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Asym./Biol. Unit - manually (Jmol Viewer)

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Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF HUMAN SENP2 IN COMPLEX WITH PRESUMO-2

Authors :   D. Reverter, C. D. Lima

Date :   09 Oct 06 (Deposition) - 14 Nov 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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

Keywords :   Sumo, Ubiquitin, Senp, Ulp, Complex, Protein Binding, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. Reverter, C. D. Lima
Structural Basis For Senp2 Protease Interactions With Sumo Precursors And Conjugated Substrates.
Nat. Struct. Mol. Biol. V. 13 1060 2006
PubMed-ID: 17099700 | Reference-DOI: 10.1038/NSMB1168
(for further references see the PDB file header)

Molecule 1 - SENTRIN-SPECIFIC PROTEASE 2
	Chains	:	A
	EC Number	:	3.4.22.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28B
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	CATALYTIC DOMAIN
	Gene	:	SENP2, KIAA1331
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	SENTRIN/SUMO-SPECIFIC PROTEASE SENP2, SMT3- SPECIFIC ISOPEPTIDASE 2, SMT3IP2, AXAM2

Molecule 2 - SMALL UBIQUITIN-RELATED MODIFIER 2 PRECURSOR
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28B
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	SUMO2, SMT3B, SMT3H2
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	SUMO-2, UBIQUITIN-LIKE PROTEIN SMT3B, SMT3 HOMOLOG 2, SENTRIN-2, HSMT3

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 3)

No.	Name	Count	Type	Full Name
1	SO4	3	Ligand/Ion	SULFATE ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH A:65 , HOH A:76 , HOH A:95 , ALA A:392 , PHE A:393 , LYS A:394 , ARG A:396	BINDING SITE FOR RESIDUE SO4 A 300
2	AC2	SOFTWARE	ARG A:475 , LYS A:476	BINDING SITE FOR RESIDUE SO4 A 301
3	AC3	SOFTWARE	ARG A:396 , ASN B:68 , GLU B:69 , THR B:70 , HOH B:306 , HOH B:333	BINDING SITE FOR RESIDUE SO4 B 302

(no "SS Bond" information available for 2IO0)

(no "Cis Peptide Bond" information available for 2IO0)

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	16	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:16-93
2	ULP_PROTEASE	PS50600	Ubiquitin-like protease family profile.	SENP2_HUMAN	395-559	1	A:395-559

Asymmetric/Biological Unit (7, 7)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.2a	ENST00000296257	2a	ENSE00001875109	chr3:185303962-185304302	341	SENP2_HUMAN	1-34	34	0	-	-
1.3	ENST00000296257	3	ENSE00001324023	chr3:185307902-185307957	56	SENP2_HUMAN	34-53	20	0	-	-
1.4b	ENST00000296257	4b	ENSE00001308929	chr3:185316200-185316333	134	SENP2_HUMAN	53-97	45	0	-	-
1.5a	ENST00000296257	5a	ENSE00001631097	chr3:185316746-185316812	67	SENP2_HUMAN	98-120	23	0	-	-
1.6b	ENST00000296257	6b	ENSE00001756942	chr3:185318553-185318643	91	SENP2_HUMAN	120-150	31	0	-	-
1.8c	ENST00000296257	8c	ENSE00001644564	chr3:185324118-185324286	169	SENP2_HUMAN	150-206	57	0	-	-
1.9d	ENST00000296257	9d	ENSE00001632364	chr3:185327035-185327138	104	SENP2_HUMAN	207-241	35	0	-	-
1.10b	ENST00000296257	10b	ENSE00001611859	chr3:185329439-185329533	95	SENP2_HUMAN	241-273	33	0	-	-
1.11b	ENST00000296257	11b	ENSE00001697885	chr3:185330395-185330446	52	SENP2_HUMAN	273-290	18	0	-	-
1.12b	ENST00000296257	12b	ENSE00001732674	chr3:185331133-185331196	64	SENP2_HUMAN	290-311	22	0	-	-
1.13b	ENST00000296257	13b	ENSE00001602918	chr3:185332352-185332528	177	SENP2_HUMAN	312-370	59	1	A:364-370	7
1.14b	ENST00000296257	14b	ENSE00001738954	chr3:185335268-185335399	132	SENP2_HUMAN	371-414	44	1	A:371-414	44
1.15a	ENST00000296257	15a	ENSE00001645647	chr3:185337087-185337290	204	SENP2_HUMAN	415-482	68	1	A:415-482	68
1.16	ENST00000296257	16	ENSE00001639235	chr3:185339614-185339693	80	SENP2_HUMAN	483-509	27	1	A:483-509	27
1.17	ENST00000296257	17	ENSE00001806686	chr3:185341786-185341870	85	SENP2_HUMAN	509-537	29	1	A:509-537	29
1.18b	ENST00000296257	18b	ENSE00001689492	chr3:185344086-185344181	96	SENP2_HUMAN	538-569	32	1	A:538-569	32
1.19c	ENST00000296257	19c	ENSE00001887141	chr3:185347570-185351339	3770	SENP2_HUMAN	570-589	20	1	A:570-589	20

