1JAZ - JenaLib

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Title :   CRYSTAL STRUCTURE OF MONOCLINIC FORM OF D90E MUTANT OF ESCHERICHIA COLI ASPARAGINASE II

Authors :   D. Borek, M. Kozak, M. Jaskolski

Date :   01 Jun 01 (Deposition) - 09 Sep 03 (Release) - 19 Oct 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.27

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

Keywords :   L-Asparaginase, Leukemia, Zinc-Binding Site, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. Borek, M. Kozak, J. Pei, M. Jaskolski
Crystal Structure Of Active Site Mutant Of Antileukemic L-Asparaginase Reveals Conserved Zinc-Binding Site.
Febs J. V. 281 4097 2014
PubMed-ID: 25040257 | Reference-DOI: 10.1111/FEBS.12906
(for further references see the PDB file header)

Molecule 1 - L-ASPARAGINASE II
	Chains	:	A, B
	EC Number	:	3.5.1.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	L-ASNASE II

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 3)

No.	Name	Count	Type	Full Name
1	ZN	3	Ligand/Ion	ZINC ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:100 , HIS A:197 , HOH A:415 , HOH A:416	BINDING SITE FOR RESIDUE ZN A 401
2	AC2	SOFTWARE	ASP B:100 , HIS B:197 , HOH B:415 , HOH B:416	BINDING SITE FOR RESIDUE ZN B 402
3	AC3	SOFTWARE	ASP B:200	BINDING SITE FOR RESIDUE ZN B 403

Asymmetric Unit

No.	Residues
1	A:77	-	A:105
2	B:77	-	B:105

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

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

Asymmetric Unit (3, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ASN_GLN_ASE_3	PS51732	Asparaginase / glutaminase domain profile.	ASPG2_ECOLI	24-348	2	A:2-326 B:2-326
2	ASN_GLN_ASE_1	PS00144	Asparaginase / glutaminase active site signature 1.	ASPG2_ECOLI	28-36	2	A:6-14 B:6-14
3	ASN_GLN_ASE_2	PS00917	Asparaginase / glutaminase active site signature 2.	ASPG2_ECOLI	104-114	2	A:82-92 B:82-92

Biological Unit 1 (3, 12)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ASN_GLN_ASE_3	PS51732	Asparaginase / glutaminase domain profile.	ASPG2_ECOLI	24-348	4	A:2-326 B:2-326
2	ASN_GLN_ASE_1	PS00144	Asparaginase / glutaminase active site signature 1.	ASPG2_ECOLI	28-36	4	A:6-14 B:6-14
3	ASN_GLN_ASE_2	PS00917	Asparaginase / glutaminase active site signature 2.	ASPG2_ECOLI	104-114	4	A:82-92 B:82-92

(no "Exon" information available for 1JAZ)

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:307
 aligned with ASPG2_ECOLI | P00805 from UniProtKB/Swiss-Prot  Length:348

