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Title :   AN EXTENDED CONFORMATION OF THE RWD DOMAIN OF HUMAN RING FINGER PROTEIN 25

Authors :   M. Yoneyama, N. Tochio, S. Koshiba, S. Watabe, T. Harada, T. Kigawa, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)

Date :   21 Apr 06 (Deposition) - 21 Oct 06 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A  (20x)

Keywords :   Ligase, Metal-Binding, Ub1 Conjugation, Ub1 Conjugation Pathway, Rwd Domain, Alpha+Beta Sandwich Fold, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Yoneyama, N. Tochio, S. Koshiba, S. Watabe, T. Harada, T. Kigawa, S. Yokoyama
An Extended Conformation Of The Rwd Domain Of Human Ring Finger Protein 25
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - RING FINGER PROTEIN 25
	Chains	:	A
	EC Number	:	6.3.2.-
	Engineered	:	YES
	Expression System	:	CELL FREE SYNTHESIS
	Expression System Plasmid	:	P051212-01
	Expression System Vector Type	:	PLASMID
	Fragment	:	RWD DOMAIN
	Gene	:	RNF25
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	CELL-FREE PROTEIN SYNTHESIS


NMR Structure (20x)	:

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2DMF)

(no "Site" information available for 2DMF)

(no "SS Bond" information available for 2DMF)

NMR Structure

No.	Model	Residues
1	1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20	Tyr A:71	-	Pro A:72

(no "SAP(SNP)/Variant" information available for 2DMF)

NMR Structure (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RWD	PS50908	RWD domain profile.	RNF25_HUMAN	18-128	1	A:15-125
2	ZF_RING_2	PS50089	Zinc finger RING-type profile.	RNF25_HUMAN	135-202	1	A:133-133

NMR Structure (8, 8)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000295704	1a	ENSE00001940096	chr2:219537134-219536653	482	RNF25_HUMAN	1-14	14	1	A:1-11	11
1.2a	ENST00000295704	2a	ENSE00001075113	chr2:219533402-219533328	75	RNF25_HUMAN	14-39	26	1	A:11-36	26
1.2d	ENST00000295704	2d	ENSE00001075105	chr2:219533064-219532962	103	RNF25_HUMAN	39-73	35	1	A:36-70	35
1.2f	ENST00000295704	2f	ENSE00001608322	chr2:219532869-219532802	68	RNF25_HUMAN	74-96	23	1	A:71-93	23
1.3	ENST00000295704	3	ENSE00001759572	chr2:219532704-219532635	70	RNF25_HUMAN	96-119	24	1	A:93-116	24
1.4	ENST00000295704	4	ENSE00001753147	chr2:219530953-219530882	72	RNF25_HUMAN	120-143	24	1	A:117-131	15
1.5c	ENST00000295704	5c	ENSE00001630208	chr2:219530782-219530639	144	RNF25_HUMAN	144-191	48	1	A:132-133	2
1.6a	ENST00000295704	6a	ENSE00001075116	chr2:219529970-219529878	93	RNF25_HUMAN	192-222	31	0	-	-
1.7c	ENST00000295704	7c	ENSE00001075108	chr2:219529596-219529462	135	RNF25_HUMAN	223-267	45	1	A:134-137	4
1.8c	ENST00000295704	8c	ENSE00001144106	chr2:219529258-219528587	672	RNF25_HUMAN	268-459	192	0	-	-

NMR Structure

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:137
 aligned with RNF25_HUMAN | Q96BH1 from UniProtKB/Swiss-Prot  Length:459

