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(-) Description

Title :  CRYSTAL STRUCTURE OF METHYLTRANSFERASE DOMAIN OF HUMAN PR DOMAIN-CONTAINING PROTEIN 4
 
Authors :  M. F. Amaya, H. Zeng, P. Loppnau, C. Bountra, J. Weigelt, C. H. Arrowsmit A. M. Edwards, A. Bochkarev, J. Min, A. N. Plotnikov, H. Wu, Structural Consortium (Sgc)
Date :  30 May 08  (Deposition) - 12 Aug 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Methyltransferase, Prdm4, Structural Genomics, Structural Genomics Consortium, Sgc, Dna-Binding, Metal-Binding, Nucleus, Transcription, Transcription Regulation, Zinc-Finger, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. Zeng, M. F. Amaya, P. Loppnau, A. Bochkarev, J. Min, A. N. Plotnikov, H. Wu
The Crystal Structure Of Methyltransferase Domain Of Human Pr Domain-Containing Protein 4.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PR DOMAIN ZINC FINGER PROTEIN 4
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28A
    Expression System StrainBL21
    Expression System Vector TypePLASMID
    FragmentRESIDUES 390-540
    GenePRDM4, PFM1
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPR DOMAIN-CONTAINING PROTEIN 4

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 5)

Asymmetric Unit (1, 5)
No.NameCountTypeFull Name
1MSE5Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1MSE2Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 3)
No.NameCountTypeFull Name
1MSE3Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 3DB5)

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1B:49 -B:124

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gly A:51 -Pro A:52
2Gly B:51 -Pro B:52

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3DB5)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SETPS50280 SET domain profile.PRDM4_HUMAN412-529
 
  2A:23-140
B:23-140
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SETPS50280 SET domain profile.PRDM4_HUMAN412-529
 
  1A:23-140
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SETPS50280 SET domain profile.PRDM4_HUMAN412-529
 
  1-
B:23-140

(-) Exons   (0, 0)

(no "Exon" information available for 3DB5)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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  UniProt sequence: complete  aligned part    
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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:124
 aligned with PRDM4_HUMAN | Q9UKN5 from UniProtKB/Swiss-Prot  Length:801

    Alignment length:138
                                   402       412       422       432       442       452       462       472       482       492       502       512       522        
          PRDM4_HUMAN   393 PVTFVPDTPIESRARLSLPKQLVLRQSIVGAEVGVWTGETIPVRTCFGPLIGQQSHSMEVAEWTDKAVNHIWKIYHNGVLEFCIITTDENECNWMMFVRKARNREEQNLVAYPHDGKIFFCTSQDIPPENELLFYYSR 530
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...........hhhhhh....eeeee..---.eeeee........ee.....eee.-----------...eeeeee..eeeeeee.......hhhhhhee........eeeeee..eeeeee..........eeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------SET  PDB: A:23-140 UniProt: 412-529                                                                                   - PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3db5 A   4 PVTFVPDTPIESRARLSLPKQLVLRQSI---EVGVWTGETIPVRTCFGPLIGQQSH-----------VNHIWKIYHNGVLEFCIITTDENECNWmmFVRKARNREEQNLVAYPHDGKIFFCTSQDIPPENELLFYYSR 141
                                    13        23       | - |      43        53     |   -       |73        83        93    || 103       113       123       133        
                                                      31  35                      59          71                         98-MSE                                       
                                                                                                                          99-MSE                                      

Chain B from PDB  Type:PROTEIN  Length:134
 aligned with PRDM4_HUMAN | Q9UKN5 from UniProtKB/Swiss-Prot  Length:801

    Alignment length:147
                                   400       410       420       430       440       450       460       470       480       490       500       510       520       530       
          PRDM4_HUMAN   391 HGPVTFVPDTPIESRARLSLPKQLVLRQSIVGAEVGVWTGETIPVRTCFGPLIGQQSHSMEVAEWTDKAVNHIWKIYHNGVLEFCIITTDENECNWMMFVRKARNREEQNLVAYPHDGKIFFCTSQDIPPENELLFYYSRDYAQQIG 537
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhh....eeeee..--..eeeee........ee.....eee...-----------.eeeeee..eeeeeee.......hhhhhhee........eeeeee..eeeeee..........eeeehhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------SET  PDB: B:23-140 UniProt: 412-529                                                                                   -------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3db5 B   2 HGPVTFVPDTPIESRARLSLPKQLVLRQSI--AEVGVWTGETIPVRTCFGPLIGQQSHSm-----------HIWKIYHNGVLEFCIITTDENECNWmmFVRKARNREEQNLVAYPHDGKIFFCTSQDIPPENELLFYYSRDYAQQIG 148
                                    11        21        31  |     41        51        61         - |      81        91      |101       111       121       131       141       
                                                        31 34                         61-MSE      73                       98-MSE                                              
                                                                                                                            99-MSE                                             

   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 3DB5)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3DB5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3DB5)

(-) Gene Ontology  (22, 22)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (PRDM4_HUMAN | Q9UKN5)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0005123    death receptor binding    Interacting selectively and non-covalently with any member of the death receptor (DR) family. The DR family falls within the tumor necrosis factor receptor superfamily and is characterized by a cytoplasmic region of ~80 residues termed the death domain (DD).
    GO:1990226    histone methyltransferase binding    Interacting selectively and non-covalently with a histone methyltransferase enzyme.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    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:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0008283    cell proliferation    The multiplication or reproduction of cells, resulting in the expansion of a cell population.
    GO:0071363    cellular response to growth factor stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a growth factor stimulus.
    GO:0031670    cellular response to nutrient    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a nutrient stimulus.
    GO:0043985    histone H4-R3 methylation    The modification of histone H4 by addition of a methyl group to arginine at position 3 of the histone.
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
    GO:0030308    negative regulation of cell growth    Any process that stops, prevents, or reduces the frequency, rate, extent or direction of cell growth.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
    GO:0006366    transcription from RNA polymerase II promoter    The synthesis of RNA from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs).
    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:0035097    histone methyltransferase complex    A multimeric complex that is able to catalyze the addition of methyl groups to histone proteins.
    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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