    Alignment length:326
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342      
          ASPG2_ECOLI    23 LPNITILATGGTIAGGGDSATKSNYTVGKVGVENLVNAVPQLKDIANVKGEQVVNIGSQDMNDNVWLTLAKKINTDCDKTDGFVITHGTDTMEETAYFLDLTVKCDKPVVMVGAMRPSTSMSADGPFNLYNAVVTAADKASANRGVLVVMNDTVLDGRDVTKTNTTDVATFKSVNYGPLGYIHNGKIDYQRTPARKHTSDTPFDVSKLNELPKVGIVYNYANASDLPAKALVDAGYDGIVSAGVGNGNLYKSVFDTLATAAKTGTAVVRSSRVPTGATTQDAEVDDAKYGFVASGTLNPQKARVLLQLALTQTKDPQQIQQIFNQY 348
               SCOP domains d1jaza_ A: Aspa                   raginase type II                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 1jazA01 A:1-212                     [code=3.40.50.1170, no name defined]                                                                                                                                            1jazA02 A:213-325  [code=3.40.50.40, no name defined]                                                            - CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.......-------------------....hhhhhhh.eeeeee....hhhhhhhhhhhhhhhhhhhhhhhh.eeeee....hhhhhhhhhhhhh.....eeee...........hhhhhhhhhhhhhhhhhhh....eeee..eeee...eee........eee......eeee..eeee.......hhhhh............eeeee......hhhhhhhhhh...eeeeee......hhhhhhhhhhhhhh..eeeeee.............hhhhhh.ee....hhhhhhhhhhhhh....hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -ASN_GLN_ASE_3  PDB: A:2-326 UniProt: 24-348                                                                                                                                                                                                                                                                                           PROSITE (1)
                PROSITE (2) -----ASN_GLN_A-------------------------------------------------------------------ASN_GLN_ASE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jaz A   1 LPNITILATGGTIAG-------------------LVNAVPQLKDIANVKGEQVVNIGSQDMNDNVWLTLAKKINTDCDKTDGFVITHGTETMEETAYFLDLTVKCDKPVVMVGAMRPSTSMSADGPFNLYNAVVTAADKASANRGVLVVMNDTVLDGRDVTKTNTTDVATFKSVNYGPLGYIHNGKIDYQRTPARKHTSDTPFDVSKLNELPKVGIVYNYANASDLPAKALVDAGYDGIVSAGVGNGNLYKSVFDTLATAAKTGTAVVRSSRVPTGATTQDAEVDDAKYGFVASGTLNPQKARVLLQLALTQTKDPQQIQQIFNQY 326
                                    10    |    -         -    |   40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320      
                                         15                  35

Chain B from PDB  Type:PROTEIN  Length:305
 aligned with ASPG2_ECOLI | P00805 from UniProtKB/Swiss-Prot  Length:348

    Alignment length:326
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342      
          ASPG2_ECOLI    23 LPNITILATGGTIAGGGDSATKSNYTVGKVGVENLVNAVPQLKDIANVKGEQVVNIGSQDMNDNVWLTLAKKINTDCDKTDGFVITHGTDTMEETAYFLDLTVKCDKPVVMVGAMRPSTSMSADGPFNLYNAVVTAADKASANRGVLVVMNDTVLDGRDVTKTNTTDVATFKSVNYGPLGYIHNGKIDYQRTPARKHTSDTPFDVSKLNELPKVGIVYNYANASDLPAKALVDAGYDGIVSAGVGNGNLYKSVFDTLATAAKTGTAVVRSSRVPTGATTQDAEVDDAKYGFVASGTLNPQKARVLLQLALTQTKDPQQIQQIFNQY 348
               SCOP domains d1jazb_ B: Aspa                     raginase type II                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 1jazB01 B:1-212                       [code=3.40.50.1170, no name defined]                                                                                                                                          1jazB02 B:213-325  [code=3.40.50.40, no name defined]                                                            - CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.......---------------------..hhhhhhh.eeeeee....hhhhhhhhhhhhhhhhhhhhhhhh.eeeee....hhhhhhhhhhhhh.....eeee...........hhhhhhhhhhhhhhhhhhh....eeee..eeee...eee........eee......eeee..eeee.......hhhhh..hhhhh.....eeeee......hhhhhhhhhh...eeeeee......hhhhhhhhhhhhhh..eeeeee.............hhhhhheee....hhhhhhhhhhhhh....hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -ASN_GLN_ASE_3  PDB: B:2-326 UniProt: 24-348                                                                                                                                                                                                                                                                                           PROSITE (1)
                PROSITE (2) -----ASN_GLN_A-------------------------------------------------------------------ASN_GLN_ASE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jaz B   1 LPNITILATGGTIAG---------------------NAVPQLKDIANVKGEQVVNIGSQDMNDNVWLTLAKKINTDCDKTDGFVITHGTETMEETAYFLDLTVKCDKPVVMVGAMRPSTSMSADGPFNLYNAVVTAADKASANRGVLVVMNDTVLDGRDVTKTNTTDVATFKSVNYGPLGYIHNGKIDYQRTPARKHTSDTPFDVSKLNELPKVGIVYNYANASDLPAKALVDAGYDGIVSAGVGNGNLYKSVFDTLATAAKTGTAVVRSSRVPTGATTQDAEVDDAKYGFVASGTLNPQKARVLLQLALTQTKDPQQIQQIFNQY 326
                                    10    |    -         -      | 40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320      
                                         15                    37

