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(-) Description

Title :  STRUCTURE OF C351A MUTANT OF 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 :  1.48
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
    Mutation: YES
    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, 21)

Asymmetric/Biological Unit (4, 21)
No.NameCountTypeFull Name
1ALA1Mod. Amino AcidALANINE
2ARG1Mod. Amino AcidARGININE
3EDO18Ligand/Ion1,2-ETHANEDIOL
4NA1Ligand/IonSODIUM ION

(-) Sites  (20, 20)

Asymmetric Unit (20, 20)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:147 , PHE A:148 , ASP A:158 , HOH A:2114 , HOH A:2134BINDING SITE FOR RESIDUE NA A1466
02AC2SOFTWARETYR A:61 , GLU A:62 , PRO A:246 , TYR A:361 , TYR A:449 , HOH A:2023 , HOH A:2363BINDING SITE FOR RESIDUE EDO A1467
03AC3SOFTWARESER A:125 , TYR A:126 , TRP A:127 , EDO A:1472BINDING SITE FOR RESIDUE EDO A1468
04AC4SOFTWARELYS A:248 , GLU A:283 , TYR A:285 , ALA A:326 , PRO A:328 , ASP A:456 , EDO A:1474 , HOH A:2291BINDING SITE FOR RESIDUE EDO A1469
05AC5SOFTWAREILE A:58 , GLU A:60 , ARG A:129 , MET A:185 , THR A:186 , GLU A:355 , HOH A:2019 , HOH A:2021BINDING SITE FOR RESIDUE EDO A1470
06AC6SOFTWARELYS A:365 , TYR A:367 , GLU A:381 , ASP A:383 , HIS A:419 , HOH A:2366 , HOH A:2455BINDING SITE FOR RESIDUE EDO A1471
07AC7SOFTWAREARG A:70 , TYR A:126 , EDO A:1468 , HOH A:2041BINDING SITE FOR RESIDUE EDO A1472
08AC8SOFTWARELYS A:176 , ASN A:202 , HOH A:2209 , HOH A:2211BINDING SITE FOR RESIDUE EDO A1473
09AC9SOFTWAREASN A:247 , PRO A:450 , ASP A:456 , PRO A:457 , PHE A:458 , EDO A:1469 , EDO A:1483 , HOH A:2291BINDING SITE FOR RESIDUE EDO A1474
10BC1SOFTWAREPRO A:54 , ARG A:56 , TYR A:138 , THR A:140 , TYR A:363 , HOH A:2457BINDING SITE FOR RESIDUE EDO A1475
11BC2SOFTWARETYR A:270 , HOH A:2236 , HOH A:2273BINDING SITE FOR RESIDUE EDO A1476
12BC3SOFTWARETYR A:399 , TYR A:422 , PHE A:424 , THR A:425 , LEU A:427BINDING SITE FOR RESIDUE EDO A1477
13BC4SOFTWAREASP A:117 , PHE A:118 , TYR A:167 , LYS A:281 , HOH A:2283 , HOH A:2458BINDING SITE FOR RESIDUE EDO A1478
14BC5SOFTWAREARG A:63 , ARG A:445 , LYS A:446 , GLU A:447BINDING SITE FOR RESIDUE EDO A1479
15BC6SOFTWAREPRO A:455 , LYS A:459 , HOH A:2430BINDING SITE FOR RESIDUE EDO A1480
16BC7SOFTWAREALA A:409 , ALA A:410 , ASP A:411BINDING SITE FOR RESIDUE EDO A1481
17BC8SOFTWAREPRO A:54 , VAL A:55 , LYS A:215 , GLY A:219 , THR A:221 , HOH A:2230BINDING SITE FOR RESIDUE EDO A1482
18BC9SOFTWAREALA A:245 , ASN A:247 , LYS A:248 , TRP A:278 , PRO A:450 , ILE A:452 , ASP A:456 , EDO A:1474 , HOH A:2258 , HOH A:2329 , HOH A:2461BINDING SITE FOR RESIDUE EDO A1483
19CC1SOFTWAREASP A:228 , ASN A:230 , GLY A:231 , GLU A:232 , ILE A:234 , ASN A:235 , HOH A:2242 , HOH A:2244BINDING SITE FOR RESIDUE EDO A1484
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 , ALA A:351 , HOH A:2113 , HOH A:2355 , HOH A:2462BINDING SITE FOR DI-PEPTIDE ALA A1001 AND ARG A1002

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5AK8)

(-) 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 5AK8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5AK8)

(-) Exons   (0, 0)

(no "Exon" information available for 5AK8)

(-) 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.....hhhhhhhhhhhh.eeeee.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
                5ak8 A   47 SMNPPAGPVRAIAEYERSAAVLVRYPFGIPMELIKELAKNDKVITIVASESQKNTVITQYTQSGVNLSNCDFIIAKTDSYWTRDYTGWFAMYDTNKVGLVDFIYNRPRPNDDEFPKYEAQYLGIEMFGMKLKQTGGNYMTDGYGSAVQSHIAYTENSSLSQAQVNQKMKDYLGITHHDVVQDPNGEYINHVDCWGKYLAPNKILIRKVPDNHPQHQALEDMAAYFAAQTCAWGTKYEVYRALATNEQPYTNSLILNNRVFVPVNGPASVDNDALNVYKTAMPGYEIIGVKGASGTPWLGTDALHARTHEVADKGYLYIKHYPILGEQAGPDYKIEADVVSCANATISPVQCYYRINGSGSFKAADMTMESTGHYTYSFTGLNKNDKVEYYISAADNSGRKETYPFIGEPDPFKFTCMNEAR 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)
  - → 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 5AK8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5AK8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5AK8)

(-) 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 ]  
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    Tyr A:71 - Pro A:72   [ RasMol ]  
 

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

(-) Related Entries Specified in the PDB File

5ak7 STRUCTURE OF WT PORPHYROMONAS GINGIVALIS PEPTIDYLARGININE DEIMINASE