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Asym./Biol. Unit (Jmol Viewer)

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Title :   CRYSTAL STRUCTURE OF PUTATIVE ASPARAGINASE ENCODED BY ESCHERICHIA COLI YBIK GENE

Authors :   D. Borek, M. Jaskolski

Date :   30 Sep 01 (Deposition) - 09 Sep 03 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.65

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

Keywords :   Ntn Hydrolase, Asparginase, Autoproteolysis, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Michalska, D. Borek, A. Hernandez-Santoyo, M. Jaskolski
Crystal Packing Of Plant-Type L-Asparaginase From Escherichia Coli.
Acta Crystallogr. , Sect. D V. 64 309 2008
PubMed-ID: 18323626 | Reference-DOI: 10.1107/S0907444907068072
(for further references see the PDB file header)

Molecule 1 - PUTATIVE L-ASPARAGINASE
	Chains	:	A, C
	EC Number	:	3.5.1.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET11D
	Expression System Strain	:	JM109
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	N-TERMINUS (RESIDUES 2-178)
	Gene	:	YBIK
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	L-ASPARAGINE AMIDOHYDROLASE

Molecule 2 - PUTATIVE L-ASPARAGINASE
	Chains	:	B, D
	EC Number	:	3.5.1.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET11D
	Expression System Strain	:	JM109
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	C-TERMINUS (RESIDUES 179-321)
	Gene	:	YBIK
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	L-ASPARAGINE AMIDOHYDROLASE

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 13)

No.	Name	Count	Type	Full Name
1	CL	9	Ligand/Ion	CHLORIDE ION
2	CME	2	Mod. Amino Acid	S,S-(2-HYDROXYETHYL)THIOCYSTEINE
3	NA	2	Ligand/Ion	SODIUM ION

Asymmetric Unit (11, 11)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	LEU A:60 , GLU A:61 , CME A:63 , PHE A:66 , ALA A:68 , ILE A:70	BINDING SITE FOR RESIDUE NA A 801
02	AC2	SOFTWARE	GLN A:23 , ILE D:310 , TYR D:311	BINDING SITE FOR RESIDUE CL A 803
03	AC3	SOFTWARE	THR A:146 , SER A:147	BINDING SITE FOR RESIDUE CL A 808
04	AC4	SOFTWARE	GLY A:13 , ALA A:14 , HOH A:1038 , THR B:292 , GLU B:293	BINDING SITE FOR RESIDUE CL A 810
05	AC5	SOFTWARE	ARG A:104 , VAL A:139 , HOH A:841	BINDING SITE FOR RESIDUE CL A 811
06	AC6	SOFTWARE	LEU C:60 , GLU C:61 , CME C:63 , PHE C:66 , ALA C:68 , ILE C:70	BINDING SITE FOR RESIDUE NA C 802
07	AC7	SOFTWARE	ILE B:310 , TYR B:311 , HOH B:353 , GLN C:23	BINDING SITE FOR RESIDUE CL C 804
08	AC8	SOFTWARE	ARG C:104 , VAL C:139 , HOH C:897	BINDING SITE FOR RESIDUE CL C 807
09	AC9	SOFTWARE	THR C:146 , SER C:147	BINDING SITE FOR RESIDUE CL C 809
10	BC1	SOFTWARE	TYR B:251 , ARG D:262 , LYS D:267	BINDING SITE FOR RESIDUE CL D 805
11	BC2	SOFTWARE	THR D:292 , GLU D:293	BINDING SITE FOR RESIDUE CL D 806

(no "SS Bond" information available for 1K2X)

(no "Cis Peptide Bond" information available for 1K2X)

(no "SAP(SNP)/Variant" information available for 1K2X)

(no "PROSITE Motif" information available for 1K2X)

(no "Exon" information available for 1K2X)

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:156
 aligned with IAAA_ECOLI | P37595 from UniProtKB/Swiss-Prot  Length:321

