1Z7L - JenaLib

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Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF FRAGMENT OF MOUSE UBIQUITIN-ACTIVATING ENZYME

Authors :   R. H. Szczepanowski, R. Filipek, M. Bochtler

Date :   25 Mar 05 (Deposition) - 12 Apr 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

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

Keywords :   Scch, Ubiquitin-Activating Enzyme, Second Catalytic Cysteine Half-Domain, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. H. Szczepanowski, R. Filipek, M. Bochtler
Crystal Structure Of A Fragment Of Mouse Ubiquitin-Activating Enzyme.
J. Biol. Chem. V. 280 22006 2005
PubMed-ID: 15774460 | Reference-DOI: 10.1074/JBC.M502583200
(for further references see the PDB file header)

Molecule 1 - UBIQUITIN-ACTIVATING ENZYME E1 1
	Chains	:	A, B, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET15-SCCH
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PET15MOD
	Fragment	:	SECOND CATALYTIC CYSTEINE HALF-DOMAIN (RESIDUES 626-891)
	Gene	:	UBE1X, UBA1, UBE1
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

		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 (1, 3)

No.	Name	Count	Type	Full Name
1	TBR	3	Ligand/Ion	HEXATANTALUM DODECABROMIDE

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	TBR	1	Ligand/Ion	HEXATANTALUM DODECABROMIDE

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	TBR	1	Ligand/Ion	HEXATANTALUM DODECABROMIDE

Biological Unit 3 (1, 1)

No.	Name	Count	Type	Full Name
1	TBR	1	Ligand/Ion	HEXATANTALUM DODECABROMIDE

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLN A:646 , ARG A:649 , ASP A:650	BINDING SITE FOR RESIDUE TBR A 999
2	AC2	SOFTWARE	GLN B:646 , ARG B:649 , ASP B:650	BINDING SITE FOR RESIDUE TBR B 1000
3	AC3	SOFTWARE	GLN C:646 , ARG C:649 , ASP C:650 , GLU C:653	BINDING SITE FOR RESIDUE TBR C 1001

(no "SS Bond" information available for 1Z7L)

(no "Cis Peptide Bond" information available for 1Z7L)

(no "SAP(SNP)/Variant" information available for 1Z7L)

Asymmetric Unit (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	UBIQUITIN_ACTIVAT_2	PS00865	Ubiquitin-activating enzyme active site.	UBA1_MOUSE	630-638	3	A:630-638 B:630-638 C:630-638

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	UBIQUITIN_ACTIVAT_2	PS00865	Ubiquitin-activating enzyme active site.	UBA1_MOUSE	630-638	1	A:630-638 - -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	UBIQUITIN_ACTIVAT_2	PS00865	Ubiquitin-activating enzyme active site.	UBA1_MOUSE	630-638	1	- B:630-638 -

Biological Unit 3 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	UBIQUITIN_ACTIVAT_2	PS00865	Ubiquitin-activating enzyme active site.	UBA1_MOUSE	630-638	1	- - C:630-638

(no "Exon" information available for 1Z7L)

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:255
 aligned with UBA1_MOUSE | Q02053 from UniProtKB/Swiss-Prot  Length:1058

    Alignment length:261
                                   638       648       658       668       678       688       698       708       718       728       738       748       758       768       778       788       798       808       818       828       838       848       858       868       878       888 
           UBA1_MOUSE   629 IPICTLKNFPNAIEHTLQWARDEFEGLFKQPAENVNQYLTDSKFVERTLRLAGTQPLEVLEAVQRSLVLQRPQTWGDCVTWACHHWHTQYCNNIRQLLHNFPPDQLTSSGAPFWSGPKRCPHPLTFDVNNTLHLDYVMAAANLFAQTYGLTGSQDRAAVASLLQSVQVPEFTPKSGVKIHVSDQELQSANASVDDSRLEELKATLPSPDKLPGFKMYPIDFEKDDDSNFHMDFIVAASNLRAENYDISPADRHKSKLIAGK 889
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh...hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh............................hhhhhhhhhhhhhhhhhhh......hhhhhhhhhhh.....................------..hhhhhhhhhhh.hhhhh.................hhhhhhhhhhhhhhhhh.....hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -UBIQUITIN----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1z7l A 629 IPICTLKNFPNAIEHTLQWARDEFEGLFKQPAENVNQYLTDSKFVERTLRLAGTQPLEVLEAVQRSLVLQRPQTWGDCVTWACHHWHTQYCNNIRQLLHNFPPDQLTSSGAPFWSGPKRCPHPLTFDVNNTLHLDYVMAAANLFAQTYGLTGSQDRAAVASLLQSVQVPEFTPKSGVKIHVSDQEL------VDDSRLEELKATLPSPDKLPGFKMYPIDFEKDDDSNFHMDFIVAASNLRAENYDISPADRHKSKLIAGK 889
                                   638       648       658       668       678       688       698       708       718       728       738       748       758       768       778       788       798       808     |   -  |    828       838       848       858       868       878       888 
                                                                                                                                                                                                                   814    821

