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Asym./Biol. Unit (Jmol Viewer)

Title :   SENP1 COVALENT COMPLEX WITH SUMO-2

Authors :   C. Dong, J. H. Naismith

Date :   14 Jul 06 (Deposition) - 08 Aug 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.20

Chains :   Asym./Biol. Unit : A,B

Keywords :   Protease, Hydrolase, Thiol Protease, Nuclear Protein, Ubl Conjugation Pathway (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Dong, J. H. Naismith
Senp1 Native Structure
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - SENTRIN-SPECIFIC PROTEASE 1
	Chains	:	A
	EC Number	:	3.4.22.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	CATALYTIC FRAGMENT, RESIDUES 419-643
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	SENP1, SENTRIN/SUMO-SPECIFIC PROTEASE SENP1

Molecule 2 - SMALL UBIQUITIN-RELATED MODIFIER 2
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	CATALYTIC FRAGMENT, RESIDUES 15-95
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	SUMO2, UBIQUITIN-LIKE PROTEIN SMT3B, SMT3 HOMOLOG 2, SENTRIN-2, HSMT3, SUMO-2

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

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

(no "Site" information available for 2IYD)

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

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

Asymmetric/Biological Unit (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_047508	D	16	N	SUMO2_HUMAN	Polymorphism	17850328	B	D	15	N

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric/Biological Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	UBIQUITIN_2	PS50053	Ubiquitin domain profile.	SUMO2_HUMAN	16-93	1	B:15-92
2	ULP_PROTEASE	PS50600	Ubiquitin-like protease family profile.	SENP1_HUMAN	450-614	1	A:450-614

(no "Exon" information available for 2IYD)

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
	(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:226
 aligned with SENP1_HUMAN | Q9P0U3 from UniProtKB/Swiss-Prot  Length:644

    Alignment length:226
                                   428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628       638      
          SENP1_HUMAN   419 EFPEITEEMEKEIKNVFRNGNQDEVLSEAFRLTITRKDIQTLNHLNWLNDEIINFYMNMLMERSKEKGLPSVHAFNTFFFTKLKTAGYQAVKRWTKKVDVFSVDILLVPIHLGVHWCLAVVDFRKKNITYYDSMGGINNEACRILLQYLKQESIDKKRKEFDTNGWQLFSKKSQEIPQQMNGSDCGMFACKYADCITKDRPINFTQQHMPYFRKRMVWEILHRKLL 644
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhh......eeeee..eeeehhhhhh.......hhhhhhhhhhhhhhh........eee...hhhhhhhhhhhhhhhhhhh........eeeeeeee..eeeeeeee....eeeee......hhhhhhhhhhhhhhhhhhhh.........eeee.............hhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------ULP_PROTEASE  PDB: A:450-614 UniProt: 450-614                                                                                                                        ------------------------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2iyd A 419 EFPEITEEMEKEIKNVFRNGNQDEVLSEAFRLTITRKDIQTLNHLNWLNDEIINFYMNMLMERSKEKGLPSVHAFNTFFFTKLKTAGYQAVKRWTKKVDVFSVDILLVPIHLGVHWCLAVVDFRKKNITYYDSMGGINNEACRILLQYLKQESIDKKRKEFDTNGWQLFSKKSQEIPQQMNGSDCGMFACKYADCITKDRPINFTQQHMPYFRKRMVWEILHRKLL 644
                                   428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628       638

Chain B from PDB  Type:PROTEIN  Length:79
 aligned with SUMO2_HUMAN | P61956 from UniProtKB/Swiss-Prot  Length:95

    Alignment length:79
                                    24        34        44        54        64        74        84         
          SUMO2_HUMAN    15 NDHINLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQGLSMRQIRFRFDGQPINETDTPAQLEMEDEDTIDVFQQQTGG  93
               SCOP domains d2iydb1 B:14-92 SUMO-2                                                          SCOP domains
               CATH domains 2iydB00 B:14-92                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee...eeeeeeee....hhhhhhhhhhh.......eeeee..ee......hhhhh....eeeeeee..... Sec.struct. author
                 SAPs(SNPs) -N----------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -UBIQUITIN_2  PDB: B:15-92 UniProt: 16-93                                       PROSITE
                 Transcript ------------------------------------------------------------------------------- Transcript
                 2iyd B  14 NDHINLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQGLSMRQIRFRFDGQPINETDTPAQLEMEDEDTIDVFQQQTGG  92
                                    23        33        43        53        63        73        83

