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Title :   STRUCTURE OF A SUMO-BINDING-MOTIF MIMIC BOUND TO SMT3P-UBC9P: CONSERVATION OF A NONCOVALENT UBIQUITIN-LIKE PROTEIN-E2 COMPLEX AS A PLATFORM FOR SELECTIVE INTERACTIONS WITHIN A SUMO PATHWAY

Authors :   D. M. Duda, B. A. Schulman

Date :   23 Mar 07 (Deposition) - 29 May 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

Keywords :   Ubc9, Smt3, Sumo Binding Motif, Sbm, Ligase/Protein Binding Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. M. Duda, R. C. A. M. Van Waardenburg, L. A. Borg, S. Mcgarity, A. Nourse, M. B. Waddell, M. A. Bjornsti, B. A. Schulman
Structure Of A Sumo-Binding-Motif Mimic Bound To Smt3P-Ubc9P: Conservation Of A Non-Covalent Ubiquitin-Like Protein-E2 Complex As A Platform For Selective Interactions Within A Sumo Pathway
J. Mol. Biol. V. 369 619 2007
PubMed-ID: 17475278 | Reference-DOI: 10.1016/J.JMB.2007.04.007
(for further references see the PDB file header)

Molecule 1 - SUMO-CONJUGATING ENZYME UBC9
	Chains	:	A, B
	EC Number	:	6.3.2.19
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PRSF-DUET
	Expression System Strain	:	BL21(DE3) GOLD
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	UBC9
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Synonym	:	UBIQUITIN-CONJUGATING ENZYME E2-18 KDA, UBIQUITIN- PROTEIN LIGASE, UBIQUITIN CARRIER PROTEIN 9

Molecule 2 - UBIQUITIN-LIKE PROTEIN SMT3
	Chains	:	C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PRSF-DUET
	Expression System Strain	:	BL21(DE3) GOLD
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	SMT3
	Mutation	:	YES
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A		C
Biological Unit 2 (1x)	:		B		D

Summary Information (see also Sequences/Alignments below)

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

(no "Site" information available for 2EKE)

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

Asymmetric Unit

No.	Residues
1	Tyr A:68	-	Pro A:69
2	Tyr B:68	-	Pro B:69

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

Asymmetric Unit (3, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	UBIQUITIN_CONJUGAT_2	PS50127	Ubiquitin-conjugating enzymes family profile.	UBC9_YEAST	7-146	2	A:7-146 B:7-146
2	UBIQUITIN_2	PS50053	Ubiquitin domain profile.	SMT3_YEAST	22-98	2	C:1022-1095 D:1022-1094
3	UBIQUITIN_CONJUGAT_1	PS00183	Ubiquitin-conjugating enzymes active site.	UBC9_YEAST	82-97	2	A:82-97 B:82-97

Biological Unit 1 (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	UBIQUITIN_CONJUGAT_2	PS50127	Ubiquitin-conjugating enzymes family profile.	UBC9_YEAST	7-146	1	A:7-146 -
2	UBIQUITIN_2	PS50053	Ubiquitin domain profile.	SMT3_YEAST	22-98	1	C:1022-1095 -
3	UBIQUITIN_CONJUGAT_1	PS00183	Ubiquitin-conjugating enzymes active site.	UBC9_YEAST	82-97	1	A:82-97 -

Biological Unit 2 (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	UBIQUITIN_CONJUGAT_2	PS50127	Ubiquitin-conjugating enzymes family profile.	UBC9_YEAST	7-146	1	- B:7-146
2	UBIQUITIN_2	PS50053	Ubiquitin domain profile.	SMT3_YEAST	22-98	1	- D:1022-1094
3	UBIQUITIN_CONJUGAT_1	PS00183	Ubiquitin-conjugating enzymes active site.	UBC9_YEAST	82-97	1	- B:82-97

Asymmetric Unit (3, 6)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YDL064W	1	YDL064W.1	IV:337487-337524	38	UBC9_YEAST	1-13	13	2	A:3-13 B:3-13	11 11
1.2	YDL064W	2	YDL064W.2	IV:337635-338070	436	UBC9_YEAST	13-157	145	2	A:13-156 B:13-156	144 144

2.1	YDR510W	1	YDR510W.1	IV:1469393-1469698	306	SMT3_YEAST	1-101	101	2	C:105-1095 (gaps) D:105-1094 (gaps)	93 92

Asymmetric Unit

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	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:154
 aligned with UBC9_YEAST | P50623 from UniProtKB/Swiss-Prot  Length:157

