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(-) Description

Title :  CALCIUM FREE FORM OF HUMAN PEPTIDYLARGININE DEIMINASE TYPE4 (PAD4)
 
Authors :  K. Arita, H. Hashimoto, T. Shimizu, K. Nakashima, M. Yamada, M. Sato
Date :  12 May 04  (Deposition) - 13 Jul 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Post-Translational Enzyme, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. Arita, H. Hashimoto, T. Shimizu, K. Nakashima, M. Yamada, M. Sato
Structural Basis For Ca(2+)-Induced Activation Of Human Pad
Nat. Struct. Mol. Biol. V. 11 777 2004
PubMed-ID: 15247907  |  Reference-DOI: 10.1038/NSMB799

(-) Compounds

Molecule 1 - PROTEIN-ARGININE DEIMINASE TYPE IV
    ChainsA
    EC Number3.5.3.15
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX6P-1
    Expression System StrainBL21 (DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPEPTIDYLARGININE DEIMINASE IV, HL-60 PAD

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (2x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1WD8)

(-) Sites  (0, 0)

(no "Site" information available for 1WD8)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1WD8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1WD8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (8, 8)

Asymmetric Unit (8, 8)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_053560R8HPADI4_HUMANPolymorphism35381732AR8H
2UniProtVAR_053561T79MPADI4_HUMANPolymorphism35809521AT79M
3UniProtVAR_020640V82APADI4_HUMANPolymorphism11203367AA82A
4UniProtVAR_027401D89NPADI4_HUMANPolymorphism143187209AD89N
5UniProtVAR_027402P102TPADI4_HUMANPolymorphism34309058AP102T
6UniProtVAR_020641G112APADI4_HUMANPolymorphism874881AA112A
7UniProtVAR_053562D260NPADI4_HUMANPolymorphism35903413AD260N
8UniProtVAR_020642S275FPADI4_HUMANPolymorphism1748020AS275F

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (8, 16)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_053560R8HPADI4_HUMANPolymorphism35381732AR8H
2UniProtVAR_053561T79MPADI4_HUMANPolymorphism35809521AT79M
3UniProtVAR_020640V82APADI4_HUMANPolymorphism11203367AA82A
4UniProtVAR_027401D89NPADI4_HUMANPolymorphism143187209AD89N
5UniProtVAR_027402P102TPADI4_HUMANPolymorphism34309058AP102T
6UniProtVAR_020641G112APADI4_HUMANPolymorphism874881AA112A
7UniProtVAR_053562D260NPADI4_HUMANPolymorphism35903413AD260N
8UniProtVAR_020642S275FPADI4_HUMANPolymorphism1748020AS275F

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1WD8)

(-) Exons   (16, 16)

Asymmetric Unit (16, 16)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000003754481bENSE00001883200chr1:17634692-17634809118PADI4_HUMAN1-31311A:2-3130
1.2ENST000003754482ENSE00001268578chr1:17657464-17657644181PADI4_HUMAN31-91611A:31-91 (gaps)61
1.3ENST000003754483ENSE00001044965chr1:17660438-1766050467PADI4_HUMAN92-114231A:92-11423
1.6ENST000003754486ENSE00001044983chr1:17662654-1766272168PADI4_HUMAN114-136231A:114-136 (gaps)23
1.7ENST000003754487ENSE00001044981chr1:17664533-17664650118PADI4_HUMAN137-176401A:137-176 (gaps)40
1.8ENST000003754488ENSE00001044989chr1:17666183-17666308126PADI4_HUMAN176-218431A:176-21843
1.9ENST000003754489ENSE00001268541chr1:17668438-17668616179PADI4_HUMAN218-277601A:218-277 (gaps)60
1.10ENST0000037544810ENSE00001044974chr1:17668794-17668897104PADI4_HUMAN278-312351A:278-31235
1.11aENST0000037544811aENSE00001044969chr1:17672523-17672634112PADI4_HUMAN312-349381A:312-349 (gaps)38
1.12bENST0000037544812bENSE00001044980chr1:17674436-17674543108PADI4_HUMAN350-385361A:350-37021
1.14ENST0000037544814ENSE00001044967chr1:17681028-17681182155PADI4_HUMAN386-437521A:388-437 (gaps)50
1.15ENST0000037544815ENSE00001044986chr1:17682478-17682622145PADI4_HUMAN437-485491A:437-48549
1.16bENST0000037544816bENSE00001044971chr1:17682852-17682954103PADI4_HUMAN486-520351A:486-51530
1.17bENST0000037544817bENSE00001044973chr1:17685333-1768540371PADI4_HUMAN520-543241A:522-54322
1.18ENST0000037544818ENSE00001044963chr1:17685775-17685903129PADI4_HUMAN544-586431A:544-58643
1.19ENST0000037544819ENSE00001467124chr1:17690017-17690499483PADI4_HUMAN587-663771A:587-663 (gaps)77

