3K4P - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   ASPERGILLUS NIGER PHYTASE

Authors :   A. J. Oakley

Date :   06 Oct 09 (Deposition) - 30 Jun 10 (Release) - 21 Jul 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

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

Keywords :   Phytase, Phya, 3-Phosphotase, Myo-Inositol Hexakis Phosphate Phosphohydrolase, 37288-11-2, Disulfide Bond, Glycoprotein, Hydrolase, Secreted (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. J. Oakley
The Structure Of Aspergillus Niger Phytase Phya In Complex With A Phytate Mimetic
Biochem. Biophys. Res. Commun. V. 397 745 2010
PubMed-ID: 20541524 | Reference-DOI: 10.1016/J.BBRC.2010.06.024

Molecule 1 - 3-PHYTASE A
	Chains	:	A, B
	EC Number	:	3.1.3.8
	Engineered	:	YES
	Expression System	:	ASPERGILLUS NIGER
	Expression System Taxid	:	5061
	Gene	:	PHYA
	Organism Scientific	:	ASPERGILLUS NIGER
	Organism Taxid	:	5061
	Synonym	:	3 PHYTASE A, MYO-INOSITOL-HEXAPHOSPHATE 3-PHOSPHOHYDROLASE A, MYO-INOSITOL HEXAKISPHOSPHATE PHOSPHOHYDROLASE A

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 6)

No.	Name	Count	Type	Full Name
1	NAG	6	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 1 (1, 3)

No.	Name	Count	Type	Full Name
1	NAG	3	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 2 (1, 3)

No.	Name	Count	Type	Full Name
1	NAG	3	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:78 , ASN A:82 , VAL A:227 , THR A:228 , HOH A:471	BINDING SITE FOR RESIDUE NAG A 1001
2	AC2	SOFTWARE	SER A:182 , SER A:183 , ASN A:184 , ASN A:316 , HOH A:466	BINDING SITE FOR RESIDUE NAG A 1002
3	AC3	SOFTWARE	ASN A:353 , GLY A:412 , GLY A:429 , PHE A:432 , HOH A:593 , HOH A:598 , ASN B:130 , ARG B:163 , ALA B:164 , GLN B:165	BINDING SITE FOR RESIDUE NAG A 1003
4	AC4	SOFTWARE	GLU B:78 , ASN B:82 , VAL B:227 , THR B:228 , HOH B:484	BINDING SITE FOR RESIDUE NAG B 1001
5	AC5	SOFTWARE	SER B:183 , ASN B:184 , ASN B:316 , HOH B:471	BINDING SITE FOR RESIDUE NAG B 1002
6	AC6	SOFTWARE	ASN A:130 , ARG A:163 , ALA A:164 , GLN A:165 , ASN B:353 , HIS B:411 , GLY B:412 , GLY B:429 , PHE B:432 , HOH B:451 , HOH B:549	BINDING SITE FOR RESIDUE NAG B 1003

Asymmetric Unit

No.	Residues
1	A:8	-	A:17
2	A:48	-	A:391
3	A:192	-	A:442
4	A:241	-	A:259
5	A:413	-	A:421
6	B:8	-	B:17
7	B:48	-	B:391
8	B:192	-	B:442
9	B:241	-	B:259
10	B:413	-	B:421

(no "Cis Peptide Bond" information available for 3K4P)

(no "SAP(SNP)/Variant" information available for 3K4P)

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HIS_ACID_PHOSPHAT_1	PS00616	Histidine acid phosphatases phosphohistidine signature.	PHYA_ASPNG	73-87	2	A:50-64 B:50-64
2	HIS_ACID_PHOSPHAT_2	PS00778	Histidine acid phosphatases active site signature.	PHYA_ASPNG	355-371	2	A:332-348 B:332-348

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HIS_ACID_PHOSPHAT_1	PS00616	Histidine acid phosphatases phosphohistidine signature.	PHYA_ASPNG	73-87	1	A:50-64 -
2	HIS_ACID_PHOSPHAT_2	PS00778	Histidine acid phosphatases active site signature.	PHYA_ASPNG	355-371	1	A:332-348 -

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HIS_ACID_PHOSPHAT_1	PS00616	Histidine acid phosphatases phosphohistidine signature.	PHYA_ASPNG	73-87	1	- B:50-64
2	HIS_ACID_PHOSPHAT_2	PS00778	Histidine acid phosphatases active site signature.	PHYA_ASPNG	355-371	1	- B:332-348

