2BWB - JenaLib

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Title :   CRYSTAL STRUCTURE OF THE UBA DOMAIN OF DSK2 FROM S. CEREVISIAE

Authors :   E. D. Lowe, N. Hasan, J. -F. Trempe, L. Fonso, M. E. M. Noble, J. A. Endicott, L. N. Johnson, N. R. Brown

Date :   13 Jul 05 (Deposition) - 25 Jan 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

Chains :   Asym. Unit : A,B,C,D,E,F,G,H,I
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: D  (1x)
Biol. Unit 5: E  (1x)
Biol. Unit 6: F  (1x)
Biol. Unit 7: G  (1x)
Biol. Unit 8: H  (1x)
Biol. Unit 9: I  (1x)

Keywords :   Ubiquitin, Uba, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. D. Lowe, N. Hasan, J. -F. Trempe, L. Fonso, M. E. M. Noble, J. A. Endicott, L. N. Johnson, N. R. Brown
Structures Of The Dsk2 Ubl And Uba Domains And Their Complex.
Acta Crystallogr. , Sect. D V. 62 177 2006
PubMed-ID: 16421449 | Reference-DOI: 10.1107/S0907444905037777

Molecule 1 - UBIQUITIN-LIKE PROTEIN DSK2
	Chains	:	A, B, C, D, E, F, G, H, I
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX-KG
	Expression System Strain	:	B834(DE3)PLYSS
	Expression System Taxid	:	562
	Fragment	:	UBA DOMAIN, RESIDUES 326-371
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Other Details	:	UBIQUITIN BINDING DOMAIN OF DSK2 PROTEIN

		1	2	3	4	5	6	7	8	9
Asymmetric Unit	:	A	B	C	D	E	F	G	H	I
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:			C
Biological Unit 4 (1x)	:				D
Biological Unit 5 (1x)	:					E
Biological Unit 6 (1x)	:						F
Biological Unit 7 (1x)	:							G
Biological Unit 8 (1x)	:								H
Biological Unit 9 (1x)	:									I

Summary Information (see also Sequences/Alignments below)

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

(no "Site" information available for 2BWB)

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

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

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

Asymmetric Unit (1, 9)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	UBA	PS50030	Ubiquitin-associated domain (UBA) profile.	DSK2_YEAST	327-371	9	A:328-371 B:328-370 C:328-371 D:328-371 E:328-370 F:328-370 G:328-371 H:328-370 I:328-370

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	UBA	PS50030	Ubiquitin-associated domain (UBA) profile.	DSK2_YEAST	327-371	1	A:328-371 - - - - - - - -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	UBA	PS50030	Ubiquitin-associated domain (UBA) profile.	DSK2_YEAST	327-371	1	- B:328-370 - - - - - - -

Biological Unit 3 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	UBA	PS50030	Ubiquitin-associated domain (UBA) profile.	DSK2_YEAST	327-371	1	- - C:328-371 - - - - - -

Biological Unit 4 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	UBA	PS50030	Ubiquitin-associated domain (UBA) profile.	DSK2_YEAST	327-371	1	- - - D:328-371 - - - - -

Biological Unit 5 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	UBA	PS50030	Ubiquitin-associated domain (UBA) profile.	DSK2_YEAST	327-371	1	- - - - E:328-370 - - - -

Biological Unit 6 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	UBA	PS50030	Ubiquitin-associated domain (UBA) profile.	DSK2_YEAST	327-371	1	- - - - - F:328-370 - - -

Biological Unit 7 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	UBA	PS50030	Ubiquitin-associated domain (UBA) profile.	DSK2_YEAST	327-371	1	- - - - - - G:328-371 - -

Biological Unit 8 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	UBA	PS50030	Ubiquitin-associated domain (UBA) profile.	DSK2_YEAST	327-371	1	- - - - - - - H:328-370 -