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 SENP2_HUMAN | Q9HC62 from UniProtKB/Swiss-Prot  Length:589

    Alignment length:226
                                   373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583      
          SENP2_HUMAN   364 DLLELTEDMEKEISNALGHGPQDEILSSAFKLRITRGDIQTLKNYHWLNDEVINFYMNLLVERNKKQGYPALHVFSTFFYPKLKSGGYQAVKRWTKGVNLFEQEIILVPIHRKVHWSLVVIDLRKKCLKYLDSMGQKGHRICEILLQYLQDESKTKRNSDLNLLEWTHHSMKPHEIPQQLNGSDCGMFTCKYADYISRDKPITFTQHQMPLFRKKMVWEILHQQLL 589
               SCOP domains d2io0a1 A:364-589 Sentrin-specific protease 2, SENP2                                                                                                                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhh......eeeee..eeeehhhhhhhh.....hhhhhhhhhhhhhhhhhhh....eee...hhhhhhhhhhhhhhhhhhh..hhhhh.eeeeeee....eeeeeee....eeeee.......hhhhhhhhhhhhhhhhhhhh.............hhhhh....hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------ULP_PROTEASE  PDB: A:395-559 UniProt: 395-559                                                                                                                        ------------------------------ PROSITE
           Transcript 1 (1) 1.13b  Exon 1.14b  PDB: A:371-414 UniProt: 371-414 Exon 1.15a  PDB: A:415-482 UniProt: 415-482                         Exon 1.16  PDB: A:483-509  ----------------------------Exon 1.18b  PDB: A:538-569      Exon 1.19c           Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.17  PDB: A:509-537    ---------------------------------------------------- Transcript 1 (2)
                 2io0 A 364 DLLELTEDMEKEISNALGHGPQDEILSSAFKLRITRGDIQTLKNYHWLNDEVINFYMNLLVERNKKQGYPALHVFSTFFYPKLKSGGYQAVKRWTKGVNLFEQEIILVPIHRKVHWSLVVIDLRKKCLKYLDSMGQKGHRICEILLQYLQDESKTKRNSDLNLLEWTHHSMKPHEIPQQLNGSDSGMFTCKYADYISRDKPITFTQHQMPLFRKKMVWEILHQQLL 589
                                   373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583

Chain B from PDB  Type:PROTEIN  Length:84
 aligned with SUMO2_HUMAN | P61956 from UniProtKB/Swiss-Prot  Length:95

    Alignment length:84
                                                                                                          95    
                                    25        35        45        55        65        75        85        95    
          SUMO2_HUMAN    16 DHINLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQGLSMRQIRFRFDGQPINETDTPAQLEMEDEDTIDVFQQQTGGVY----   -
               SCOP domains d2io0b_ B: SUMO-2                                                                    SCOP domains
               CATH domains 2io0B00 B:16-99 Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1   CATH domains
               Pfam domains ------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeee.....eeeeeee....hhhhhhhhhhhh......eeeee..ee...............eeeeeee........... Sec.struct. author
                 SAPs(SNPs) N----------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE UBIQUITIN_2  PDB: B:16-93 UniProt: 16-93                                      ------ PROSITE
                 Transcript ------------------------------------------------------------------------------------ Transcript
                 2io0 B  16 DHINLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQGLSMRQIRFRFDGQPINETDTPAQLEMEDEDTIDVFQQQTGGVYLEHH  99
                                    25        35        45        55        65        75        85        95

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)

d2io0b_

Fold: Cysteine proteinases (392)

Superfamily: Cysteine proteinases (392)

Family: Adenain-like (26)

Protein domain: Sentrin-specific protease 2, SENP2 (6)

Human (Homo sapiens) [TaxId: 9606] (6)

d2io0a1

A:364-589

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)

2io0B00

B:16-99

(no "Pfam Domain" information available for 2IO0)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (SENP2_HUMAN | Q9HC62)