(no "Exon" information available for 3K4P)

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:438
 aligned with PHYA_ASPNG | P34752 from UniProtKB/Swiss-Prot  Length:467

    Alignment length:438
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459        
           PHYA_ASPNG    30 SCDTVDQGYQCFSETSHLWGQYAPFFSLANESVISPEVPAGCRVTFAQVLSRHGARYPTDSKGKKYSALIEEIQQNATTFDGKYAFLKTYNYSLGADDLTPFGEQELVNSGIKFYQRYESLTRNIVPFIRSSGSSRVIASGKKFIEGFQSTKLKDPRAQPGQSSPKIDVVISEASSSNNTLDPGTCTVFEDSELADTVEANFTATFVPSIRQRLENDLSGVTLTDTEVTYLMDMCSFDTISTSTVDTKLSPFCDLFTHDEWINYDYLQSLKKYYGHGAGNPLGPTQGVGYANELIARLTHSPVHDDTSSNHTLDSSPATFPLNSTLYADFSHDNGIISILFALGLYNGTKPLSTTTVENITQTDGFSSAWTVPFASRLYVEMMQCQAEQEPLVRVLVNDRVVPLHGCPVDALGRCTRDSFVRGLSFARSGGDWAECFA 467
               SCOP domains d3k4pa_ A: Phytase (myo-inositol-hexakisphosphate-3-phosphohydrolase)                                                                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..ee...ee..hhhhhhhhhhhh....hhhhh..........eeeeeeeeee......hhhhhhhhhhhhhhhhhhh...hhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhh....eeeee.hhhhhhhhhhhhhhhhhhhhh..............eee..............hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.........hhhhhh..........eeeeeehhhhhhhhhhhh.......................hhhhhh....eeeeeeee.......eeeeee..ee.............eehhhhhhhhhhhhh..hhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------HIS_ACID_PHOSPH---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------HIS_ACID_PHOSPHAT------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3k4p A   7 SCDTVDQGYQCFSETSHLWGQYAPFFSLANESVISPEVPAGCRVTFAQVLSRHGARYPTDSKGKKYSALIEEIQQNATTFDGKYAFLKTYNYSLGADDLTPFGEQELVNSGIKFYQRYESLTRNIVPFIRSSGSSRVIASGKKFIEGFQSTKLKDPRAQPGQSSPKIDVVISEASSSNNTLDPGTCTVFEDSELADTVEANFTATFVPSIRQRLENDLSGVTLTDTEVTYLMDMCSFDTISTSTVDTKLSPFCDLFTHDEWINYDYLQSLKKYYGHGAGNPLGPTQGVGYANELIARLTHSPVHDDTSSNHTLDSSPATFPLNSTLYADFSHDNGIISILFALGLYNGTKPLSTTTVENITQTDGFSSAWTVPFASRLYVEMMQCQAEQEPLVRVLVNDRVVPLHGCPVDALGRCTRDSFVRGLSFARSGGDWAECFA 444
                                    16        26        36        46        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       346       356       366       376       386       396       406       416       426       436

Chain B from PDB  Type:PROTEIN  Length:438
 aligned with PHYA_ASPNG | P34752 from UniProtKB/Swiss-Prot  Length:467

