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Asym./Biol. Unit (Jmol Viewer)

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

Title :   CRYSTAL STRUCTURE OF THE GLYCOSYLASPARAGINASE T152C APO-PRECURSOR

Authors :   Y. Wang, H. -C. Guo

Date :   26 Jan 10 (Deposition) - 24 Nov 10 (Release) - 24 Nov 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

Keywords :   Aspartylglucosylaminase, Active Precursors, Precursor Structure, Reversible Inhibitor, Constrained Conformation, Autoproteolysis, Catalytic Mechanism, N-Terminal Nucleophile Hydrolases, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Wang, H. C. Guo
Crystallographic Snapshot Of Glycosylasparaginase Precursor Poised For Autoprocessing.
J. Mol. Biol. V. 403 120 2010
PubMed-ID: 20800597 | Reference-DOI: 10.1016/J.JMB.2010.08.038

Molecule 1 - N(4)-(BETA-N-ACETYLGLUCOSAMINYL)-L-ASPARAGINASE
	Chains	:	A, C
	EC Number	:	3.5.1.26
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PMAL-C2X
	Expression System Strain	:	BP-1
	Expression System Taxid	:	562
	Fragment	:	UNP RESIDUES 46-340
	Gene	:	GA(1-295)
	Mutation	:	YES
	Organism Scientific	:	FLAVOBACTERIUM MENINGOSEPTICUM
	Organism Taxid	:	238
	Synonym	:	GLYCOSYLASPARAGINASE, ASPARTYLGLUCOSAMINIDASE, AGA, N4-(N- ACETYL-BETA-GLUCOSAMINYL)-L-ASPARAGINE AMIDASE, GLYCOSYLASPARAGINASE ALPHA CHAIN, GLYCOSYLASPARAGINASE BETA CHAIN

		1	2
Asymmetric/Biological Unit	:	A	C

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 3)

No.	Name	Count	Type	Full Name
1	GLY	1	Mod. Amino Acid	GLYCINE
2	NA	2	Ligand/Ion	SODIUM ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP C:451 , GLY C:472 , MET C:473 , ARG C:480 , ASP C:483 , SER C:484 , GLY C:504 , GLY C:506 , HOH C:625 , HOH C:654	BINDING SITE FOR RESIDUE GLY C 596
2	AC2	SOFTWARE	VAL A:42 , GLU A:43 , ASP A:45 , GLU A:48 , VAL A:51 , TYR A:53	BINDING SITE FOR RESIDUE NA A 597
3	AC3	SOFTWARE	VAL C:342 , ASP C:345 , GLU C:348 , VAL C:351 , TYR C:353	BINDING SITE FOR RESIDUE NA C 597

(no "SS Bond" information available for 3LJQ)

Asymmetric/Biological Unit

No.	Residues
1	Lys A:4	-	Pro A:5
2	Lys C:304	-	Pro C:305

(no "SAP(SNP)/Variant" information available for 3LJQ)

(no "PROSITE Motif" information available for 3LJQ)

(no "Exon" information available for 3LJQ)

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:281
 aligned with ASPG_ELIMR | Q47898 from UniProtKB/Swiss-Prot  Length:340

    Alignment length:294
                                    56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336    
           ASPG_ELIMR    47 TNKPIVLSTWNFGLHANVEAWKVLSKGGKALDAVEKGVRLVEDDPTERSVGYGGRPDRDGRVTLDACIMDENYNIGSVACMEHIKNPISVARAVMEKTPHVMLVGDGALEFALSQGFKKENLLTAESEKEWKEWLKTSQYKPIVNIENHDTIGMIALDAQGNLSGACTTSGMAYKMHGRVGDSPIIGAGLFVDNEIGAATATGHGEEVIRTVGTHLVVELMNQGRTPQQACKEAVERIVKIVNRRGKNLKDIQVGFIALNKKGEYGAYCIQDGFNFAVHDQKGNRLETPGFALK 340
               SCOP domains d3ljqa_ A: automated matches                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeee.hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh...................eeeeee.....eeeeeee....hhhhhhhhhhhhh...eeehhhhhhhhhhh........hhhhhhhhhhhhh-------------..eeeeee.....eeeeeee....................eeee...eeeeeeehhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh..hhhhh.eeeeeee....eeeee......eeeee..eeeee..ee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ljq A   2 TNKPIVLSTWNFGLHANVEAWKVLSKGGKALDAVEKGVRLVEDDPTERSVGYGGRPDRDGRVTLDACIMDENYNIGSVACMEHIKNPISVARAVMEKTPHVMLVGDGALEFALSQGFKKENLLTAESEKEWKEWLK-------------DCIGMIALDAQGNLSGACTTSGMAYKMHGRVGDSPIIGAGLFVDNEIGAATATGHGEEVIRTVGTHLVVELMNQGRTPQQACKEAVERIVKIVNRRGKNLKDIQVGFIALNKKGEYGAYCIQDGFNFAVHDQKGNRLETPGFALK 295
                                    11        21        31        41        51        61        71        81        91       101       111       121       131     |   -       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291    
                                                                                                                                                                 137           151