    Alignment length:156
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151      
           IAAA_ECOLI     2 GKAVIAIHGGAGAISRAQMSLQQELRYIEALSAIVETGQKMLEAGESALDVVTEAVRLLEECPLFNAGIGAVFTRDETHELDACVMDGNTLKAGAVAGVSHLRNPVLAARLVMEQSPHVMMIGEGAENFAFARGMERVSPEIFSTSLRYEQLLAAR 157
               SCOP domains d1k2x.1 A:,B: Glycosylasparaginase (aspartylglucosaminidase, AGA)                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh..................eeeeeee.....eeeeeee....hhhhhhhhhhhhh...eeehhhhhhhhhh......hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1k2x A   2 GKAVIAIHGGAGAISRAQMSLQQELRYIEALSAIVETGQKMLEAGESALDVVTEAVRLLEEcPLFNAGIGAVFTRDETHELDACVMDGNTLKAGAVAGVSHLRNPVLAARLVMEQSPHVMMIGEGAENFAFARGMERVSPEIFSTSLRYEQLLAAR 157
                                    11        21        31        41        51        61 |      71        81        91       101       111       121       131       141       151      
                                                                                        63-CME

Chain B from PDB  Type:PROTEIN  Length:135
 aligned with IAAA_ECOLI | P37595 from UniProtKB/Swiss-Prot  Length:321

    Alignment length:135
                                   188       198       208       218       228       238       248       258       268       278       288       298       308     
           IAAA_ECOLI   179 TVGAVALDLDGNLAAATSTGGMTNKLPGRVGDSPLVGAGCYANNASVAVSCTGTGEVFIRALAAYDIAALMDYGGLSLAEACERVVMEKLPALGGSGGLIAIDHEGNVALPFNTEGMYRAWGYAGDTPTTGIYRE 313
               SCOP domains d1k2x.1 A:,B: Glycosylasparaginase (aspartylglucosaminidase, AGA)                                                                       SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....eeeeeee.........ee.........eee....eeeeeeehhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh...eeeeeee....ee......eeeeeeee.....eeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1k2x B 179 TVGAVALDLDGNLAAATSTGGMTNKLPGRVGDSPLVGAGCYANNASVAVSCTGTGEVFIRALAAYDIAALMDYGGLSLAEACERVVMEKLPALGGSGGLIAIDHEGNVALPFNTEGMYRAWGYAGDTPTTGIYRE 313
                                   188       198       208       218       228       238       248       258       268       278       288       298       308

Chain C from PDB  Type:PROTEIN  Length:156
 aligned with IAAA_ECOLI | P37595 from UniProtKB/Swiss-Prot  Length:321

    Alignment length:156
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151      
           IAAA_ECOLI     2 GKAVIAIHGGAGAISRAQMSLQQELRYIEALSAIVETGQKMLEAGESALDVVTEAVRLLEECPLFNAGIGAVFTRDETHELDACVMDGNTLKAGAVAGVSHLRNPVLAARLVMEQSPHVMMIGEGAENFAFARGMERVSPEIFSTSLRYEQLLAAR 157
               SCOP domains d1k2x.2 C:,D: Glycosylasparaginase (aspartylglucosaminidase, AGA)                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh..................eeeeeee.....eeeeeee....hhhhhhhhhhhhh...eeehhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1k2x C   2 GKAVIAIHGGAGAISRAQMSLQQELRYIEALSAIVETGQKMLEAGESALDVVTEAVRLLEEcPLFNAGIGAVFTRDETHELDACVMDGNTLKAGAVAGVSHLRNPVLAARLVMEQSPHVMMIGEGAENFAFARGMERVSPEIFSTSLRYEQLLAAR 157
                                    11        21        31        41        51        61 |      71        81        91       101       111       121       131       141       151      
                                                                                        63-CME

Chain D from PDB  Type:PROTEIN  Length:135
 aligned with IAAA_ECOLI | P37595 from UniProtKB/Swiss-Prot  Length:321

