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Title :   CRYSTAL STRUCTURE OF S. POMBE AMSH-LIKE PROTEASE SST2 CATALYTIC DOMAIN FROM P212121 SPACE GROUP

Authors :   R. K. Shrestha, J. A. Ronau, C. Das

Date :   18 Sep 13 (Deposition) - 18 Jun 14 (Release) - 18 Jun 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

Chains :   Asym. Unit : A,B,C
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)

Keywords :   Helix-Beta-Helix Sandwich, Ubiquitin, Deubiquitination, Zinc Metalloprotease, Lysine 63-Linked Polyubiquitin, Cytosol, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. K. Shrestha, J. A. Ronau, C. W. Davies, R. G. Guenette, E. R. Strieter L. N. Paul, C. Das
Insights Into The Mechanism Of Deubiquitination By Jamm Deubiquitinases From Cocrystal Structures Of The Enzyme Wit The Substrate And Product.
Biochemistry V. 53 3199 2014
PubMed-ID: 24787148 | Reference-DOI: 10.1021/BI5003162

Molecule 1 - AMSH-LIKE PROTEASE SST2
	Chains	:	A, B, C
	EC Number	:	3.4.19.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX-6P-1
	Expression System Strain	:	ROSETTA
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Fragment	:	CATALYTIC DOMAIN, UNP RESIDUES 245-435
	Gene	:	SST2, SPAC19B12.10
	Organism Common	:	FISSION YEAST
	Organism Scientific	:	SCHIZOSACCHAROMYCES POMBE
	Organism Taxid	:	284812
	Strain	:	972/ATCC 24843
	Synonym	:	SUPPRESSOR OF STE12 DELETION PROTEIN 2

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 18)

No.	Name	Count	Type	Full Name
1	EDO	8	Ligand/Ion	1,2-ETHANEDIOL
2	GLY	1	Mod. Amino Acid	GLYCINE
3	PO4	3	Ligand/Ion	PHOSPHATE ION
4	ZN	6	Ligand/Ion	ZINC ION

Biological Unit 1 (3, 8)

No.	Name	Count	Type	Full Name
1	EDO	5	Ligand/Ion	1,2-ETHANEDIOL
2	GLY	1	Mod. Amino Acid	GLYCINE
3	PO4	2	Ligand/Ion	PHOSPHATE ION
4	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	EDO	2	Ligand/Ion	1,2-ETHANEDIOL
2	GLY	-1	Mod. Amino Acid	GLYCINE
3	PO4	-1	Ligand/Ion	PHOSPHATE ION
4	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 3 (2, 2)

No.	Name	Count	Type	Full Name
1	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
2	GLY	-1	Mod. Amino Acid	GLYCINE
3	PO4	1	Ligand/Ion	PHOSPHATE ION
4	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (18, 18)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	CYS A:288 , GLY A:318 , THR A:319 , THR A:357 , TYR A:361 , HOH A:646	BINDING SITE FOR RESIDUE EDO A 501
02	AC2	SOFTWARE	LYS A:409 , TYR A:411 , PO4 A:506 , PO4 A:507 , HOH A:617	BINDING SITE FOR RESIDUE EDO A 502
03	AC3	SOFTWARE	PRO A:388 , GLN A:392 , HOH A:724	BINDING SITE FOR RESIDUE EDO A 503
04	AC4	SOFTWARE	THR A:316 , GLY A:318 , LEU A:402 , GLY A:508 , HOH A:703	BINDING SITE FOR RESIDUE EDO A 504
05	AC5	SOFTWARE	ARG A:433	BINDING SITE FOR RESIDUE EDO A 505
06	AC6	SOFTWARE	LYS A:409 , EDO A:502 , PO4 A:507	BINDING SITE FOR RESIDUE PO4 A 506
07	AC7	SOFTWARE	LYS A:294 , LYS A:409 , THR A:412 , MET A:413 , EDO A:502 , PO4 A:506 , HOH A:652 , HOH A:671 , HOH A:710 , HOH A:728	BINDING SITE FOR RESIDUE PO4 A 507
08	AC8	SOFTWARE	GLU A:407 , EDO A:504	BINDING SITE FOR RESIDUE GLY A 508
09	AC9	SOFTWARE	HIS A:341 , HIS A:343 , ASP A:354 , HOH A:633	BINDING SITE FOR RESIDUE ZN A 509
10	BC1	SOFTWARE	HIS A:356 , CYS A:397 , HIS A:404 , HIS A:406	BINDING SITE FOR RESIDUE ZN A 510
11	BC2	SOFTWARE	GLY B:318 , THR B:319 , TYR B:361	BINDING SITE FOR RESIDUE EDO B 501
12	BC3	SOFTWARE	ALA B:415 , GLN B:416 , HOH B:639	BINDING SITE FOR RESIDUE EDO B 502
13	BC4	SOFTWARE	HIS B:341 , HIS B:343 , ASP B:354 , HOH B:612	BINDING SITE FOR RESIDUE ZN B 503
14	BC5	SOFTWARE	HIS B:356 , CYS B:397 , HIS B:404 , HIS B:406	BINDING SITE FOR RESIDUE ZN B 504
15	BC6	SOFTWARE	GLY C:318 , THR C:319 , TYR C:361	BINDING SITE FOR RESIDUE EDO C 501
16	BC7	SOFTWARE	LYS B:396 , HIS C:251	BINDING SITE FOR RESIDUE PO4 C 502
17	BC8	SOFTWARE	HIS C:341 , HIS C:343 , ASP C:354 , HOH C:601	BINDING SITE FOR RESIDUE ZN C 503
18	BC9	SOFTWARE	HIS C:356 , CYS C:397 , HIS C:404 , HIS C:406	BINDING SITE FOR RESIDUE ZN C 504