    Alignment length:438
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459        
           PHYA_ASPNG    30 SCDTVDQGYQCFSETSHLWGQYAPFFSLANESVISPEVPAGCRVTFAQVLSRHGARYPTDSKGKKYSALIEEIQQNATTFDGKYAFLKTYNYSLGADDLTPFGEQELVNSGIKFYQRYESLTRNIVPFIRSSGSSRVIASGKKFIEGFQSTKLKDPRAQPGQSSPKIDVVISEASSSNNTLDPGTCTVFEDSELADTVEANFTATFVPSIRQRLENDLSGVTLTDTEVTYLMDMCSFDTISTSTVDTKLSPFCDLFTHDEWINYDYLQSLKKYYGHGAGNPLGPTQGVGYANELIARLTHSPVHDDTSSNHTLDSSPATFPLNSTLYADFSHDNGIISILFALGLYNGTKPLSTTTVENITQTDGFSSAWTVPFASRLYVEMMQCQAEQEPLVRVLVNDRVVPLHGCPVDALGRCTRDSFVRGLSFARSGGDWAECFA 467
               SCOP domains d3k4pb_ B: Phytase (myo-inositol-hexakisphosphate-3-phosphohydrolase)                                                                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) ------------------------------------------His_Phos_2-3k4pB01 B:49-404                                                                                                                                                                                                                                                                                                                                         ---------------------------------------- Pfam domains (1)
           Pfam domains (2) ------------------------------------------His_Phos_2-3k4pB02 B:49-404                                                                                                                                                                                                                                                                                                                                         ---------------------------------------- Pfam domains (2)
         Sec.struct. author ..ee...ee..hhhhhhhhhhhh....hhhhh..........eeeeeeeeee......hhhhhhhhhhhhhhhhhhh...hhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhh....eeeee.hhhhhhhhhhhhhhhhhhhhh..............eee..............hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh.........hhhhhh..........eeeeeehhhhhhhhhhhh.......................hhhhhh....eeeeeeee.......eeeeee..ee.............eehhhhhhhhhhhhh..hhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------HIS_ACID_PHOSPH---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------HIS_ACID_PHOSPHAT------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3k4p B   7 SCDTVDQGYQCFSETSHLWGQYAPFFSLANESVISPEVPAGCRVTFAQVLSRHGARYPTDSKGKKYSALIEEIQQNATTFDGKYAFLKTYNYSLGADDLTPFGEQELVNSGIKFYQRYESLTRNIVPFIRSSGSSRVIASGKKFIEGFQSTKLKDPRAQPGQSSPKIDVVISEASSSNNTLDPGTCTVFEDSELADTVEANFTATFVPSIRQRLENDLSGVTLTDTEVTYLMDMCSFDTISTSTVDTKLSPFCDLFTHDEWINYDYLQSLKKYYGHGAGNPLGPTQGVGYANELIARLTHSPVHDDTSSNHTLDSSPATFPLNSTLYADFSHDNGIISILFALGLYNGTKPLSTTTVENITQTDGFSSAWTVPFASRLYVEMMQCQAEQEPLVRVLVNDRVVPLHGCPVDALGRCTRDSFVRGLSFARSGGDWAECFA 444
                                    16        26        36        46        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       346       356       366       376       386       396       406       416       426       436

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: Phosphoglycerate mutase-like (103)

Superfamily: Phosphoglycerate mutase-like (103)

Family: Histidine acid phosphatase (24)

Protein domain: Phytase (myo-inositol-hexakisphosphate-3-phosphohydrolase) (15)

Aspergillus niger [TaxId: 5061] (3)

1a	d3k4pa_	A:
1b	d3k4pb_	B:

(no "CATH Domain" information available for 3K4P)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: PGM (50)

Family: His_Phos_2 (19)

Aspergillus niger (2)

1a	His_Phos_2-3k4pB01	B:49-404
1b	His_Phos_2-3k4pB02	B:49-404

Asymmetric Unit(hide GO term definitions)

Chain A,B (PHYA_ASPNG | P34752)

molecular function
	GO:0016158	3-phytase activity	Catalysis of the reaction: myo-inositol hexakisphosphate + H2O = D-myo-inositol 1,2,4,5,6-pentakisphosphate + phosphate.
	GO:0003993	acid phosphatase activity	Catalysis of the reaction: an orthophosphoric monoester + H2O = an alcohol + phosphate, with an acid pH optimum.
	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:0016791	phosphatase activity	Catalysis of the hydrolysis of phosphoric monoesters, releasing inorganic phosphate.
biological process
	GO:0016311	dephosphorylation	The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
cellular component
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

Asymmetric Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3k4p)

Biological Units
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	3k4p
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	PHYA_ASPNG \| P34752
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	3.1.3.8
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UniProtKB/Swiss-Prot
	PHYA_ASPNG \| P34752	:	1ihp 3k4q

1dkl	ESCHERICHIA COLI PHYTASE
1dkq	ESCHERICHIA COLI PHYTASE H17A MUTANT IN COMPLEX WITH MYO- INOSITOL HEXAKISPHOSPHATE
1ihp	ASPERGILLUS NIGER PHYTASE
1qfx	ASPERGILLUS NIGER PH 2.5 ACID PHOSPHATASE
2gfi	DEBARYOMYCES CASTELLII CBS 2923 PHYTASE
3k4q	ASPERGILLUS NIGER PHYTASE IN COMPLEX WITH MYO-INOSITOL HEXAKIS SULFATE

Description

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Chains, Units

Ligands, Modified Residues, Ions (1, 6)

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SS Bonds (10, 10)

Cis Peptide Bonds (0, 0)

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