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(-) Description

Title :  CRYSTAL STRUCTURE OF PORPHYROMONAS GINGIVALIS PEPTIDYLARGININE DEIMINASE (PPAD) IN COMPLEX WITH DIPEPTIDE ASP-GLN.
 
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) - 15 Jul 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
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
    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  (8, 14)

Asymmetric/Biological Unit (8, 14)
No.NameCountTypeFull Name
1ASP1Mod. Amino AcidASPARTIC ACID
2AZI1Ligand/IonAZIDE ION
3CL1Ligand/IonCHLORIDE ION
4GLN1Mod. Amino AcidGLUTAMINE
5GOL3Ligand/IonGLYCEROL
6IMD1Ligand/IonIMIDAZOLE
7NA1Ligand/IonSODIUM ION
8PO45Ligand/IonPHOSPHATE ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:147 , PHE A:148 , ASP A:158 , HOH A:816 , HOH A:862binding site for residue NA A 501
02AC2SOFTWARETRP A:127 , ARG A:154 , TYR A:233 , GLN A:503 , HOH A:1142 , HOH A:1261binding site for residue ASP A 502
03AC3SOFTWARETRP A:127 , ASP A:130 , ARG A:152 , ARG A:154 , TYR A:233 , ILE A:234 , THR A:346 , ASP A:347 , CYS A:351 , ASP A:502 , HOH A:809 , HOH A:810 , HOH A:916 , HOH A:1261binding site for residue GLN A 503
04AC4SOFTWAREASP A:266 , MET A:267 , TYR A:270 , PRO A:455 , HOH A:612 , HOH A:637 , HOH A:659 , HOH A:675 , HOH A:881 , HOH A:1005binding site for residue GOL A 504
05AC5SOFTWARELYS A:176 , ASN A:202 , SER A:204 , HOH A:890 , HOH A:962 , HOH A:1105 , HOH A:1140 , HOH A:1148binding site for residue GOL A 505
06AC6SOFTWARESER A:206 , GLN A:207 , ALA A:208 , GLU A:283 , LYS A:459 , HOH A:604 , HOH A:618 , HOH A:627 , HOH A:632 , HOH A:636 , HOH A:647 , HOH A:649 , HOH A:661 , HOH A:707 , HOH A:734 , HOH A:751binding site for residue GOL A 506
07AC7SOFTWAREALA A:390 , THR A:391 , ASN A:442 , HOH A:638binding site for residue PO4 A 507
08AC8SOFTWAREPRO A:76 , MET A:77 , ALA A:338 , HOH A:878 , HOH A:941 , HOH A:1008 , HOH A:1168 , HOH A:1181binding site for residue PO4 A 508
09AC9SOFTWAREGLN A:212 , LYS A:215 , HOH A:983 , HOH A:1243binding site for residue PO4 A 509
10AD1SOFTWARETHR A:280 , LYS A:281 , HOH A:605 , HOH A:608 , HOH A:656binding site for residue PO4 A 510
11AD2SOFTWAREASN A:428 , LYS A:429 , GLU A:465binding site for residue PO4 A 511
12AD3SOFTWAREARG A:70 , PRO A:72binding site for residue IMD A 512
13AD4SOFTWAREHIS A:196 , TYR A:199 , VAL A:225 , PRO A:455 , HOH A:602 , HOH A:610 , HOH A:696 , HOH A:705binding site for residue AZI A 514

(-) SS Bonds  (0, 0)

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

(-) 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 4YTB)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4YTB)

(-) 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:424
                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eee......eeeeeee.....hhhhhhhhhhhh.eeeee.hhhhhhhhhhhhhhhh.hhh.eeeee......hhhhhh.eeeee...eeeeeeeee...hhhhhhhhhhhhhhhh..eeeeeeeehhhhhee....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
                 4ytb A  44 AFQETNPPAGPVRAIAEYERSAAVLVRYPFGIPMELIKELAKNDKVITIVASESQKNTVITQYTQSGVNLSNCDFIIAKTDSYWTRDYTGWFAMYDTNKVGLVDFIYNRPRPNDDEFPKYEAQYLGIEMFGMKLKQTGGNYMTDGYGSAVQSHIAYTENSSLSQAQVNQKMKDYLGITHHDVVQDPNGEYINHVDCWGKYLAPNKILIRKVPDNHPQHQALEDMAAYFAAQTCAWGTKYEVYRALATNEQPYTNSLILNNRVFVPVNGPASVDNDALNVYKTAMPGYEIIGVKGASGTPWLGTDALHCRTHEVADKGYLYIKHYPILGEQAGPDYKIEADVVSCANATISPVQCYYRINGSGSFKAADMTMESTGHYTYSFTGLNKNDKVEYYISAADNSGRKETYPFIGEPDPFKFTCMNEDQ 503
                                    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 || 
                                                                                                                                                                                                                                                                                                                                                                                                                                                               465| 
                                                                                                                                                                                                                                                                                                                                                                                                                                                                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 4YTB)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Gly A:311 - Pro A:312   [ RasMol ]  
    Gly A:375 - Pro A:376   [ RasMol ]  
    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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4yt9