    Alignment length:227
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       
          RNF25_HUMAN     4 SASAAAGEEDWVLPSEVEVLESIYLDELQVIKGNGRTSPWEIYITLHPATAEDQDSQYVCFTLVLQVPAEYPHEVPQISIRNPRGLSDEQIHTILQVLGHVAKAGLGTAMLYELIEKGKEILTDNNIPHGQCVICLYGFQEKEAFTKTPCYHYFHCHCLARYIQHMEQELKAQGQEQEQERQHATTKQKAVGVQCPVCREPLVYDLASLKAAPEPQQPMELYQPSAE 230
               SCOP domains -------d2dmfa1 A:8-131 E3 ubiquitin-protein ligase RNF25                                                                           ------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhhh...eeee........eeeeeee....hhhhh....eeeeeeee.........eeeeeeee..hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh......-----------------------------------------..-------------------------------------------------.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------RWD  PDB: A:15-125 UniProt: 18-128                                                                             ------ZF_RING_2  PDB: A:133-133 UniProt: 135-202                          ---------------------------- PROSITE
           Transcript 1 (1) Exon 1.1a  ------------------------Exon 1.2d  PDB: A:36-70            Exon 1.2f  PDB: A:71-93-----------------------Exon 1.4  PDB: A:117-131Exon 1.5c  PDB: A:132-133 UniProt: 144-191      Exon 1.6a  PDB: -              1.7c     Transcript 1 (1)
           Transcript 1 (2) ----------Exon 1.2a  PDB: A:11-36   --------------------------------------------------------Exon 1.3  PDB: A:93-116 --------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 2dmf A   1 GSSGSSGEEDWVLPSEVEVLESIYLDELQVIKGNGRTSPWEIYITLHPATAEDQDSQYVCFTLVLQVPAEYPHEVPQISIRNPRGLSDEQIHTILQVLGHVAKAGLGTAMLYELIEKGKEILTDNNIPHGQ-----------------------------------------SG-------------------------------------------------PSSG 137
                                    10        20        30        40        50        60        70        80        90       100       110       120       130|        -         -         -         -  ||     -         -         -         -         -   |   
                                                                                                                                                            131                                       132|                                               134   
                                                                                                                                                                                                       133

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 '\|'

NMR Structure

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: UBC-like (176)

Superfamily: UBC-like (176)

Family: RWD domain (5)

Protein domain: E3 ubiquitin-protein ligase RNF25 (2)

Human (Homo sapiens) [TaxId: 9606] (2)

d2dmfa1

A:8-131

(no "CATH Domain" information available for 2DMF)

(no "Pfam Domain" information available for 2DMF)

NMR Structure(hide GO term definitions)

Chain A (RNF25_HUMAN | Q96BH1)

molecular function
	GO:0051059	NF-kappaB binding	Interacting selectively and non-covalently with NF-kappaB, a transcription factor for eukaryotic RNA polymerase II promoters.
	GO:0016874	ligase activity	Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0061630	ubiquitin protein ligase activity	Catalysis of the transfer of ubiquitin to a substrate protein via the reaction X-ubiquitin + S -> X + S-ubiquitin, where X is either an E2 or E3 enzyme, the X-ubiquitin linkage is a thioester bond, and the S-ubiquitin linkage is an amide bond: an isopeptide bond between the C-terminal glycine of ubiquitin and the epsilon-amino group of lysine residues in the substrate or, in the linear extension of ubiquitin chains, a peptide bond the between the C-terminal glycine and N-terminal methionine of ubiquitin residues.
	GO:0004842	ubiquitin-protein transferase activity	Catalysis of the transfer of ubiquitin from one protein to another via the reaction X-Ub + Y --> Y-Ub + X, where both X-Ub and Y-Ub are covalent linkages.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0051092	positive regulation of NF-kappaB transcription factor activity	Any process that activates or increases the frequency, rate or extent of activity of the transcription factor NF-kappaB.
	GO:0016567	protein ubiquitination	The process in which one or more ubiquitin groups are added to a protein.
cellular component
	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: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.

NMR Structure
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	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 2dmf)

	Sites
(no "Sites" information available for 2dmf)

	Cis Peptide Bonds
		Tyr A:71 - Pro A:72	[ RasMol ]

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	RNF25_HUMAN \| Q96BH1
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	6.3.2.-
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	RNF25_HUMAN \| Q96BH1
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UniProtKB/Swiss-Prot
	RNF25_HUMAN \| Q96BH1	:	2day 5d1k 5d1l 5d1m

2day	THE SAME PROTEIN DOMAIN OF THE DIFFERENT LENGTH RELATED ID: HSS001000178.2 RELATED DB: TARGETDB

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Ligands, Modified Residues, Ions (0, 0)

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Cis Peptide Bonds (1, 20)

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PROSITE Motifs (2, 2)

Exons (8, 8)

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