Biological Unit 9 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	UBA	PS50030	Ubiquitin-associated domain (UBA) profile.	DSK2_YEAST	327-371	1	- - - - - - - - I:328-370

Asymmetric Unit (1, 9)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YMR276W	1	YMR276W.1	XIII:818826-819947	1122	DSK2_YEAST	1-373	373	9	A:326-371 (gaps) B:327-370 (gaps) C:326-371 (gaps) D:327-371 (gaps) E:327-370 (gaps) F:327-370 (gaps) G:327-371 (gaps) H:327-370 (gaps) I:327-370 (gaps)	68 47 68 48 47 47 48 47 47

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:46
 aligned with DSK2_YEAST | P48510 from UniProtKB/Swiss-Prot  Length:373

    Alignment length:68
                                   313       323       333       343       353       363        
           DSK2_YEAST   304 FDPALLASMFQPPVQASQAEDTRPPEERYEHQLRQLNDMGFFDFDRNVAALRRSGGSVQGALDSLLNG 371
               SCOP domains d2                      bwba_ A: automated matches                   SCOP domains
               CATH domains -------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------- Pfam domains
         Sec.struct. author .h----------------------hhhhhhhhhhhhhhh...hhhhhhhhhhhhh.hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------UBA  PDB: A:328-371 UniProt: 327-371          PROSITE
               Transcript 1 Exon 1.1  PDB: A:326-371 (gaps) UniProt: 1-373 [INCOMPLETE]          Transcript 1
                 2bwb A 326 LD----------------------PEERYEHQLRQLNDMGFFDFDRNVAALRRSGGSVQGALDSLLNG 371
                             |       -         -    |  333       343       353       363        
                             |                    328                                           
                           327

Chain B from PDB  Type:PROTEIN  Length:44
 aligned with DSK2_YEAST | P48510 from UniProtKB/Swiss-Prot  Length:373

    Alignment length:47
                                   333       343       353       363       
           DSK2_YEAST   324 DTRPPEERYEHQLRQLNDMGFFDFDRNVAALRRSGGSVQGALDSLLN 370
               SCOP domains d   2bwbb_ B: automated matches                 SCOP domains
               CATH domains ----------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------- Pfam domains
         Sec.struct. author h---hhhhhhhhhhhhhhh...hhhhhhhhhhhh..hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------- SAPs(SNPs)
                    PROSITE ---UBA  PDB: B:328-370 UniProt: 327-371         PROSITE
               Transcript 1 Exon 1.1  PDB: B:327-370 (gaps) UniProt: 1-373  Transcript 1
                 2bwb B 327 D---PEERYEHQLRQLNDMGFFDFDRNVAALRRSGGSVQGALDSLLN 370
                            |   |  333       343       353       363       
                          327 328

Chain C from PDB  Type:PROTEIN  Length:46
 aligned with DSK2_YEAST | P48510 from UniProtKB/Swiss-Prot  Length:373

    Alignment length:68
                                   313       323       333       343       353       363        
           DSK2_YEAST   304 FDPALLASMFQPPVQASQAEDTRPPEERYEHQLRQLNDMGFFDFDRNVAALRRSGGSVQGALDSLLNG 371
               SCOP domains d2                      bwbc_ C: automated matches                   SCOP domains
               CATH domains -------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------- Pfam domains
         Sec.struct. author .h----------------------hhhhhhhhhhhhhhh...hhhhhhhhhhhh..hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------UBA  PDB: C:328-371 UniProt: 327-371          PROSITE
               Transcript 1 Exon 1.1  PDB: C:326-371 (gaps) UniProt: 1-373 [INCOMPLETE]          Transcript 1
                 2bwb C 326 LD----------------------PEERYEHQLRQLNDMGFFDFDRNVAALRRSGGSVQGALDSLLNG 371
                             |       -         -    |  333       343       353       363        
                           327                    328

