2WT4 - JenaLib

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Biol. Unit 1 - sites (Jmol Viewer)

Title :   ROOM TEMPERATURE CRYSTAL STRUCTURE OF HELICOBACTER PYLORI L-ASPARAGINASE AT 1.8 A RESOLUTION

Authors :   P. Dhavala, A. C. Papageorgiou

Date :   11 Sep 09 (Deposition) - 24 Nov 09 (Release) - 30 May 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

Chains :   Asym. Unit : A
Biol. Unit 1: A  (4x)

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

Reference :   P. Dhavala, A. C. Papageorgiou
Structure Of Helicobacter Pylori L-Asparaginase At 1. 4 A Resolution
Acta Crystallogr. , Sect. D V. 65 1253 2009
PubMed-ID: 19966411 | Reference-DOI: 10.1107/S0907444909038244

Molecule 1 - L-ASPARAGINASE
	Chains	:	A
	EC Number	:	3.5.1.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Scientific	:	HELICOBACTER PYLORI
	Organism Taxid	:	210
	Synonym	:	L-ASNASE

		1
Asymmetric Unit	:	A
Biological Unit 1 (4x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 1)

No.	Name	Count	Type	Full Name
1	ASP	1	Mod. Amino Acid	ASPARTIC ACID

Biological Unit 1 (1, 4)

No.	Name	Count	Type	Full Name
1	ASP	4	Mod. Amino Acid	ASPARTIC ACID

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:15 , THR A:16 , GLY A:61 , SER A:62 , GLN A:63 , GLY A:94 , THR A:95 , ASP A:96 , ALA A:120 , ASN A:255 , GLU A:289 , HOH A:2040 , HOH A:2041	BINDING SITE FOR RESIDUE ASP A3613

(no "SS Bond" information available for 2WT4)

Asymmetric Unit

No.	Residues
1	Val A:36	-	Lys A:37
2	Lys A:37	-	Glu A:38
3	Thr A:216	-	Pro A:217

(no "SAP(SNP)/Variant" information available for 2WT4)

Asymmetric Unit (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ASN_GLN_ASE_3	PS51732	Asparaginase / glutaminase domain profile.	ASPG_HELPJ	6-332	1	A:6-332
2	ASN_GLN_ASE_1	PS00144	Asparaginase / glutaminase active site signature 1.	ASPG_HELPJ	10-18	1	A:10-18
3	ASN_GLN_ASE_2	PS00917	Asparaginase / glutaminase active site signature 2.	ASPG_HELPJ	88-98	1	A:88-98

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.	ASPG_HELPJ	6-332	4	A:6-332
2	ASN_GLN_ASE_1	PS00144	Asparaginase / glutaminase active site signature 1.	ASPG_HELPJ	10-18	4	A:10-18
3	ASN_GLN_ASE_2	PS00917	Asparaginase / glutaminase active site signature 2.	ASPG_HELPJ	88-98	4	A:88-98

(no "Exon" information available for 2WT4)

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:316
 aligned with ASPG_HELPJ | Q9ZLB9 from UniProtKB/Swiss-Prot  Length:332

    Alignment length:329
                                                                                                                                                                                                                                                                                                                                                                 332 
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       | 
          ASPG_HELPJ      5 LPTIALLATGGTIAGSGVDASLGSYKSGELGVKELLKAIPSLNKIARIQGEQVSNIGSQDMNEEIWFKLAQRAQELLDDSRIQGVVITHGTDTLEESAYFLNLVLHSTKPVVLVGAMRNASSLSADGALNLYYAVSVAVNEKSANKGVLVVMDDTIFRVREVVKTHTTHISTFKALNSGAIGSVYYGKTRYYMQPLRKHTTESEFSLSQLKTPLPKVDIIYTHAGMTPDLFQASLNSHAKGVVIAGVGNGNVSAGFLKAMQEASQMGVVIVRSSRVGSGGVTSGEIDDKAYGFITSDNLNPQKARVLLQLALTKTNDKAKIQEMFEEY-    -
               SCOP domains d2wt4a_ A: automa             ted matches                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains 2wt4A01 A:5-219               [code=3.40.50.1170, no name defined]                                                                                                                                                     2wt4A02 A:220-331  [code=3.40.50.40, no name defined]                                                           -- CATH domains
               Pfam domains --Asparaginase-2w             t4A01 A:7-326                                                                                                                                                                                                                                                                                       ------- Pfam domains
         Sec.struct. author ..eeeeee.........-------------........hhhhhhh.eeeeee.........hhhhhhhhhhhhhhhhh.......eee....hhhhhhhhhhhhh......eee.............hhhhhhhhhhhhhhhhh....eeee..eeee....ee........ee........................hhhhh..hhhhh........eee......hhhhhhhhhh.....eee..........hhhhhhhhhhh....ee.....................ee....hhhhhhhhhhhhhh...hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -ASN_GLN_ASE_3  PDB: A:6-332 UniProt: 6-332                                                                                                                                                                                                                                                                                             - PROSITE (1)
                PROSITE (2) -----ASN_GLN_A---------------------------------------------------------------------ASN_GLN_ASE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2wt4 A    5 LPTIALLATGGTIAGSG-------------GVKELLKAIPSLNKIARIQGEQVSNIGSQDMNEEIWFKLAQRAQELLDDSRIQGVVITHGTDTLEESAYFLNLVLHSTKPVVLVGAMRNASSLSADGALNLYEAVSVAVNEKSANKGVLVVMDDTIFSVREVVKTHTTHVSTFKALNSGAIGSVYYGKTRYYMQPLRKHTTESEFSLSQLKTPLPKVDIIYTHAGMTPDLFQASLNSHAKGVVIAGVGNGNVSAGFLKAMQEASQMGVVIVRSSRVGSGGVTSGEIDDKAYGFITSDNLNPQKARVLLQLALTKTNDKAKIQEMFEEYD 3613
                                    14      |  -         -|       44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       ||
                                           21            35                                                                                                                                                                                                                                                                                                      332|
                                                                                                                                                                                                                                                                                                                                                                 3613

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: automated matches (4)

Protein domain: automated matches (4)

Helicobacter pylori [TaxId: 210] (2)

d2wt4a_

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)

Helicobacter pylori. Organism_taxid: 210. (2)

2wt4A01

A:5-219

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

Helicobacter pylori. Organism_taxid: 210. (2)

2wt4A02

A:220-331

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Asparaginase] (13)

Family: Asparaginase (13)

Helicobacter pylori J99 (Campylobacter pylori J99) (2)

Asparaginase-2wt4A01

A:7-326

Asymmetric Unit(hide GO term definitions)

Chain A (ASPG_HELPJ | Q9ZLB9)

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.
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.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric Unit
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	Cis Peptide Bonds
		Lys A:37 - Glu A:38	[ RasMol ]
		Thr A:216 - Pro A:217	[ RasMol ]
		Val A:36 - Lys A:37	[ RasMol ]

Biological Unit
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		Biological Unit 1	[ Jena3D ]

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	2wt4
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	ASPG_HELPJ \| Q9ZLB9	:	2wlt

2wlt	THE CRYSTAL STRUCTURE OF HELICOBACTER PYLORI L-ASPARAGINASE AT ATOMIC RESOLUTION

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (0, 0)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (3, 3)

Exons (0, 0)

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