(no "SS Bond" information available for 4MSJ)

Asymmetric Unit

No.	Residues
1	Asp A:387	-	Pro A:388
2	Gln A:416	-	Pro A:417
3	Asp B:387	-	Pro B:388
4	Gln B:416	-	Pro B:417
5	Asp C:387	-	Pro C:388
6	Gln C:416	-	Pro C:417

(no "SAP(SNP)/Variant" information available for 4MSJ)

(no "PROSITE Motif" information available for 4MSJ)

(no "Exon" information available for 4MSJ)

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:190
                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........ee.....ee..eeee.hhhhhhhhhhhhhhhh....eeeeeeeee..eeeeeeeee.............hhhhhhhhhhhh..eeeeeeee........hhhhhhhhhhhhhhh...eeeeeehhhheeeeeee..hhhhhhhhhh.............eee......eeee....eeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4msj A 244 MAGTFKIHAYTEGGKPLRTIYLPKLLKKVFLDVVKPNTKKNLETCGILCGKLRQNAFFITHLVIPLQEATSDTCGTTDEASLFEFQDKHNLLTLGWIHTHPTQTCFMSSVDLHTHCSYQLMLPEAIAIVMAPSKNTSGIFRLLDPEGLQTIVKCRKPGLFHPHEGKVYTMVAQPGHVREINSKLQVVDLR 433
                                   253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433

Chain B from PDB  Type:PROTEIN  Length:188
                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................eeee.hhhhhhhhhhhhhhhh....eeeeeeeee..eeeeeeeee..............hhhhhhhhhhh..eeeeeeee........hhhhhhhhhhhhhhh...eeeeeehhhheeeeeee..hhhhhhhhhh.............eee......eeee....eeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4msj B 247 TFKIHAYTEGGKPLRTIYLPKLLKKVFLDVVKPNTKKNLETCGILCGKLRQNAFFITHLVIPLQEATSDTCGTTDEASLFEFQDKHNLLTLGWIHTHPTQTCFMSSVDLHTHCSYQLMLPEAIAIVMAPSKNTSGIFRLLDPEGLQTIVKCRKPGLFHPHEGKVYTMVAQPGHVREINSKLQVVDLRV 434
                                   256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426

Chain C from PDB  Type:PROTEIN  Length:187
                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee.....ee.eeeee.hhhhhhhhhhhhhhhh....eeeeeeeee..eeeeeeeee..eee....eee..hhhhhhhhhhh..eeeeeeee........hhhhhhhhhhhhhhh...eeeeeehhhheeeeeee..hhhhhhhhhh.............eee......eeee....eeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4msj C 247 TFKIHAYTEGGKPLRTIYLPKLLKKVFLDVVKPNTKKNLETCGILCGKLRQNAFFITHLVIPLQEATSDTCGTTDEASLFEFQDKHNLLTLGWIHTHPTQTCFMSSVDLHTHCSYQLMLPEAIAIVMAPSKNTSGIFRLLDPEGLQTIVKCRKPGLFHPHEGKVYTMVAQPGHVREINSKLQVVDLR 433
                                   256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426

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 '\|'

(no "SCOP Domain" information available for 4MSJ)

(no "CATH Domain" information available for 4MSJ)

(no "Pfam Domain" information available for 4MSJ)

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
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	Cis Peptide Bonds
		Asp A:387 - Pro A:388	[ RasMol ]
		Asp B:387 - Pro B:388	[ RasMol ]
		Asp C:387 - Pro C:388	[ RasMol ]
		Gln A:416 - Pro A:417	[ RasMol ]
		Gln B:416 - Pro B:417	[ RasMol ]
		Gln C:416 - Pro C:417	[ RasMol ]

Biological Units
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	3.4.19.-
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	SST2_SCHPO \| Q9P371	:	4jxe 4k1r 4ms7 4msd 4msm 4msq 4nql 4pqt 4zd4 4zd5 4zfr 4zft

3rzu	STRUCTURE OF CATALYTIC DOMAIN, HUMAN PROTEIN AMSH
4jxe	STRUCTURE OF CATALYTIC DOMAIN, S.POMBE SSTE
4ms7	CRYSTAL STRUCTURE OF SCHIZOSACCHAROMYCES POMBE SST2 CATALYTIC DOMAIN
4msd	CRYSTAL STRUCTURE OF SCHIZOSACCHAROMYCES POMBE AMSH-LIKE PROTEIN SST2 T319I MUTANT
4msm	CRYSTAL STRUCTURE OF SCHIZOSACCHAROMYCES POMBE AMSH-LIKE PROTEASE SST2 E286A MUTANT BOUND TO UBIQUITIN
4msq	CRYSTAL STRUCTURE OF SCHIZOSACCHAROMYCES POMBE AMSH-LIKE PROTEASE SST2 CATALYTIC DOMAIN BOUND TO UBIQUITIN

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 18)

Sites (18, 18)

SS Bonds (0, 0)

Cis Peptide Bonds (6, 6)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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Gene Ontology (14, 14)

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