Chain D from PDB  Type:PROTEIN  Length:45
 aligned with DSK2_YEAST | P48510 from UniProtKB/Swiss-Prot  Length:373

    Alignment length:48
                                   333       343       353       363        
           DSK2_YEAST   324 DTRPPEERYEHQLRQLNDMGFFDFDRNVAALRRSGGSVQGALDSLLNG 371
               SCOP domains d   2bwbd_ D: automated matches                  SCOP domains
               CATH domains ------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------ Pfam domains
         Sec.struct. author h---hhhhhhhhhhhhhhh...hhhhhhhhhhhhh.hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------ SAPs(SNPs)
                    PROSITE ---UBA  PDB: D:328-371 UniProt: 327-371          PROSITE
               Transcript 1 Exon 1.1  PDB: D:327-371 (gaps) UniProt: 1-373   Transcript 1
                 2bwb D 327 D---PEERYEHQLRQLNDMGFFDFDRNVAALRRSGGSVQGALDSLLNG 371
                            |   |  333       343       353       363        
                          327 328

Chain E from PDB  Type:PROTEIN  Length:44
 aligned with DSK2_YEAST | P48510 from UniProtKB/Swiss-Prot  Length:373

    Alignment length:47
                                   333       343       353       363       
           DSK2_YEAST   324 DTRPPEERYEHQLRQLNDMGFFDFDRNVAALRRSGGSVQGALDSLLN 370
               SCOP domains d   2bwbe_ E: automated matches                 SCOP domains
               CATH domains ----------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------- Pfam domains
         Sec.struct. author h---hhhhhhhhhhhhhhh...hhhhhhhhhhhh..hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------- SAPs(SNPs)
                    PROSITE ---UBA  PDB: E:328-370 UniProt: 327-371         PROSITE
               Transcript 1 Exon 1.1  PDB: E:327-370 (gaps) UniProt: 1-373  Transcript 1
                 2bwb E 327 D---PEERYEHQLRQLNDMGFFDFDRNVAALRRSGGSVQGALDSLLN 370
                            |   |  333       343       353       363       
                          327 328

Chain F from PDB  Type:PROTEIN  Length:44
 aligned with DSK2_YEAST | P48510 from UniProtKB/Swiss-Prot  Length:373

    Alignment length:47
                                   333       343       353       363       
           DSK2_YEAST   324 DTRPPEERYEHQLRQLNDMGFFDFDRNVAALRRSGGSVQGALDSLLN 370
               SCOP domains d   2bwbf_ F: automated matches                 SCOP domains
               CATH domains ----------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------- Pfam domains
         Sec.struct. author .---....hhhhhhhhhhh...hhhhhhhhhhhh..hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------- SAPs(SNPs)
                    PROSITE ---UBA  PDB: F:328-370 UniProt: 327-371         PROSITE
               Transcript 1 Exon 1.1  PDB: F:327-370 (gaps) UniProt: 1-373  Transcript 1
                 2bwb F 327 D---PEERYEHQLRQLNDMGFFDFDRNVAALRRSGGSVQGALDSLLN 370
                            |   |  333       343       353       363       
                          327 328

Chain G from PDB  Type:PROTEIN  Length:45
 aligned with DSK2_YEAST | P48510 from UniProtKB/Swiss-Prot  Length:373

    Alignment length:48
                                   333       343       353       363        
           DSK2_YEAST   324 DTRPPEERYEHQLRQLNDMGFFDFDRNVAALRRSGGSVQGALDSLLNG 371
               SCOP domains d   2bwbg_ G: automated matches                  SCOP domains
               CATH domains ------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------ Pfam domains
         Sec.struct. author h---hhhhhhhhhhhhhhh...hhhhhhhhhhhh..hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------ SAPs(SNPs)
                    PROSITE ---UBA  PDB: G:328-371 UniProt: 327-371          PROSITE
               Transcript 1 Exon 1.1  PDB: G:327-371 (gaps) UniProt: 1-373   Transcript 1
                 2bwb G 327 D---PEERYEHQLRQLNDMGFFDFDRNVAALRRSGGSVQGALDSLLNG 371
                            |   |  333       343       353       363        
                          327 328

