4PV3 - JenaLib

Title :   CRYSTAL STRUCTURE OF POTASSIUM-DEPENDENT PLANT-TYPE L-ASPARAGINASE FROM PHASEOLUS VULGARIS IN COMPLEX WITH NA+ CATIONS

Authors :   M. Bejger, M. Gilski, B. Imiolczyk, M. Jaskolski

Date :   14 Mar 14 (Deposition) - 03 Sep 14 (Release) - 03 Sep 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.09

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

Keywords :   Metal Binding Sites, Potassium Coordination, K-Dependent Enzyme, Ntn- Hydrolase, Plant Protein, L-Asparaginase, Isoaspartyl Aminopeptidase, Amidohydrolase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Bejger, B. Imiolczyk, D. Clavel, M. Gilski, A. Pajak, F. Marsolais, M. Jaskolski
Na+/K+ Exchange Switches The Catalytic Apparatus Of Potassium-Dependent Plant L-Asparaginase
Acta Crystallogr. , Sect. D V. 70 1854 2014
PubMed-ID: 25004963 | Reference-DOI: 10.1107/S1399004714008700
(for further references see the PDB file header)

Compounds

Molecule 1 - L-ASPARAGINASE ALPHA SUBUNIT
	Chains	:	A, C
	EC Number	:	3.5.1.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	N-TERMINAL SUBUNIT ALPHA (UNP RESIDUES 1-195)
	Gene	:	PHAVU_001G025000G
	Organism Common	:	FRENCH BEAN,KIDNEY BEAN,STRING BEAN
	Organism Scientific	:	PHASEOLUS VULGARIS
	Organism Taxid	:	3885
	Synonym	:	L-ASPARAGINE AMIDOHYDROLASE

Molecule 2 - L-ASPARAGINASE BETA SUBUNIT
	Chains	:	B, D
	EC Number	:	3.5.1.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	C-TERMINAL SUBUNIT BETA (UNP RESIDUES 196-326)
	Gene	:	PHAVU_001G025000G
	Organism Common	:	FRENCH BEAN,KIDNEY BEAN,STRING BEAN
	Organism Scientific	:	PHASEOLUS VULGARIS
	Organism Taxid	:	3885
	Other Details	:	SUBUNITS ALPHA (CHAINS A, C) AND BETA (CHAINS B, D) ARE, RESPECTIVELY, THE N- AND C-TERMINAL PRODUCTS OF AUTOPROTEOLYTIC CLEAVAGE OF A PRECURSOR
	Synonym	:	L-ASPARAGINE AMIDOHYDROLASE

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 4)

Sites (4, 4)

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LEU A:58 , GLU A:59 , ASP A:61 , PHE A:64 , SER A:66 , ARG A:68	BINDING SITE FOR RESIDUE NA A 201
2	AC2	SOFTWARE	VAL A:111 , MET A:112 , SER A:115 , HIS A:117 , HOH A:352 , HOH A:353	BINDING SITE FOR RESIDUE NA A 202
3	AC3	SOFTWARE	LEU C:58 , GLU C:59 , ASP C:61 , PHE C:64 , SER C:66 , ARG C:68	BINDING SITE FOR RESIDUE NA C 201
4	AC4	SOFTWARE	VAL C:111 , MET C:112 , SER C:115 , HIS C:117 , HOH C:353	BINDING SITE FOR RESIDUE NA C 202

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

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
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Chain A from PDB  Type:PROTEIN  Length:157
                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee......hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh..................eeeeeee.hhheeeeeeee....hhhhhhhhhhhhh...eeehhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pv3 A   2 GGWAIAVHGGAGVDPTLPLERQEEAKQLLTRCLNLGISALNSNVPAIDVVELVVRELETDPLFNSGRGSALTEKGTVEMEASIMDGPKRRCGAVSGLTTVKNPISLARLVMDKSPHSYIAFSGAEDFARQQGVEVVDNEYFVTPDNVGMLKLAKEAN 158
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151

Chain B from PDB  Type:PROTEIN  Length:131
                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....eeeeeee....................eee...eeeeeeehhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh....eeeeeee....eeeee....eeeeeee....eeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pv3 B 196 TVGCVVVDREGRCAAATSTGGLMNKMTGRIGDSPLIGAGTYACDVCGVSCTGEGEAIIRGTLAREVAAVMEYKGLKLHQAVDFVIKHRLDEGKAGLIAVSNTGEVACGFNCNGMFRACATEDGFMEVAIWD 326
                                   205       215       225       235       245       255       265       275       285       295       305       315       325

Chain C from PDB  Type:PROTEIN  Length:155
                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee......hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh..................eeeeeee....eeeeeeee....hhhhhhhhhhhhh...eeehhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pv3 C   2 GGWAIAVHGGAGVDPTLPLERQEEAKQLLTRCLNLGISALNSNVPAIDVVELVVRELETDPLFNSGRGSALTEKGTVEMEASIMDGPKRRCGAVSGLTTVKNPISLARLVMDKSPHSYIAFSGAEDFARQQGVEVVDNEYFVTPDNVGMLKLAKE 156
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151

Chain D from PDB  Type:PROTEIN  Length:131
                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....eeeeeee....................eee...eeeeeeehhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh....eeeeeee....eeeee....eeeeeee....eeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pv3 D 196 TVGCVVVDREGRCAAATSTGGLMNKMTGRIGDSPLIGAGTYACDVCGVSCTGEGEAIIRGTLAREVAAVMEYKGLKLHQAVDFVIKHRLDEGKAGLIAVSNTGEVACGFNCNGMFRACATEDGFMEVAIWD 326
                                   205       215       225       235       245       255       265       275       285       295       305       315       325

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	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 '\|'

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (1, 1)

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File

1jn9	ESCHERICHIA COLI L-ASPARAGINASE (ECAIII)
1k2x	ESCHERICHIA COLI L-ASPARAGINASE (ECAIII)
1t3m	ESCHERICHIA COLI L-ASPARAGINASE (ECAIII)
2gez	LUPINUS LUTEUS L-ASPARAGINASE (LLA)
2zak	ESCHERICHIA COLI L-ASPARAGINASE MUTANT (ECAIII T179A)
2zal	ESCHERICHIA COLI L-ASPARAGINASE (ECAIII)
3c17	ESCHERICHIA COLI L-ASPARAGINASE MUTANT (ECAIII T179A)
4gdt	HUMAN ASPARAGINASE-LIKE PROTEIN (HASNASE3)
4gdu	HUMAN ASPARAGINASE-LIKE PROTEIN (HASNASE3)
4gdv	HUMAN ASPARAGINASE-LIKE PROTEIN (HASNASE3)
4gdw	HUMAN ASPARAGINASE-LIKE PROTEIN (HASNASE3)
4hlo	HUMAN ASPARAGINASE-LIKE PROTEIN (HASNASE3)
4hlp	HUMAN ASPARAGINASE-LIKE PROTEIN (HASNASE3)
4pu6	CRYSTAL STRUCTURE OF POTASSIUM-DEPENDENT PLANT-TYPE L- ASPARAGINASE FROM PHASEOLUS VULGARIS IN COMPLEX WITH K+ CATIONS
4pv2	CRYSTAL STRUCTURE OF POTASSIUM-DEPENDENT PLANT-TYPE L- ASPARAGINASE FROM PHASEOLUS VULGARIS IN COMPLEX WITH K+ AND NA+ CATIONS

Description