Chain B from PDB  Type:PROTEIN  Length:255
 aligned with UBA1_MOUSE | Q02053 from UniProtKB/Swiss-Prot  Length:1058

    Alignment length:261
                                   638       648       658       668       678       688       698       708       718       728       738       748       758       768       778       788       798       808       818       828       838       848       858       868       878       888 
           UBA1_MOUSE   629 IPICTLKNFPNAIEHTLQWARDEFEGLFKQPAENVNQYLTDSKFVERTLRLAGTQPLEVLEAVQRSLVLQRPQTWGDCVTWACHHWHTQYCNNIRQLLHNFPPDQLTSSGAPFWSGPKRCPHPLTFDVNNTLHLDYVMAAANLFAQTYGLTGSQDRAAVASLLQSVQVPEFTPKSGVKIHVSDQELQSANASVDDSRLEELKATLPSPDKLPGFKMYPIDFEKDDDSNFHMDFIVAASNLRAENYDISPADRHKSKLIAGK 889
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh...hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh............................hhhhhhhhhhhhhhhhhhh......hhhhhhhhhhh.....................------..hhhhhhhhhhh.hhhhh.................hhhhhhhhhhhhhhhhh.....hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -UBIQUITIN----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1z7l B 629 IPICTLKNFPNAIEHTLQWARDEFEGLFKQPAENVNQYLTDSKFVERTLRLAGTQPLEVLEAVQRSLVLQRPQTWGDCVTWACHHWHTQYCNNIRQLLHNFPPDQLTSSGAPFWSGPKRCPHPLTFDVNNTLHLDYVMAAANLFAQTYGLTGSQDRAAVASLLQSVQVPEFTPKSGVKIHVSDQEL------VDDSRLEELKATLPSPDKLPGFKMYPIDFEKDDDSNFHMDFIVAASNLRAENYDISPADRHKSKLIAGK 889
                                   638       648       658       668       678       688       698       708       718       728       738       748       758       768       778       788       798       808     |   -  |    828       838       848       858       868       878       888 
                                                                                                                                                                                                                   814    821

Chain C from PDB  Type:PROTEIN  Length:255
 aligned with UBA1_MOUSE | Q02053 from UniProtKB/Swiss-Prot  Length:1058

    Alignment length:261
                                   638       648       658       668       678       688       698       708       718       728       738       748       758       768       778       788       798       808       818       828       838       848       858       868       878       888 
           UBA1_MOUSE   629 IPICTLKNFPNAIEHTLQWARDEFEGLFKQPAENVNQYLTDSKFVERTLRLAGTQPLEVLEAVQRSLVLQRPQTWGDCVTWACHHWHTQYCNNIRQLLHNFPPDQLTSSGAPFWSGPKRCPHPLTFDVNNTLHLDYVMAAANLFAQTYGLTGSQDRAAVASLLQSVQVPEFTPKSGVKIHVSDQELQSANASVDDSRLEELKATLPSPDKLPGFKMYPIDFEKDDDSNFHMDFIVAASNLRAENYDISPADRHKSKLIAGK 889
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) UBA_e1_thiolCys-1z7lC07      ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UBACT-1z7lC01 C:848-889                    Pfam domains (1)
           Pfam domains (2) UBA_e1_thiolCys-1z7lC08      ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UBACT-1z7lC02 C:848-889                    Pfam domains (2)
           Pfam domains (3) UBA_e1_thiolCys-1z7lC09      ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UBACT-1z7lC03 C:848-889                    Pfam domains (3)
           Pfam domains (4) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UBACT-1z7lC04 C:848-889                    Pfam domains (4)
           Pfam domains (5) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UBACT-1z7lC05 C:848-889                    Pfam domains (5)
           Pfam domains (6) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UBACT-1z7lC06 C:848-889                    Pfam domains (6)
         Sec.struct. author .hhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh...hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh............................hhhhhhhhhhhhhhhhhhh......hhhhhhhhhhh.....................------..hhhhhhhhhhh.hhhhh.................hhhhhhhhhhhhhhhhh.....hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -UBIQUITIN----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1z7l C 629 IPICTLKNFPNAIEHTLQWARDEFEGLFKQPAENVNQYLTDSKFVERTLRLAGTQPLEVLEAVQRSLVLQRPQTWGDCVTWACHHWHTQYCNNIRQLLHNFPPDQLTSSGAPFWSGPKRCPHPLTFDVNNTLHLDYVMAAANLFAQTYGLTGSQDRAAVASLLQSVQVPEFTPKSGVKIHVSDQEL------VDDSRLEELKATLPSPDKLPGFKMYPIDFEKDDDSNFHMDFIVAASNLRAENYDISPADRHKSKLIAGK 889
                                   638       648       658       668       678       688       698       708       718       728       738       748       758       768       778       788       798       808     |   -  |    828       838       848       858       868       878       888 
                                                                                                                                                                                                                   814    821

