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(-) Description

Title :  STRUCTURE OF WT PORPHYROMONAS GINGIVALIS PEPTIDYLARGININE DEIMINASE
 
Authors :  J. Kopec, A. Montgomery, L. Shrestha, W. Kiyani, R. Nowak, N. Burgess-B P. J. Venables, W. W. Yue
Date :  02 Mar 15  (Deposition) - 22 Jul 15  (Release) - 25 May 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.46
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase, Ppad (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. B. Montgomery, J. Kopec, L. Shrestha, M. L. Thezenas, N. A. Burgess-Brown, R. Fischer, W. W. Yue, P. J. Venables
Crystal Structure Of Porphyromonas Gingivalis Peptidylarginine Deiminase: Implications For Autoimmunity In Rheumatoid Arthritis.
Ann. Rheum. Dis. V. 75 1255 2016
PubMed-ID: 26209657  |  Reference-DOI: 10.1136/ANNRHEUMDIS-2015-207656

(-) Compounds

Molecule 1 - PEPTIDYLARGININE DEIMINASE
    Chains: A
    EC Number: 3.5.3.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PNIC28-BSA
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: ROSETTA
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 49-484
    Organism Scientific: PORPHYROMONAS GINGIVALIS
    Organism Taxid: 837
    Synonym: PPAD

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 20)

Asymmetric/Biological Unit (4, 20)
No.NameCountTypeFull Name
1ALA1Mod. Amino AcidALANINE
2ARG1Mod. Amino AcidARGININE
3EDO17Ligand/Ion1,2-ETHANEDIOL
4NA1Ligand/IonSODIUM ION

(-) Sites  (20, 20)

Asymmetric Unit (20, 20)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:125 , TYR A:126 , TRP A:127 , EDO A:1480BINDING SITE FOR RESIDUE EDO A1466
02AC2SOFTWARETYR A:61 , GLU A:62 , PRO A:246 , TYR A:361 , TYR A:449 , HOH A:2029 , HOH A:2375BINDING SITE FOR RESIDUE EDO A1467
03AC3SOFTWARELYS A:248 , GLU A:283 , TYR A:285 , ASP A:456 , HOH A:2308BINDING SITE FOR RESIDUE EDO A1468
04AC4SOFTWAREASN A:247 , PRO A:450 , ASP A:456 , PRO A:457 , HOH A:2267 , HOH A:2269 , HOH A:2308BINDING SITE FOR RESIDUE EDO A1469
05AC5SOFTWARELYS A:365 , TYR A:367 , GLU A:381 , ASP A:383 , HIS A:419 , HOH A:2379 , HOH A:2397 , HOH A:2478BINDING SITE FOR RESIDUE EDO A1470
06AC6SOFTWAREASN A:202 , LEU A:205 , HOH A:2214BINDING SITE FOR RESIDUE EDO A1471
07AC7SOFTWARETYR A:399 , TYR A:422 , PHE A:424 , THR A:425BINDING SITE FOR RESIDUE EDO A1472
08AC8SOFTWAREPRO A:54 , THR A:140 , HOH A:2479BINDING SITE FOR RESIDUE EDO A1473
09AC9SOFTWAREPRO A:328 , PRO A:455 , LYS A:459 , HOH A:2453 , HOH A:2473BINDING SITE FOR RESIDUE EDO A1474
10BC1SOFTWARELYS A:213BINDING SITE FOR RESIDUE EDO A1475
11BC2SOFTWARETYR A:270 , HOH A:2244 , HOH A:2289 , HOH A:2480BINDING SITE FOR RESIDUE EDO A1476
12BC3SOFTWARESER A:114 , SER A:191 , GLN A:274 , THR A:275 , CYS A:276 , ALA A:277 , TYR A:282 , HOH A:2096 , HOH A:2196BINDING SITE FOR RESIDUE EDO A1477
13BC4SOFTWAREASP A:117 , PHE A:118 , TYR A:167 , LYS A:281 , HOH A:2099BINDING SITE FOR RESIDUE EDO A1478
14BC5SOFTWAREASN A:211 , THR A:221 , HIS A:222 , HIS A:223 , HOH A:2229BINDING SITE FOR RESIDUE EDO A1479
15BC6SOFTWAREARG A:70 , TYR A:126 , EDO A:1466 , HOH A:2048BINDING SITE FOR RESIDUE EDO A1480
16BC7SOFTWAREVAL A:284 , TYR A:285 , HOH A:2306BINDING SITE FOR RESIDUE EDO A1481
17BC8SOFTWARESER A:203 , SER A:204 , SER A:206BINDING SITE FOR RESIDUE EDO A1482
18BC9SOFTWAREASP A:147 , PHE A:148 , ASP A:158 , HOH A:2123 , HOH A:2143BINDING SITE FOR RESIDUE NA A1483
19CC1SOFTWARETRP A:127 , ARG A:154 , TYR A:233 , ARG A:1002BINDING SITE FOR RESIDUE ALA A1001
20CC2SOFTWARETRP 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 , CYS A:351 , ALA A:1001 , HOH A:2122 , HOH A:2259 , HOH A:2368BINDING SITE FOR RESIDUE ARG A1002

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5AK7)

(-) 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 5AK7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5AK7)

(-) Exons   (0, 0)

(no "Exon" information available for 5AK7)

(-) 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.hhhhhhhhhhhhhhh..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
                5ak7 A   47 SMNPPAGPVRAIAEYERSAAVLVRYPFGIPMELIKELAKNDKVITIVASESQKNTVITQYTQSGVNLSNCDFIIAKTDSYWTRDYTGWFAMYDTNKVGLVDFIYNRPRPNDDEFPKYEAQYLGIEMFGMKLKQTGGNYMTDGYGSAVQSHIAYTENSSLSQAQVNQKMKDYLGITHHDVVQDPNGEYINHVDCWGKYLAPNKILIRKVPDNHPQHQALEDMAAYFAAQTCAWGTKYEVYRALATNEQPYTNSLILNNRVFVPVNGPASVDNDALNVYKTAMPGYEIIGVKGASGTPWLGTDALHCRTHEVADKGYLYIKHYPILGEQAGPDYKIEADVVSCANATISPVQCYYRINGSGSFKAADMTMESTGHYTYSFTGLNKNDKVEYYISAADNSGRKETYPFIGEPDPFKFTCMNEAR 1002
                                    56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456      1001 
                                                                                                                                                                                                                                                                                                                                                                                                                                                            465| 
                                                                                                                                                                                                                                                                                                                                                                                                                                                            1001
   Legend:   → Mismatch (orange background)
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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 5AK7)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5AK7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5AK7)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
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    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: 4yt9 4ytb 4ytg 5ak8

(-) Related Entries Specified in the PDB File

5ak8 STRUCTURE OF C351A MUTANT OF PORPHYROMONAS GINGIVALIS PEPTIDYLARGININE DEIMINASE