)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
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    Gly A:53 - Pro A:54   [ RasMol ]  
    Ser A:393 - Pro A:394   [ RasMol ]  
    Tyr A:449 - Pro A:450   [ RasMol ]  
    Tyr A:71 - Pro A:72   [ RasMol ]  
 

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 Related Entries

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        PAD_PORGI | Q9RQJ2: 4ytb 4ytg 5ak7 5ak8

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