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 1Z7L)

(no "CATH Domain" information available for 1Z7L)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: UBACT] (10)

Family: UBACT (10)

Mus musculus (Mouse) (1)

1a	UBACT-1z7lC01	C:848-889
1b	UBACT-1z7lC02	C:848-889
1c	UBACT-1z7lC03	C:848-889
1d	UBACT-1z7lC04	C:848-889
1e	UBACT-1z7lC05	C:848-889
1f	UBACT-1z7lC06	C:848-889

Clan: no clan defined [family: UBA_e1_thiolCys] (10)

Family: UBA_e1_thiolCys (10)

Mus musculus (Mouse) (1)

2a	UBA_e1_thiolCys-1z7lC07	C:629-657
2b	UBA_e1_thiolCys-1z7lC08	C:629-657
2c	UBA_e1_thiolCys-1z7lC09	C:629-657

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (UBA1_MOUSE | Q02053)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	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: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:0008641	small protein activating enzyme activity	Catalysis of the activation of small proteins, such as ubiquitin or ubiquitin-like proteins, through the formation of an ATP-dependent high-energy thiolester bond.
	GO:0004839	ubiquitin activating enzyme activity	Catalysis of the reaction: E1 + ubiquitin + ATP--> E1-ubiquitin + AMP + PPi, where the E1-ubiquitin linkage is a thioester bond between the C-terminal glycine of Ub and a sulfhydryl side group of an E1 cysteine residue. This is the first step in a cascade of reactions in which ubiquitin is ultimately added to a protein substrate.
	GO:0004842	ubiquitin-protein transferase activity	Catalysis of the transfer of ubiquitin from one protein to another via the reaction X-Ub + Y --> Y-Ub + X, where both X-Ub and Y-Ub are covalent linkages.
biological process
	GO:0006464	cellular protein modification process	The covalent alteration of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications) occurring at the level of an individual cell. Includes the modification of charged tRNAs that are destined to occur in a protein (pre-translation modification).
	GO:0006974	cellular response to DNA damage stimulus	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
	GO:0019941	modification-dependent protein catabolic process	The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent modification of the target protein.
	GO:0016567	protein ubiquitination	The process in which one or more ubiquitin groups are added to a protein.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0030057	desmosome	A cell-cell junction in which: on the cytoplasmic surface of each interacting plasma membrane is a dense plaque composed of a mixture of intracellular anchor proteins; a bundle of keratin intermediate filaments is attached to the surface of each plaque; transmembrane adhesion proteins of the cadherin family bind to the plaques and interact through their extracellular domains to hold the adjacent membranes together by a Ca2+-dependent mechanism.
	GO:0010008	endosome membrane	The lipid bilayer surrounding an endosome.
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	GO:0000792	heterochromatin	A compact and highly condensed form of chromatin.
	GO:0005765	lysosomal membrane	The lipid bilayer surrounding the lysosome and separating its contents from the cell cytoplasm.
	GO:0005739	mitochondrion	A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
	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:0030867	rough endoplasmic reticulum membrane	The lipid bilayer surrounding the rough endoplasmic reticulum.

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	1z7l
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(no "Related Entries Specified in the PDB File" available for 1Z7L)

Description

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Ligands, Modified Residues, Ions (1, 3)

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