    Alignment length:154
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152    
          UBC9_YEAST      3 SLCLQRLQEERKKWRKDHPFGFYAKPVKKADGSMDLQKWEAGIPGKEGTNWAGGVYPITVEYPNEYPSKPPKVKFPAGFYHPNVYPSGTICLSILNEDQDWRPAITLKQIVLGVQDLLDSPNPNSPAQEPAWRSFSRNKAEYDKKVLLQAKQYS  156
               SCOP domains d2ekea_ A: Ubiquitin conjugating enzyme, UBC                                                                                                               SCOP domains
               CATH domains 2ekeA00 A:3-156 Ubiquitin Conjugating Enzyme                                                                                                               CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhh.....eeeeee.....eeeeeeeeeee..........eeeeeee..........eee.................hhhhh.........hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----UBIQUITIN_CONJUGAT_2  PDB: A:7-146 UniProt: 7-146                                                                                           ---------- PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) -------------------------------------------------------------------------------UBIQUITIN_CONJUG----------------------------------------------------------- PROSITE (3)
           Transcript 1 (1) Exon 1.1   ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ----------Exon 1.2  PDB: A:13-156 UniProt: 13-157 [INCOMPLETE]                                                                                             Transcript 1 (2)
                2eke A    3 SLCLQRLQEERKKWRKDHPFGFYAKPVKKADGSMDLQKWEAGIPGKEGTNWAGGVYPITVEYPNEYPSKPPKVKFPAGFYHPNVYPSGTICLSILNEDQDWRPAITLKQIVLGVQDLLDSPNPNSPAQEPAWRSFSRNKAEYDKKVLLQAKQYS  156
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152

Chain B from PDB  Type:PROTEIN  Length:154
 aligned with UBC9_YEAST | P50623 from UniProtKB/Swiss-Prot  Length:157

    Alignment length:154
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152    
          UBC9_YEAST      3 SLCLQRLQEERKKWRKDHPFGFYAKPVKKADGSMDLQKWEAGIPGKEGTNWAGGVYPITVEYPNEYPSKPPKVKFPAGFYHPNVYPSGTICLSILNEDQDWRPAITLKQIVLGVQDLLDSPNPNSPAQEPAWRSFSRNKAEYDKKVLLQAKQYS  156
               SCOP domains d2ekeb_ B: Ubiquitin conjugating enzyme, UBC                                                                                                               SCOP domains
               CATH domains 2ekeB00 B:3-156 Ubiquitin Conjugating Enzyme                                                                                                               CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhh.....eeeeee.....eeeeeeeeeee..........eeeeeee..........eee.................hhhhh.........hhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----UBIQUITIN_CONJUGAT_2  PDB: B:7-146 UniProt: 7-146                                                                                           ---------- PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) -------------------------------------------------------------------------------UBIQUITIN_CONJUG----------------------------------------------------------- PROSITE (3)
           Transcript 1 (1) Exon 1.1   ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ----------Exon 1.2  PDB: B:13-156 UniProt: 13-157 [INCOMPLETE]                                                                                             Transcript 1 (2)
                2eke B    3 SLCLQRLQEERKKWRKDHPFGFYAKPVKKADGSMDLQKWEAGIPGKEGTNWAGGVYPITVEYPNEYPSKPPKVKFPAGFYHPNVYPSGTICLSILNEDQDWRPAITLKQIVLGVQDLLDSPNPNSPAQEPAWRSFSRNKAEYDKKVLLQAKQYS  156
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152

Chain C from PDB  Type:PROTEIN  Length:91
 aligned with SMT3_YEAST | Q12306 from UniProtKB/Swiss-Prot  Length:101

    Alignment length:93
                                    12        22        32        42        52        62        72        82        92   
          SMT3_YEAST      3 DSEVNQEAKPEVKPEVKPETHINLKVSDGSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHREQ   95
               SCOP domains d2ekec_   C: SUMO-1 (smt3 homologue)                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........--..........eeeeeee....eeeeeee....hhhhhhhhhhhhh.hhh.eeeee..ee...............eeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) -------------------UBIQUITIN_2  PDB: C:1022-1095 UniProt: 22-98                               PROSITE (2)
               Transcript 2 Exon 2.1  PDB: C:105-1095 (gaps) UniProt: 1-101 [INCOMPLETE]                                  Transcript 2
                2eke C  105 DPLVPRGS--EVKPEVKPETHINLKVSDGSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHREQ 1095
                                   | -|     1022      1032      1042      1052      1062      1072      1082      1092   
                                 112  |                                                                                  
                                   1013

Chain D from PDB  Type:PROTEIN  Length:88
 aligned with SMT3_YEAST | Q12306 from UniProtKB/Swiss-Prot  Length:101