Chain H from PDB  Type:PROTEIN  Length:44
 aligned with DSK2_YEAST | P48510 from UniProtKB/Swiss-Prot  Length:373

    Alignment length:47
                                   333       343       353       363       
           DSK2_YEAST   324 DTRPPEERYEHQLRQLNDMGFFDFDRNVAALRRSGGSVQGALDSLLN 370
               SCOP domains d   2bwbh_ H: automated matches                 SCOP domains
               CATH domains ----------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------- Pfam domains
         Sec.struct. author h---hhhhhhhhhhhhhhh...hhhhhhhhhhhh..hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------- SAPs(SNPs)
                    PROSITE ---UBA  PDB: H:328-370 UniProt: 327-371         PROSITE
               Transcript 1 Exon 1.1  PDB: H:327-370 (gaps) UniProt: 1-373  Transcript 1
                 2bwb H 327 D---PEERYEHQLRQLNDMGFFDFDRNVAALRRSGGSVQGALDSLLN 370
                            |   |  333       343       353       363       
                          327 328

Chain I from PDB  Type:PROTEIN  Length:40
 aligned with DSK2_YEAST | P48510 from UniProtKB/Swiss-Prot  Length:373

    Alignment length:47
                                   333       343       353       363       
           DSK2_YEAST   324 DTRPPEERYEHQLRQLNDMGFFDFDRNVAALRRSGGSVQGALDSLLN 370
               SCOP domains d   2bwbi_ I: aut    omated matches             SCOP domains
               CATH domains ----------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------- Pfam domains
         Sec.struct. author h---hhhhhhhhhhhh.----.hhhhhhhhhhhh..hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------- SAPs(SNPs)
                    PROSITE ---UBA  PDB: I:328-370 UniProt: 327-371         PROSITE
               Transcript 1 Exon 1.1  PDB: I:327-370 (gaps) UniProt: 1-373  Transcript 1
                 2bwb I 327 D---PEERYEHQLRQLN----FDFDRNVAALRRSGGSVQGALDSLLN 370
                            |   |  333      |  - |     353       363       
                          327 328         340  345

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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: RuvA C-terminal domain-like (106)

Superfamily: UBA-like (64)

Family: UBA domain (48)

Protein domain: automated matches (9)

Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] (2)

1a	d2bwba_	A:
1b	d2bwbb_	B:
1c	d2bwbc_	C:
1d	d2bwbd_	D:
1e	d2bwbe_	E:
1f	d2bwbf_	F:
1g	d2bwbg_	G:
1h	d2bwbh_	H:
1i	d2bwbi_	I:

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

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

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D,E,F,G,H,I (DSK2_YEAST | P48510)

molecular function
	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.
biological process
	GO:0030474	spindle pole body duplication	Construction of a new spindle pole body.
	GO:0030433	ubiquitin-dependent ERAD pathway	The series of steps necessary to target endoplasmic reticulum (ER)-resident proteins for degradation by the cytoplasmic proteasome. Begins with recognition of the ER-resident protein, includes retrotranslocation (dislocation) of the protein from the ER to the cytosol, protein ubiquitination necessary for correct substrate transfer, transport of the protein to the proteasome, and ends with degradation of the protein by the cytoplasmic proteasome.
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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Access by PDB/NDB ID
	2bwb
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	DSK2_YEAST \| P48510
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	DSK2_YEAST \| P48510
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UniProtKB/Swiss-Prot
	DSK2_YEAST \| P48510	:	1wr1 2bwe 2bwf 3m63 4un2

1wr1	THE COMPLEX STURCTURE OF DSK2P UBA WITH UBIQUITIN

Description

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Exons (1, 9)

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