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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: Glutaminase/Asparaginase (37)

Superfamily: Glutaminase/Asparaginase (37)

Family: Glutaminase/Asparaginase (33)

Protein domain: Asparaginase type II (17)

Escherichia coli [TaxId: 562] (7)

1a	d1jaza_	A:
1b	d1jazb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: [code=3.40.50.1170, no name defined] (27)

Escherichia coli. Organism_taxid: 562. (4)

1a	1jazA01	A:1-212
1b	1jazB01	B:1-212

Homologous Superfamily: [code=3.40.50.40, no name defined] (27)

Escherichia coli. Organism_taxid: 562. (4)

2a	1jazA02	A:213-325
2b	1jazB02	B:213-325

(no "Pfam Domain" information available for 1JAZ)

Asymmetric Unit(hide GO term definitions)

Chain A,B (ASPG2_ECOLI | P00805)

molecular function
	GO:0004067	asparaginase activity	Catalysis of the reaction: L-asparagine + H2O = L-aspartate + NH3.
	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:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
biological process
	GO:0006528	asparagine metabolic process	The chemical reactions and pathways involving asparagine, 2-amino-3-carbamoylpropanoic acid.
	GO:0006520	cellular amino acid metabolic process	The chemical reactions and pathways involving amino acids, carboxylic acids containing one or more amino groups, as carried out by individual cells.
	GO:0051289	protein homotetramerization	The formation of a protein homotetramer, a macromolecular structure consisting of four noncovalently associated identical subunits.
cellular component
	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:0030288	outer membrane-bounded periplasmic space	The region between the inner (cytoplasmic or plasma) membrane and outer membrane of organisms with two membranes such as Gram negative bacteria. These periplasmic spaces are relatively thick and contain a thin peptidoglycan layer (PGL), also referred to as a thin cell wall.
	GO:0042597	periplasmic space	The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

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	ASPG2_ECOLI \| P00805	:	1ho3 1ihd 1jja 1nns 3eca 4eca

1agx	STRUCTURE OF ACINETOBACTER GLUTAMINASIFICANS GLUTAMINASE- ASPARAGINASE
1djo	STRUCTURE OF PSEUDOMONAS 7A GLUTAMINASE-ASPARAGINASE WITH THE INHIBITOR DONV COVALENTLY BOUND IN THE ACTIVE SITE
1djp	STRUCTURE OF PSEUDOMONAS 7A GLUTAMINASE-ASPARAGINASE WITH THE INHIBITOR DON COVALENTLY BOUND IN THE ACTIVE SITE
1hfj	ASPARAGINASE FROM ERWINIA CHRYSANTHEMI, HEXAGONAL FORM WITH SULFATE
1hfk	ASPARAGINASE FROM ERWINIA CHRYSANTHEMI, HEXAGONAL FORM WITH WEAK SULFATE
1ho3	STRUCTURE OF Y25F MUTANT OF ESCHERICHIA COLI ASPARAGINASE II
1ihd	CRYSTAL STRUCTURE OF TRIGONAL FORM OF D90E MUTANT OF ESCHERICHIA COLI ASPARAGINASE II
1wsa	STRUCTURE OF WOLINELLA SUCCINOGENES L-ASPARAGINASE II PRECURSOR
3eca	STRUCTURE OF NATIVE ESCHERICHIA COLI ASPARAGINASE II
3pga	STRUCTURAL CHARACTERIZATION OF PSEUDOMONAS 7A GLUTAMINASE- ASPARAGINASE
4eca	STRUCTURE OF T89V MUTANT OF ESCHERICHIA COLI ASPARAGINASE II
4pga	GLUTAMINASE-ASPARAGINASE FROM PSEUDOMONAS 7A

Description

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Ligands, Modified Residues, Ions (1, 3)

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