(-) Sequences/Alignments

Asymmetric 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:559
 aligned with PADI4_HUMAN | Q9UM07 from UniProtKB/Swiss-Prot  Length:663

    Alignment length:662
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661  
          PADI4_HUMAN     2 AQGTLIRVTPEQPTHAVCVLGTLTQLDICSSAPEDCTSFSINASPGVVVDIAHGPPAKKKSTGSSTWPLDPGVEVTLTMKVASGSTGDQKVQISYYGPKTPPVKALLYLTGVEISLCADITRTGKVKPTRAVKDQRTWTWGPCGQGAILLVNCDRDNLESSAMDCEDDEVLDSEDLQDMSLMTLSTKTPKDFFTNHTLVLHVARSEMDKVRVFQATRGKLSSKCSVVLGPKWPSHYLMVPGGKHNMDFYVEALAFPDTDFPGLITLTISLLDTSNLELPEAVVFQDSVVFRVAPWIMTPNTQPPQEVYACSIFENEDFLKSVTTLAMKAKCKLTICPEEENMDDQWMQDEMEIGYIQAPHKTLPVVFDSPRNRGLKEFPIKRVMGPDFGYVTRGPQTGGISGLDSFGNLEVSPPVTVRGKEYPLGRILFGDSCYPSNDSRQMHQALQDFLSAQQVQAPVKLYSDWLSVGHVDEFLSFVPAPDRKGFRLLLASPRSCYKLFQEQQNEGHGEALLFEGIKKKKQQKIKNILSNKTLREHNSFVERCIDWNRELLKRELGLAESDIIDIPQLFKLKEFSKAEAFFPNMVNMLVLGKHLGIPKPFGPVINGRCCLEEKVCSLLEPLGLQCTFINDFFTYHIRHGEVHCGTNVRRKPFSFKWWNMVP 663
               SCOP domains --d1wd8a2 A:4-112 Peptidylargin      ine deiminase Pa           d4, N-terminal domain                          d1wd8a1 A:113-29       3 Peptidylarginine dei              minase Pad4, middle domain                                                                                                d1wd8a3 A:294-663 P       eptidylarginine de           iminase Pad4, catalyti                 c C-term       inal domain                                                                                                                                                                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains PAD_N-1wd8A03 A:2-111                                                                                         -PAD_M-1wd8A02 A:       113-273                                                                                                                                   ----PAD-1wd8A01 A:278-663                                                                                                                                                                                                                                                                                                                                                                              Pfam domains
         Sec.struct. author ....eee......eeeeee....eeee....------.eeeee...eeeee..-----------..........eeeee.........eeeeeee........eeeeeeeeeeeeee..........-------............eee.......--------------.hhhhh...eeeeeeeee..hhhh.eeeeeee...hhh.eeeeee..-----.eeeee.....eee.....eeeeeeeeeee..........eeeeeeeeee........eeeeeeeeeeee...........eeeeee..-------..hhhhhhhhhh.eeee.-----------....eeeeeee..eeeeeee..-----------------..eee...-------...hhh.eee...eee..eee....eeeee...........hhhhhhhhhhh.....eeee.......hhhh.eeeee......eeeeeeehhhhhhhhhhhhhh........------...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhh.eeeee..eee.hhh.eee........ee...eeeee.....ee..eehhhhhhhhhhhhhh.eeeee..------------..eeeee.....hhhhh.. Sec.struct. author
                 SAPs(SNPs) ------H----------------------------------------------------------------------M--A------N------------T---------A---------------------------------------------------------------------------------------------------------------------------------------------------N--------------F---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1b  PDB: A:2-31        ------------------------------------------------------------Exon 1.3  PDB: A:92-114----------------------Exon 1.7  PDB: A:137-176 (gaps)         -----------------------------------------Exon 1.9  PDB: A:218-277 (gaps) UniProt: 218-277            Exon 1.10  PDB: A:278-312          -------------------------------------Exon 1.12b  PDB: A:350-370          Exon 1.14  PDB: A:388-437 (gaps) UniProt: 386-437   ------------------------------------------------Exon 1.16b  PDB: A:486-515         -----------------------Exon 1.18  PDB: A:544-586 UniProt: 544-586 Exon 1.19  PDB: A:587-663 (gaps) UniProt: 587-663                             Transcript 1 (1)
           Transcript 1 (2) -----------------------------Exon 1.2  PDB: A:31-91 (gaps) UniProt: 31-91                 ----------------------Exon 1.6               ---------------------------------------Exon 1.8  PDB: A:176-218 UniProt: 176-218  ---------------------------------------------------------------------------------------------Exon 1.11a  PDB: A:312-349 (gaps)     ---------------------------------------------------------------------------------------Exon 1.15  PDB: A:437-485 UniProt: 437-485       ----------------------------------Exon 1.17b [INCOMPLETE] ------------------------------------------------------------------------------------------------------------------------ Transcript 1 (2)
                 1wd8 A   2 AQGTLIRVTPEQPTHAVCVLGTLTQLDICSS------SFSINASPGVVVDIAH-----------STWPLDPGVEVTLTMKAASGSTGDQKVQISYYGPKTPPVKALLYLTAVEISLCADITRTGKVK-------QRTWTWGPCGQGAILLVNCDRD--------------LDSEDLQDMSLMTLSTKTPKDFFTNHTLVLHVARSEMDKVRVFQATR-----KCSVVLGPKWPSHYLMVPGGKHNMDFYVEALAFPDTDFPGLITLTISLLDTSNLELPEAVVFQDSVVFRVAPWIMTPNTQPPQEVYACS-------LKSVTTLAMKAKCKLTIC-----------QDEMEIGYIQAPHKTLPVVFDS-----------------DFGYVTRG-------GLDSFGNLEVSPPVTVRGKEYPLGRILFGDSCYPSNDSRQMHQALQDFLSAQQVQAPVKLYSDWLSVGHVDEFLSFVPAPDRKGFRLLLASPRSCYKLFQEQQNEGHGEALLF------KQQKIKNILSNKTLREHNSFVERCIDWNRELLKRELGLAESDIIDIPQLFKLKEFSKAEAFFPNMVNMLVLGKHLGIPKPFGPVINGRCCLEEKVCSLLEPLGLQCTFIND------------CGTNVRRKPFSFKWWNMVP 663
                                    11        21        31|      |41        51  |      -    |   71        81        91       101       111       121      |  -    |  141       151     |   -         -|      181       191       201       211      |  -  |    231       241       251       261       271       281       291       301       311|      321       331     |   -       351       361        |-         -      |391   |     - |     411       421       431       441       451       461       471       481       491       501       511   |     -|      531       541       551       561       571       581       591       601       611       621       631|        -   |   651       661  
                                                         32     39             54          66                                                           128     136                  157            172                                           218   224                                                                                     312     320              337         349                  370               388    395     403                                                                                                             515    522                                                                                                           632          645                  