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).
	GO:0019904	protein domain specific binding	Interacting selectively and non-covalently with a specific domain of a protein.
biological process
	GO:0016055	Wnt signaling pathway	The series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell and ending with a change in cell state.
	GO:0009950	dorsal/ventral axis specification	The establishment, maintenance and elaboration of the dorsal/ventral axis. The dorsal/ventral axis is defined by a line that runs orthogonal to both the anterior/posterior and left/right axes. The dorsal end is defined by the upper or back side of an organism. The ventral end is defined by the lower or front side of an organism.
	GO:0045444	fat cell differentiation	The process in which a relatively unspecialized cell acquires specialized features of an adipocyte, an animal connective tissue cell specialized for the synthesis and storage of fat.
	GO:0007507	heart development	The process whose specific outcome is the progression of the heart over time, from its formation to the mature structure. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood.
	GO:0060711	labyrinthine layer development	The process in which the labyrinthine layer of the placenta progresses, from its formation to its mature state.
	GO:0051028	mRNA transport	The directed movement of mRNA, messenger ribonucleic acid, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0043518	negative regulation of DNA damage response, signal transduction by p53 class mediator	Any process that stops, prevents, or reduces the frequency, rate or extent of the cascade of processes induced by the cell cycle regulator phosphoprotein p53, or an equivalent protein, in response to the detection of DNA damage.
	GO:0035562	negative regulation of chromatin binding	Any process that stops or reduces the frequency, rate or extent of chromatin binding. Chromatin binding is the selective interaction with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
	GO:0032091	negative regulation of protein binding	Any process that stops, prevents, or reduces the frequency, rate or extent of protein binding.
	GO:0031397	negative regulation of protein ubiquitination	Any process that stops, prevents, or reduces the frequency, rate or extent of the addition of ubiquitin groups to a protein.
	GO:1901797	negative regulation of signal transduction by p53 class mediator	Any process that stops, prevents or reduces the frequency, rate or extent of signal transduction by p53 class mediator.
	GO:0001934	positive regulation of protein phosphorylation	Any process that activates or increases the frequency, rate or extent of addition of phosphate groups to amino acids within a protein.
	GO:0031398	positive regulation of protein ubiquitination	Any process that activates or increases the frequency, rate or extent of the addition of ubiquitin groups to a protein.
	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:0031648	protein destabilization	Any process that decreases the stability of a protein, making it more vulnerable to degradative processes or aggregation.
	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:0015031	protein transport	The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
	GO:0032875	regulation of DNA endoreduplication	Any process that modulates the frequency, rate or extent of DNA endoreduplication.
	GO:2000045	regulation of G1/S transition of mitotic cell cycle	Any cell cycle regulatory process that controls the commitment of a cell from G1 to S phase of the mitotic cell cycle.
	GO:0030111	regulation of Wnt signaling pathway	Any process that modulates the frequency, rate or extent of the activity of the Wnt signal transduction pathway.
	GO:0051246	regulation of protein metabolic process	Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving a protein.
	GO:0060712	spongiotrophoblast layer development	The process in which the spongiotrophoblast layer of the placenta progresses from its formation to its mature state.
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
	GO:0060707	trophoblast giant cell differentiation	The process in which a relatively unspecialized cell acquires specialized features of a trophoblast giant cell of the placenta. Trophoblast giant cells are the cell of the placenta that line the maternal decidua.
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:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0031410	cytoplasmic vesicle	A vesicle found in the cytoplasm of a cell.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0016604	nuclear body	Extra-nucleolar nuclear domains usually visualized by confocal microscopy and fluorescent antibodies to specific proteins.
	GO:0031965	nuclear membrane	Either of the lipid bilayers that surround the nucleus and form the nuclear envelope; excludes the intermembrane space.
	GO:0005643	nuclear pore	Any of the numerous similar discrete openings in the nuclear envelope of a eukaryotic cell, where the inner and outer nuclear membranes are joined.
	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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1tgz	CRYSTAL STRUCTURE OF HUMAN SENP2 IN COMPLEX WITH SUMO-1
2io1	CRYSTAL STRUCTURE OF HUMAN SENP2 IN COMPLEX WITH PRESUMO-3
2io2	CRYSTAL STRUCTURE OF HUMAN SENP2 IN COMPLEX WITH RANGAP1- SUMO-1
2io3	CRYSTAL STRUCTURE OF HUMAN SENP2 IN COMPLEX WITH RANGAP1- SUMO-2

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