    Alignment length:92
                                    12        22        32        42        52        62        72        82        92  
          SMT3_YEAST      3 DSEVNQEAKPEVKPEVKPETHINLKVSDGSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHRE   94
               SCOP domains d2eked_   D: S  UMO-1 (smt3 homologue)                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........--....--....eeeeeee....eeeeeee....hhhhhhhhhhhhh.hhh.eeeee..ee...............eeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) -------------------UBIQUITIN_2  PDB: D:1022-1094 UniProt: 22-98                              PROSITE (2)
               Transcript 2 Exon 2.1  PDB: D:105-1094 (gaps) UniProt: 1-101 [INCOMPLETE]                                 Transcript 2
                2eke D  105 DPLVPRGS--EVKP--KPETHINLKVSDGSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHRE 1094
                                   | -|  |  1022      1032      1042      1052      1062      1072      1082      1092  
                                 112  |  |  |                                                                           
                                   1013  |  |                                                                           
                                      1016  |                                                                           
                                         1019

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(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Roll (3276)

Topology: Ubiquitin Conjugating Enzyme (83)

Homologous Superfamily: Ubiquitin Conjugating Enzyme (83)

Baker's yeast (Saccharomyces cerevisiae) (11)

1a	2ekeA00	A:3-156
1b	2ekeB00	B:3-156

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (UBC9_YEAST | P50623)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0019789	SUMO transferase activity	Catalysis of the transfer of SUMO from one protein to another via the reaction X-SUMO + Y --> Y-SUMO + X, where both X-SUMO and Y-SUMO are covalent linkages.
	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:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	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:0031625	ubiquitin protein ligase binding	Interacting selectively and non-covalently with a ubiquitin protein ligase enzyme, any of the E3 proteins.
biological process
	GO:0007049	cell cycle	The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
	GO:0051301	cell division	The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
	GO:0000022	mitotic spindle elongation	The cell cycle process in which the distance is lengthened between poles of the mitotic spindle. Mitotic spindle elongation begins during mitotic prophase and ends during mitotic anaphase B.
	GO:0016925	protein sumoylation	The process in which a SUMO protein (small ubiquitin-related modifier) is conjugated to a target protein via an isopeptide bond between the carboxyl terminus of SUMO with an epsilon-amino group of a lysine residue of the target protein.
cellular component
	GO:0000794	condensed nuclear chromosome	A highly compacted molecule of DNA and associated proteins resulting in a cytologically distinct nuclear chromosome.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	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.

Chain C,D (SMT3_YEAST | Q12306)

molecular function
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	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:0031386	protein tag	A molecular function exhibited by a protein that is covalently attached (AKA tagged or conjugated) to another protein where it acts as a marker, recognized by the cellular apparatus to target the tagged protein for some cellular process such as modification, sequestration, transport or degradation.
biological process
	GO:0000070	mitotic sister chromatid segregation	The cell cycle process in which replicated homologous chromosomes are organized and then physically separated and apportioned to two sets during the mitotic cell cycle. Each replicated chromosome, composed of two sister chromatids, aligns at the cell equator, paired with its homologous partner. One homolog of each morphologic type goes into each of the resulting chromosome sets.
	GO:0016925	protein sumoylation	The process in which a SUMO protein (small ubiquitin-related modifier) is conjugated to a target protein via an isopeptide bond between the carboxyl terminus of SUMO with an epsilon-amino group of a lysine residue of the target protein.
cellular component
	GO:0000794	condensed nuclear chromosome	A highly compacted molecule of DNA and associated proteins resulting in a cytologically distinct nuclear chromosome.
	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.
	GO:0005940	septin ring	A tight ring-shaped structure that forms in the division plane at the site of cytokinesis; composed of members of the conserved family of filament-forming proteins called septins as well as septin-associated proteins. This type of septin structure is observed at the bud neck of budding fungal cells, at the site of cell division in animal cells, at the junction between the mother cell and a pseudohyphal projection, and also within hyphae of filamentous fungi at sites where a septum will form.

Asymmetric Unit
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(no "Sites" information available for 2eke)

	Cis Peptide Bonds
		Tyr A:68 - Pro A:69	[ RasMol ]
		Tyr B:68 - Pro B:69	[ RasMol ]

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	UBC9_YEAST \| P50623
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1euv	SOLUTION STRUCTURE OF SUMO-1 IN COMPLEX WITH A SUMO-BINDING -MOTIF (SBM)
1wyw	CRYSTAL STRUCTURE OF SUMO-1 CONJUGATED THYMINE DNA GLYCOSYLASE
1z5s	CRYSTAL STRUCTURE OF A COMPLEX BETWEEN UBC9, SUMO-1, RANGAP1, AND NUP358/RANBP2

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