   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  (3, 3)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1WD8)

(-) Pfam Domains  (3, 3)

Asymmetric Unit
(-)
Clan: GME (20)

(-) Gene Ontology  (22, 22)

Asymmetric Unit(hide GO term definitions)
Chain A   (PADI4_HUMAN | Q9UM07)
molecular function
    GO:0016990    arginine deiminase activity    Catalysis of the reaction: L-arginine + H2O = L-citrulline + NH3.
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0004668    protein-arginine deiminase activity    Catalysis of the reaction: protein L-arginine + H2O = protein L-citrulline + NH3.
biological process
    GO:0006464    cellular protein modification process    The covalent alteration of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications) occurring at the level of an individual cell. Includes the modification of charged tRNAs that are destined to occur in a protein (pre-translation modification).
    GO:0006325    chromatin organization    Any process that results in the specification, formation or maintenance of the physical structure of eukaryotic chromatin.
    GO:0006338    chromatin remodeling    Dynamic structural changes to eukaryotic chromatin occurring throughout the cell division cycle. These changes range from the local changes necessary for transcriptional regulation to global changes necessary for chromosome segregation.
    GO:0036413    histone H3-R26 citrullination    The hydrolysis of peptidyl-arginine to form peptidyl-citrulline at position 26 in histone H3.
    GO:0036414    histone citrullination    The hydrolysis of peptidyl-arginine to form peptidyl-citrulline on a histone protein.
    GO:0002376    immune system process    Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
    GO:0045087    innate immune response    Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
    GO:0006334    nucleosome assembly    The aggregation, arrangement and bonding together of a nucleosome, the beadlike structural units of eukaryotic chromatin composed of histones and DNA.
    GO:0018101    protein citrullination    The hydrolysis of peptidyl-arginine to form peptidyl-citrulline.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0019827    stem cell population maintenance    The process by which an organism or tissue maintains a population of stem cells of a single type. This can be achieved by a number of mechanisms: stem cell asymmetric division maintains stem cell numbers; stem cell symmetric division increases them; maintenance of a stem cell niche maintains the conditions for commitment to the stem cell fate for some types of stem cell; stem cells may arise de novo from other cell types.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        PADI4_HUMAN | Q9UM071wd9 1wda 2dew 2dex 2dey 2dw5 3apm 3apn 3b1t 3b1u 4dkt 4x8c 4x8g 5n0m 5n0y 5n0z 5n1b

(-) Related Entries Specified in the PDB File

1wd9 THE SAME PROTEIN, CALCIUM BOUND FORM
1wda THE SAME PROTEIN WITH BENZOYL-L-ARGININE AMIDE