    Alignment length:135
                                   188       198       208       218       228       238       248       258       268       278       288       298       308     
           IAAA_ECOLI   179 TVGAVALDLDGNLAAATSTGGMTNKLPGRVGDSPLVGAGCYANNASVAVSCTGTGEVFIRALAAYDIAALMDYGGLSLAEACERVVMEKLPALGGSGGLIAIDHEGNVALPFNTEGMYRAWGYAGDTPTTGIYRE 313
               SCOP domains d1k2x.2 C:,D: Glycosylasparaginase (aspartylglucosaminidase, AGA)                                                                       SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) Asparaginase_2-1k2xD01 D:179-313                                                                                                        Pfam domains (1)
           Pfam domains (2) Asparaginase_2-1k2xD02 D:179-313                                                                                                        Pfam domains (2)
           Pfam domains (3) Asparaginase_2-1k2xD03 D:179-313                                                                                                        Pfam domains (3)
           Pfam domains (4) Asparaginase_2-1k2xD04 D:179-313                                                                                                        Pfam domains (4)
         Sec.struct. author .eeeeee.....eeeeeee.........ee.........eee....eeeeeeehhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh...eeeeeee....ee......eeeeeeee.....eeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1k2x D 179 TVGAVALDLDGNLAAATSTGGMTNKLPGRVGDSPLVGAGCYANNASVAVSCTGTGEVFIRALAAYDIAALMDYGGLSLAEACERVVMEKLPALGGSGGLIAIDHEGNVALPFNTEGMYRAWGYAGDTPTTGIYRE 313
                                   188       198       208       218       228       238       248       258       268       278       288       298       308

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: Ntn hydrolase-like (356)

Superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases) (352)

Family: (Glycosyl)asparaginase (14)

Protein domain: Glycosylasparaginase (aspartylglucosaminidase, AGA) (13)

Escherichia coli [TaxId: 562] (3)

1a	d1k2x.1	A:,B:
1b	d1k2x.2	C:,D:

(no "CATH Domain" information available for 1K2X)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: NTN (93)

Family: Asparaginase_2 (8)

Escherichia coli (strain K12) (5)

1a	Asparaginase_2-1k2xD01	D:179-313
1b	Asparaginase_2-1k2xD02	D:179-313
1c	Asparaginase_2-1k2xD03	D:179-313
1d	Asparaginase_2-1k2xD04	D:179-313

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C,D (IAAA_ECOLI | P37595)

molecular function
	GO:0004067	asparaginase activity	Catalysis of the reaction: L-asparagine + H2O = L-aspartate + NH3.
	GO:0008798	beta-aspartyl-peptidase activity	Catalysis of the cleavage of a beta-linked aspartic residue from the N-terminus of a polypeptide.
	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.
biological process
	GO:0016540	protein autoprocessing	Processing which a protein carries out itself. This involves actions such as the autolytic removal of residues to generate the mature form of the protein.
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1k2x)

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	3.5.1.1
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UniProtKB/Swiss-Prot
	IAAA_ECOLI \| P37595	:	1jn9 1t3m 2zak 2zal 3c17

1apy	THREE-DIMENSIONAL STRUCTURE OF HUMAN LYSOSOMAL ASPARTYLGLUCOSAMINIDASE.
1apz	HUMAN ASPARTYLGLUCOSAMINIDASE COMPLEX WITH REACTION PRODUCT.
1ayy	CRYSTAL STRUCTURE OF GLYCOSYLASPARAGINASE FROM FLAVOBACTERIUM MENINGOSEPTICUM.
1jn9	STRUCTURE OF PUTATIVE ASPARAGINASE ENCODED BY ESCHERICHIA COLI YBIK GENE
2gac	T152C MUTANT GLYCOSYLASPARAGINASE FROM FLAVOBACTERIUM
2gaw	CRYSTAL STRUCTURES OF FLAVOBACTERIUM GLYCOSYLASPARAGINASE.
9gaa	PRECURSOR OF THE T152A MUTANT GLYCOSYLASPARAGINASE FROM FLAVOBACTERIUM MENINGOSEPTICUM
9gac	PRECURSOR OF THE T152C MUTANT GLYCOSYLASPARAGINASE FROM FLAVOBACTERIUM MENINGOSEPTICUM
9gaf	PRECURSOR OF THE W11F MUTANT GLYCOSYLASPARAGINASE FROM FLAVOBACTERIUM MENINGOSEPTICUM

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 13)

Sites (11, 11)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (0, 0)

Pfam Domains (1, 4)

Gene Ontology (6, 6)

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