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Description

Title :   STRUCTURE OF YEAST DCN-1

Authors :   X. Yang, J. Zhou, L. Sun, Z. Wei, J. Gao, W. Gong, R. M. Xu, Z. Rao, Y. Liu

Date :   16 Oct 06 (Deposition) - 26 Jun 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.92

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

Keywords :   Ubiquitin, Dcn1, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   X. Yang, J. Zhou, L. Sun, Z. Wei, J. Gao, W. Gong, R. M. Xu, Z. Rao, Y. Liu
Structural Basis For The Function Of Dcn-1 In Protein Neddylation.
J. Biol. Chem. V. 282 24490 2007
PubMed-ID: 17597076 | Reference-DOI: 10.1074/JBC.C700038200

Compounds

Molecule 1 - DEFECTIVE IN CULLIN NEDDYLATION PROTEIN 1
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PGEX4T-2
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 66-269
	Gene	:	DCN1
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932

Structural Features

Chains, Units

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

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (3, 6)

Asymmetric Unit (3, 6)

No.	Name	Count	Type	Full Name
1	CL	4	Ligand/Ion	CHLORIDE ION
2	MES	1	Ligand/Ion	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
3	PT	1	Ligand/Ion	PLATINUM (II) ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	MES	1	Ligand/Ion	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
3	PT	-1	Ligand/Ion	PLATINUM (II) ION

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	MES	2	Ligand/Ion	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
3	PT	-1	Ligand/Ion	PLATINUM (II) ION

Sites (6, 6)

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	MET A:230 , CL A:1110 , CL A:1118	BINDING SITE FOR RESIDUE PT A 1109
2	AC2	SOFTWARE	GLU A:128 , ASP A:129 , SER A:132 , PT A:1109	BINDING SITE FOR RESIDUE CL A 1110
3	AC3	SOFTWARE	LEU A:233	BINDING SITE FOR RESIDUE CL A 1111
4	AC4	SOFTWARE	ASP A:226	BINDING SITE FOR RESIDUE CL A 1112
5	AC5	SOFTWARE	GLU A:128 , MET A:230 , MES A:1001 , PT A:1109 , HOH A:1199	BINDING SITE FOR RESIDUE CL A 1118
6	AC6	SOFTWARE	TYR A:71 , ARG A:127 , GLU A:128 , MET A:230 , LEU A:233 , ALA A:252 , ALA A:253 , TRP A:254 , CL A:1118 , HOH A:1179 , HOH A:1209 , HOH A:1257	BINDING SITE FOR RESIDUE MES A 1001

SS Bonds (0, 0)

(no "SS Bond" information available for 2IS9)

Cis Peptide Bonds (0, 0)

(no "Cis Peptide Bond" information available for 2IS9)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

(no "SAP(SNP)/Variant" information available for 2IS9)

PROSITE Motifs (1, 1)

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DCUN1	PS51229	DCUN1 domain profile.	DCN1_YEAST	70-266	1	A:70-266

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DCUN1	PS51229	DCUN1 domain profile.	DCN1_YEAST	70-266	1	A:70-266

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DCUN1	PS51229	DCUN1 domain profile.	DCN1_YEAST	70-266	2	A:70-266

Exons (1, 1)

Asymmetric Unit (1, 1)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YLR128W	1	YLR128W.1	XII:398531-398533	3	DCN1_YEAST	1-1	1	0	-	-
1.2	YLR128W	2	YLR128W.2	XII:398628-399434	807	DCN1_YEAST	2-269	268	1	A:66-269	204

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
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Chain A from PDB  Type:PROTEIN  Length:204
 aligned with DCN1_YEAST | Q12395 from UniProtKB/Swiss-Prot  Length:269

    Alignment length:204
                                    75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265    
           DCN1_YEAST    66 AHPPVYPKELTQVFEHYINNNLFDIDSLVKFIEELGYNLEDLATLCLAHLLGYKKLEEPLKREDFLSTWFMQGCSTISDMQECIKTLDVKLHEDLQYFTQIYNYAFNLILDPNRKDIDTDEGIQYWKLFFQPEYPVRMEPDLLEAWFRFLRDEGKTTISKDTWRMLLLFFKRYPTIQKIISDYDETAAWPFIIDEFYECLQDQQ 269
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......hhhhhhhhhhhh.....hhhhhhhhhhhhh....hhhhhhhhhhhh........hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eehhhhhhhhhhhh........hhhhhhhhhhhhhhh...eehhhhhhhhhhhhhhh.hhhhhhhhh......hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----DCUN1  PDB: A:70-266 UniProt: 70-266                                                                                                                                                                 --- PROSITE
               Transcript 1 Exon 1.2  PDB: A:66-269 UniProt: 2-269 [INCOMPLETE]                                                                                                                                                          Transcript 1
                 2is9 A  66 AHPPVYPKELTQVFEHYINNNLFDIDSLVKFIEELGYNLEDLATLCLAHLLGYKKLEEPLKREDFLSTWFMQGCSTISDMQECIKTLDVKLHEDLQYFTQIYNYAFNLILDPNRKDIDTDEGIQYWKLFFQPEYPVRMEPDLLEAWFRFLRDEGKTTISKDTWRMLLLFFKRYPTIQKIISDYDETAAWPFIIDEFYECLQDQQ 269
                                    75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265

Legend:		→ Mismatch	(orange background)
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	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 2IS9)

CATH Domains (0, 0)

(no "CATH Domain" information available for 2IS9)

Pfam Domains (0, 0)

(no "Pfam Domain" information available for 2IS9)

Gene Ontology (10, 10)

Asymmetric Unit(hide GO term definitions)

Chain A (DCN1_YEAST | Q12395)

molecular function
	GO:0097602	cullin family protein binding	Interacting selectively and non-covalently with any member of the cullin family, hydrophobic proteins that act as scaffolds for ubiquitin ligases (E3).
	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:0030674	protein binding, bridging	The binding activity of a molecule that brings together two or more protein molecules, or a protein and another macromolecule or complex, through a selective, non-covalent, often stoichiometric interaction, permitting those molecules to function in a coordinated way.
	GO:0043130	ubiquitin binding	Interacting selectively and non-covalently with ubiquitin, a protein that when covalently bound to other cellular proteins marks them for proteolytic degradation.
	GO:0031624	ubiquitin conjugating enzyme binding	Interacting selectively and non-covalently with a ubiquitin conjugating enzyme, any of the E2 proteins.
	GO:0032182	ubiquitin-like protein binding	Interacting selectively and non-covalently with a small conjugating protein such as ubiquitin or a ubiquitin-like protein.
biological process
	GO:0051443	positive regulation of ubiquitin-protein transferase activity	Any process that activates, maintains or increases the rate of ubiquitin transferase activity.
	GO:0045116	protein neddylation	Covalent attachment of the ubiquitin-like protein NEDD8 (RUB1) to another protein.
cellular component
	GO:0005575	cellular_component	The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.
	GO:0000151	ubiquitin ligase complex	A protein complex that includes a ubiquitin-protein ligase and enables ubiquitin protein ligase activity. The complex also contains other proteins that may confer substrate specificity on the complex.

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Related Entries

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UniProtKB/Swiss-Prot
	DCN1_YEAST \| Q12395	:	2l4e 2l4f 3bq3 3o2p 3o6b 3tdi

Related Entries Specified in the PDB File

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