3EP0 - JenaLib

Title :   METHYLTRANSFERASE DOMAIN OF HUMAN PR DOMAIN-CONTAINING PROTEIN 12

Authors :   M. F. Amaya, H. Zeng, P. Loppnau, C. Bountra, J. Weigelt, C. H. Arrowsmith, A. M. Edwards, A. Botchkarev, J. Min, A. N. Plotnikov, H. Wu, Structural Genomics Consortium (Sgc)

Date :   29 Sep 08 (Deposition) - 04 Nov 08 (Release) - 25 Aug 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)

Keywords :   Pr Domain-Containing Protein 12, Pr Domain Zinc Finger Protein 12, Structural Genomics, Structural Genomics Consortium, Sgc, Dna-Binding, Metal-Binding, Nucleus, Transcription, Transcription Regulation, Zinc, Zinc-Finger, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Zeng, M. F. Amaya, P. Loppnau, J. Min, A. N. Plotnikov, H. Wu
The Crystal Structure Of Methyltransferase Domain Of Human Pr Domain-Containing Protein 12.
To Be Published
PubMed: search
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (4, 8)

Asymmetric Unit (4, 8)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_074618	I	102	N	PRD12_HUMAN	Disease (HSAN8)	879255636	A/B	I	43	N
2	UniProt	VAR_074619	W	160	C	PRD12_HUMAN	Disease (HSAN8)	---	A/B	W	101	C
3	UniProt	VAR_074620	R	168	C	PRD12_HUMAN	Disease (HSAN8)	767397937	A/B	R	109	C
4	UniProt	VAR_074621	E	172	D	PRD12_HUMAN	Disease (HSAN8)	---	A/B	E	113	D

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

Biological Unit 1 (4, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_074618	I	102	N	PRD12_HUMAN	Disease (HSAN8)	879255636	A	I	43	N
2	UniProt	VAR_074619	W	160	C	PRD12_HUMAN	Disease (HSAN8)	---	A	W	101	C
3	UniProt	VAR_074620	R	168	C	PRD12_HUMAN	Disease (HSAN8)	767397937	A	R	109	C
4	UniProt	VAR_074621	E	172	D	PRD12_HUMAN	Disease (HSAN8)	---	A	E	113	D

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

Biological Unit 2 (4, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_074618	I	102	N	PRD12_HUMAN	Disease (HSAN8)	879255636	B	I	43	N
2	UniProt	VAR_074619	W	160	C	PRD12_HUMAN	Disease (HSAN8)	---	B	W	101	C
3	UniProt	VAR_074620	R	168	C	PRD12_HUMAN	Disease (HSAN8)	767397937	B	R	109	C
4	UniProt	VAR_074621	E	172	D	PRD12_HUMAN	Disease (HSAN8)	---	B	E	113	D

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

PROSITE Motifs (1, 2)

Exons (0, 0)

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:113
 aligned with PRD12_HUMAN | Q9H4Q4 from UniProtKB/Swiss-Prot  Length:367

    Alignment length:129
                                    85        95       105       115       125       135       145       155       165       175       185       195         
          PRD12_HUMAN    76 VQKLSSLVLPAEVIIAQSSIPGEGLGIFSKTWIKAGTEMGPFTGRVIAPEHVDICKNNNLMWEVFNEDGTVRYFIDASQEDHRSWMTYIKCARNEQEQNLEVVQIGTSIFYKAIEMIPPDQELLVWYGN 204
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee.......eeeee.......eeeee........eeeee..eee..----------.eeeee.....eeeeee.------hhhhhhee........eeeeee..eeeeee..........eeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------N---------------------------------------------------------C-------C---D-------------------------------- SAPs(SNPs)
                    PROSITE ----------SET  PDB: A:27-144 UniProt: 86-203                                                                                    - PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ep0 A  17 VQKLSSLVLPAEVIIAQSSIPGEGLGIFSKTWIKAGTEMGPFTGRVIAP----------LMWEVFNEDGTVRYFIDA------SWMTYIKCARNEQEQNLEVVQIGTSIFYKAIEMIPPDQELLVWYGN 145
                                    26        36        46        56        |-        76        86      |  -   |   106       116       126       136         
                                                                           65         76               93    100

Chain B from PDB  Type:PROTEIN  Length:113
 aligned with PRD12_HUMAN | Q9H4Q4 from UniProtKB/Swiss-Prot  Length:367

    Alignment length:129
                                    85        95       105       115       125       135       145       155       165       175       185       195         
          PRD12_HUMAN    76 VQKLSSLVLPAEVIIAQSSIPGEGLGIFSKTWIKAGTEMGPFTGRVIAPEHVDICKNNNLMWEVFNEDGTVRYFIDASQEDHRSWMTYIKCARNEQEQNLEVVQIGTSIFYKAIEMIPPDQELLVWYGN 204
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee.......eeeee.......eeeee........eeeee..eee..----------.eeeee.....eeeeee.------hhhhhhee........eeeeee..eeeeee........eeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------N---------------------------------------------------------C-------C---D-------------------------------- SAPs(SNPs)
                    PROSITE ----------SET  PDB: B:27-144 UniProt: 86-203                                                                                    - PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ep0 B  17 VQKLSSLVLPAEVIIAQSSIPGEGLGIFSKTWIKAGTEMGPFTGRVIAP----------LMWEVFNEDGTVRYFIDA------SWMTYIKCARNEQEQNLEVVQIGTSIFYKAIEMIPPDQELLVWYGN 145
                                    26        36        46        56        |-        76        86      |  -   |   106       116       126       136         
                                                                           65         76               93    100

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	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (11, 11)

Asymmetric Unit(hide GO term definitions)

Chain A,B (PRD12_HUMAN | Q9H4Q4)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	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: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.
biological process
	GO:0032259	methylation	The process in which a methyl group is covalently attached to a molecule.
	GO:0022008	neurogenesis	Generation of cells within the nervous system.
	GO:1900111	positive regulation of histone H3-K9 dimethylation	Any process that activates or increases the frequency, rate or extent of histone H3-K9 dimethylation.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	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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	Cis Peptide Bonds
		Gly A:56 - Pro A:57	[ RasMol ]
		Gly B:56 - Pro B:57	[ RasMol ]

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