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(-) Description

Title :  CRYSTAL STRUCTURE OF PORPHYROMONAS GINGIVALIS PEPTIDYLARGININE DEIMINASE (PPAD) MUTANT C351A IN COMPLEX WITH DIPEPTIDE MET-ARG.
 
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) - 01 Jul 15  (Release) - 28 Sep 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
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: RESIDUES 44-475
    Mutation: YES
    Organism Scientific: PORPHYROMONAS GINGIVALIS
    Organism Taxid: 242619

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 12)

Asymmetric/Biological Unit (7, 12)
No.NameCountTypeFull Name
1ARG1Mod. Amino AcidARGININE
2AZI2Ligand/IonAZIDE ION
3CL1Ligand/IonCHLORIDE ION
4CYS1Mod. Amino AcidCYSTEINE
5GOL5Ligand/IonGLYCEROL
6MET1Mod. Amino AcidMETHIONINE
7NA1Ligand/IonSODIUM ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:147 , PHE A:148 , ASP A:158 , HOH A:797binding site for residue NA A 501
02AC2SOFTWARETYR A:378 , PHE A:424 , THR A:425 , GLY A:426 , LEU A:427 , PHE A:460 , CYS A:462binding site for residue CYS A 502
03AC3SOFTWARETRP A:127 , ARG A:154 , TYR A:233 , ARG A:504 , HOH A:724binding site for residue MET A 503
04AC4SOFTWARETRP A:127 , ASP A:130 , ARG A:152 , ARG A:154 , GLY A:182 , TYR A:233 , ILE A:234 , HIS A:236 , ASP A:238 , THR A:346 , ALA A:351 , MET A:503 , HOH A:764 , HOH A:914binding site for residue ARG A 504
05AC5SOFTWAREILE A:149 , LYS A:176 , ASN A:202 , SER A:204 , HOH A:798 , HOH A:804 , HOH A:824binding site for residue GOL A 505
06AC6SOFTWAREASP A:266 , TYR A:270 , HOH A:631 , HOH A:740 , HOH A:1001binding site for residue GOL A 506
07AC7SOFTWAREVAL A:55 , ARG A:56 , GLY A:219 , LYS A:365 , TYR A:367 , HOH A:643 , HOH A:771 , HOH A:904binding site for residue GOL A 507
08AC8SOFTWAREASN A:247 , LYS A:248 , GLU A:283 , PRO A:450 , ASP A:456 , AZI A:512 , HOH A:815 , HOH A:869binding site for residue GOL A 508
09AC9SOFTWARETYR A:399 , TYR A:422 , SER A:423 , PHE A:424 , THR A:425 , LEU A:427 , HOH A:674binding site for residue GOL A 509
10AD1SOFTWAREASN A:49binding site for residue CL A 510
11AD2SOFTWAREGLU A:232 , ASN A:235 , HOH A:604 , HOH A:678binding site for residue AZI A 511
12AD3SOFTWARELYS A:248 , GLU A:283 , TYR A:285 , ASP A:456 , GOL A:508binding site for residue AZI A 512

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:462 -A:502

(-) Cis Peptide Bonds  (5, 5)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4YTG)

(-) 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:420
                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ............ee......eeeeeee.....hhhhhhhhhhhheeeeee.hhhhhhhhhhhhhhh..hhh.eeeee......hhhhhh.eeeee...eeeeeeeee...hhhhhhhhhhhhhhhh.eeeeeeeeehhhhhee....eeeeehhhhhh....hhhhhhhhhhhhhh..eeeee.........hhhh.eeeee..eeeeee......hhhhhhhhhhhhhh.........eeeeee..........eee..eeeeee..hhhhhhhhhhhhhhhh...eeeeee............hhhhheeee....eeeee....eee..eeeeeeee.....eeeeeeeeee......eeee.eeee..eeeee........eeeeeeeeee....eeee........eeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4ytg A  44 AFQETNPPAGPVRAIAEYERSAAVLVRYPFGIPMELIKELAKNDKVITIVASESQKNTVITQYTQSGVNLSNCDFIIAKTDSYWTRDYTGWFAMYDTNKVGLVDFIYNRPRPNDDEFPKYEAQYLGIEMFGMKLKQTGGNYMTDGYGSAVQSHIAYTENSSLSQAQVNQKMKDYLGITHHDVVQDPNGEYINHVDCWGKYLAPNKILIRKVPDNHPQHQALEDMAAYFAAQTCAWGTKYEVYRALATNEQPYTNSLILNNRVFVPVNGPASVDNDALNVYKTAMPGYEIIGVKGASGTPWLGTDALHARTHEVADKGYLYIKHYPILGEQDYKIEADVVSCANATISPVQCYYRINGSGSFKAADMTMESTGHYTYSFTGLNKNDKVEYYISAADNSGRKETYPFIGEPDPFKFTCMCMR 504
                                    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|      386       396       406       416       426       436       446       456      |504
                                                                                                                                                                                                                                                                                                                                                                   373|                                                                                   463|  
                                                                                                                                                                                                                                                                                                                                                                    377                                                                                    502
   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 4YTG)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
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    Tyr A:71 - Pro A:72   [ RasMol ]  
 

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 Related Entries

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        PAD_PORGI | Q9RQJ2: 4yt9 4ytb 5ak7 5ak8

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4yt9