Chain C from PDB  Type:PROTEIN  Length:289
 aligned with ASPG_ELIMR | Q47898 from UniProtKB/Swiss-Prot  Length:340

    Alignment length:300
                                                                                                                                                                                                                                                                                                                                    340 
                                    51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331        |-
           ASPG_ELIMR    42 SEPKTTNKPIVLSTWNFGLHANVEAWKVLSKGGKALDAVEKGVRLVEDDPTERSVGYGGRPDRDGRVTLDACIMDENYNIGSVACMEHIKNPISVARAVMEKTPHVMLVGDGALEFALSQGFKKENLLTAESEKEWKEWLKTSQYKPIVNIENHDTIGMIALDAQGNLSGACTTSGMAYKMHGRVGDSPIIGAGLFVDNEIGAATATGHGEEVIRTVGTHLVVELMNQGRTPQQACKEAVERIVKIVNRRGKNLKDIQVGFIALNKKGEYGAYCIQDGFNFAVHDQKGNRLETPGFALK-   -
               SCOP domains d3ljqc_ C: automated matches                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) ----Asparaginase_2-3ljqC01 C:301-595                                                                                                                                                                                                                                                                       - Pfam domains (1)
           Pfam domains (2) ----Asparaginase_2-3ljqC02 C:301-595                                                                                                                                                                                                                                                                       - Pfam domains (2)
         Sec.struct. author .........eeeee..hhhhhhhhhhhhhh...hhhhhhhhhhhhhhh....................eeeeee.....eeeeeee....hhhhhhhhhhhhh...eeehhhhhhhhhhh........hhhhhhhhhhhhh-----------....eeeeee.....eeeeeee....................eeee...eeeeeeehhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh..hhhhh.eeeeeee....eeeee......eeeee..eeeee..ee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ljq C 297 SEPSTTNKPIVLSTWNFGLHANVEAWKVLSKGGKALDAVEKGVRLVEDDPTERSVGYGGRPDRDGRVTLDACIMDENYNIGSVACMEHIKNPISVARAVMEKTPHVMLVGDGALEFALSQGFKKENLLTAESEKEWKEWLK-----------NHDCIGMIALDAQGNLSGACTTSGMAYKMHGRVGDSPIIGAGLFVDNEIGAATATGHGEEVIRTVGTHLVVELMNQGRTPQQACKEAVERIVKIVNRRGKNLKDIQVGFIALNKKGEYGAYCIQDGFNFAVHDQKGNRLETPGFALKG 596
                                   306       316       326       336       346       356       366       376       386       396       406       416       426       436|        -  |    456       466       476       486       496       506       516       526       536       546       556       566       576       586       596
                                                                                                                                                                      437         449

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: automated matches (1)

Flavobacterium meningosepticum [TaxId: 238] (1)

1a	d3ljqa_	A:
1b	d3ljqc_	C:

(no "CATH Domain" information available for 3LJQ)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: NTN (93)

Family: Asparaginase_2 (8)

Elizabethkingia miricola (Chryseobacterium miricola) (3)

1a	Asparaginase_2-3ljqC01	C:301-595
1b	Asparaginase_2-3ljqC02	C:301-595

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,C (ASPG_ELIMR | Q47898)

molecular function
	GO:0003948	N4-(beta-N-acetylglucosaminyl)-L-asparaginase activity	Catalysis of the reaction: N(4)-(beta-N-acetyl-D-glucosaminyl)-L-asparagine + H(2)O = N-acetyl-beta-D-glucosaminylamine + L-aspartate + H(+).
	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:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
	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).

Asymmetric/Biological Unit
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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
		Lys A:4 - Pro A:5	[ RasMol ]
		Lys C:304 - Pro C:305	[ RasMol ]

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Access by PDB/NDB ID
	3ljq
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
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	ASPG_ELIMR \| Q47898
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	3.5.1.26
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		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
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	ASPG_ELIMR \| Q47898
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UniProtKB/Swiss-Prot
	ASPG_ELIMR \| Q47898	:	1ayy 1p4k 1p4v 2gac 2gaw 2gl9 4r4y 9gaa 9gac 9gaf

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 3)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (1, 2)

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Pfam Domains (1, 2)

Gene Ontology (5, 5)

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