3OPW - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE RPH1 CATALYTIC CORE

Authors :   Y. Chang, J. Wu, X. Tong, J. Zhou, J. Ding

Date :   02 Sep 10 (Deposition) - 22 Dec 10 (Release) - 05 Mar 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

Chains :   Asym./Biol. Unit : A

Keywords :   Rph1, Histone Demethylase, Catalytic Core, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Chang, J. Wu, X. J. Tong, J. Q. Zhou, J. Ding
Crystal Structure Of The Catalytic Core Of Saccharomyces Cerevesiae Histone Demethylase Rph1: Insights Into The Substrate Specificity And Catalytic Mechanism
Biochem. J. V. 433 295 2011
PubMed-ID: 21067515 | Reference-DOI: 10.1042/BJ20101418

Molecule 1 - DNA DAMAGE-RESPONSIVE TRANSCRIPTIONAL REPRESSOR RPH1
	Chains	:	A
	EC Number	:	1.14.11.27
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	CATALYTIC CORE DOMAIN, UNP RESIDUES 1-373
	Gene	:	RPH1, YER169W
	Organism Common	:	YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 3OPW)

(no "Site" information available for 3OPW)

(no "SS Bond" information available for 3OPW)

Asymmetric/Biological Unit

No.	Residues
1	Leu A:58	-	Pro A:59

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

Asymmetric/Biological Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	JMJN	PS51183	JmjN domain profile.	RPH1_YEAST	14-55	1	A:14-55
2	JMJC	PS51184	JmjC domain profile.	RPH1_YEAST	193-355	1	A:193-341

(no "Exon" information available for 3OPW)

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
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Chain A from PDB  Type:PROTEIN  Length:298
 aligned with RPH1_YEAST | P39956 from UniProtKB/Swiss-Prot  Length:796

    Alignment length:336
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335      
           RPH1_YEAST     6 APSEIVGGVPVFKPTYEQFEDFYAYCKAINKYGMKSGVVKVIPPKEWKDKLDLPYSAETLQKIKIKSPIQQHISGNKGLFMVQNVEKNKTYNIIQWKDLSKDYVPPEDPKARRNSRKGSVSKSTKLKLKNFESSFNIDDFEQFRTEYTIDLSDFQNTERLKFLEEYYWKTLNFTTPMYGADTPGSIFPEGLNVWNVAKLPNILDHMETKVPGVNDSYLYAGLWKASFSWHLEDQDLYSINYIHFGAPKQWYSIPQEDRFKFYKFMQEQFPEEAKNCPEFLRHKMFLASPKLLQENGIRCNEIVHHEGEFMITYPYGYHAGFNYGYNLAESVNFALE 341
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....ee...eee..hhhhhhhhhhhhhhhhhhhh...eeee..hhhhhh......hhhhhhhh.....eeeeee....eeeeee.......hhhhhhhhh........------------------------...hhhhhhhhh......hhhhhhhhhhhhhhhhhhhh......ee......................--------------..eeeee....eeeee.hhhhheeeeeeeee..eeeee.hhhhhhhhhhhhhhh..hhhhhh.......eeeehhhhhhh.....eeeee....eeee.....eeeee...eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------JMJN  PDB: A:14-55 UniProt: 14-55         -----------------------------------------------------------------------------------------------------------------------------------------JMJC  PDB: A:193-341 UniProt: 193-355                                                                                                                 PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3opw A   6 APSEIVGGVPVFKPTYEQFEDFYAYCKAINKYGMKSGVVKVIPPKEWKDKLDLPYSAETLQKIKIKSPIQQHISGNKGLFMVQNVEKNKTYNIIQWKDLSKDYVPPED------------------------SSFNIDDFEQFRTEYTIDLSDFQNTERLKFLEEYYWKTLNFTTPMYGADTPGSIFPEGLNVWNVAKLP--------------DSYLYAGLWKASFSWHLEDQDLYSINYIHFGAPKQWYSIPQEDRFKFYKFMQEQFPEEAKNCPEFLRHKMFLASPKLLQENGIRCNEIVHHEGEFMITYPYGYHAGFNYGYNLAESVNFALE 341
                                    15        25        35        45        55        65        75        85        95       105       | -         -         -  |    145       155       165       175       185       195       205         -    |  225       235       245       255       265       275       285       295       305       315       325       335      
                                                                                                                                     113                      138                                                                205            220

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 '\|'

(no "SCOP Domain" information available for 3OPW)

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

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (RPH1_YEAST | P39956)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0051864	histone demethylase activity (H3-K36 specific)	Catalysis of the reaction: histone H3 N6-methyl-L-lysine (position 36) + alpha-ketoglutarate + O2 = succinate + CO2 + formaldehyde + lysine. This reaction is the removal of a methyl group from lysine at position 36 of the histone H3 protein.
	GO:0032454	histone demethylase activity (H3-K9 specific)	Catalysis of the reaction: histone H3 N6-methyl-L-lysine (position 9) + alpha-ketoglutarate + O2 = succinate + CO2 + formaldehyde + lysine. This reaction is the removal of a methyl group from lysine at position 9 of the histone H3 protein.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0003676	nucleic acid binding	Interacting selectively and non-covalently with any nucleic acid.
	GO:0043565	sequence-specific DNA binding	Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
	GO:0001078	transcriptional repressor activity, RNA polymerase II core promoter proximal region sequence-specific binding	Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II (RNAP II) in order to stop, prevent, or reduce the frequency, rate or extent of transcription from an RNA polymerase II promoter.
biological process
	GO:0070544	histone H3-K36 demethylation	The modification of histone H3 by the removal of a methyl group from lysine at position 36 of the histone.
	GO:0033169	histone H3-K9 demethylation	The modification of histone H3 by the removal of a methyl group from lysine at position 9 of the histone.
	GO:0016577	histone demethylation	The modification of histones by removal of methyl groups.
	GO:0010507	negative regulation of autophagy	Any process that stops, prevents, or reduces the frequency, rate or extent of autophagy. Autophagy is the process in which cells digest parts of their own cytoplasm.
	GO:0000122	negative regulation of transcription from RNA polymerase II promoter	Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
	GO:0032968	positive regulation of transcription elongation from RNA polymerase II promoter	Any process that activates or increases the frequency, rate or extent of transcription elongation, the extension of an RNA molecule after transcription initiation and promoter clearance by the addition of ribonucleotides, catalyzed by RNA polymerase II.
	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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(no "Sites" information available for 3opw)

	Cis Peptide Bonds
		Leu A:58 - Pro A:59	[ RasMol ]

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	RPH1_YEAST \| P39956
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	1.14.11.27
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	RPH1_YEAST \| P39956	:	3opt

Description

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Ligands, Modified Residues, Ions (0, 0)

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SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

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Exons (0, 0)

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