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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: beta-Grasp (ubiquitin-like) (1032)

Superfamily: Ubiquitin-like (546)

Family: Ubiquitin-related (337)

Protein domain: SUMO-2 (8)

Human (Homo sapiens) [TaxId: 9606] (8)

d2iydb1

B:14-92

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Roll (3276)

Topology: Ubiquitin-like (UB roll) (674)

Homologous Superfamily: Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 (286)

Human (Homo sapiens) (177)

2iydB00

B:14-92

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (SENP1_HUMAN | Q9P0U3)

molecular function
	GO:0070139	SUMO-specific endopeptidase activity	Catalysis of the hydrolysis of peptide bonds between an alpha-carboxyl group and an alpha-amino group within the small conjugating protein SUMO.
	GO:0016929	SUMO-specific protease activity	Catalysis of the hydrolysis of SUMO, a small ubiquitin-related modifier, from previously sumoylated substrates.
	GO:0008234	cysteine-type peptidase activity	Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
	GO:0004175	endopeptidase activity	Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0008233	peptidase activity	Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
	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).
biological process
	GO:0006919	activation of cysteine-type endopeptidase activity involved in apoptotic process	Any process that initiates the activity of the inactive enzyme cysteine-type endopeptidase in the context of an apoptotic process.
	GO:0097190	apoptotic signaling pathway	A series of molecular signals which triggers the apoptotic death of a cell. The pathway starts with reception of a signal, and ends when the execution phase of apoptosis is triggered.
	GO:0032435	negative regulation of proteasomal ubiquitin-dependent protein catabolic process	Any process that stops, prevents, or reduces the frequency, rate or extent of the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of ubiquitin, and mediated by the proteasome.
	GO:0045944	positive regulation of transcription from RNA polymerase II promoter	Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
	GO:0016926	protein desumoylation	The process in which a SUMO protein (small ubiquitin-related modifier) is cleaved from its target protein.
	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.
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
	GO:0010724	regulation of definitive erythrocyte differentiation	Any process that modulates the rate, frequency, or extent of definitive erythrocyte differentiation. Definitive erythrocyte differentiation occurs as part of the process of definitive hemopoiesis.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005925	focal adhesion	Small region on the surface of a cell that anchors the cell to the extracellular matrix and that forms a point of termination of actin filaments.
	GO:0031965	nuclear membrane	Either of the lipid bilayers that surround the nucleus and form the nuclear envelope; excludes the intermembrane space.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	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 B (SUMO2_HUMAN | P61956)

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: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.
	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:0070911	global genome nucleotide-excision repair	The nucleotide-excision repair process in which DNA lesions are removed from nontranscribed strands and from transcriptionally silent regions over the entire genome.
	GO:0032436	positive regulation of proteasomal ubiquitin-dependent protein catabolic process	Any process that activates or increases the frequency, rate or extent of the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of ubiquitin, and mediated by the proteasome.
	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:0016605	PML body	A class of nuclear body; they react against SP100 auto-antibodies (PML, promyelocytic leukemia); cells typically contain 10-30 PML bodies per nucleus; alterations in the localization of PML bodies occurs after viral infection.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
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	SUMO2_HUMAN \| P61956
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1wm2	CRYSTAL STRUCTURE OF HUMAN SUMO-2 PROTEIN
1wm3	CRYSTAL STRUCTURE OF HUMAN SUMO-2 PROTEIN
1wz0	SOLUTION STRUCTURE OF HUMAN SUMO-2 (SMT3B ), A UBIQUITIN-LIKE PROTEIN
2ckg	THE STRUCTURE OF SENP1 SUMO-2 CO-COMPLEX SUGGESTS A STRUCTURAL BASIS FOR DISCRIMINATION BETWEEN SUMO PARALOGUES DURING PROCESSING
2ckh	SENP1-SUMO2 COMPLEX
2d07	CRYSTAL STRUCTURE OF SUMO-3-MODIFIED THYMINE -DNA GLYCOSYLASE
2iy0	SENP1 (MUTANT) SUMO1 RANGAP
2iy1	SENP1 (MUTANT) FULL LENGTH SUMO1
2iyc	SENP1 NATIVE STRUCTURE

Description

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Ligands, Modified Residues, Ions (0, 0)

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SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 1)

PROSITE Motifs (2, 2)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (1, 1)

Pfam Domains (0, 0)

Gene Ontology (25, 29)

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