2WNH - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE ANALYSIS OF KLEBSIELLA SP ASR1 PHYTASE

Authors :   K. Bohm, J. J. Mueller, U. Heinemann

Date :   09 Jul 09 (Deposition) - 28 Apr 10 (Release) - 24 Nov 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.68

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

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

Reference :   K. Bohm, T. Herter, J. J. Mueller, R. Borriss, U. Heinemann
Crystal Structure Of Klebsiella Sp. Asr1 Phytase Suggests Substrate Binding To A Preformed Active Site That Meets The Requirements Of A Plant Rhizosphere Enzyme.
Febs J. V. 277 1284 2010
PubMed-ID: 20392204 | Reference-DOI: 10.1111/J.1742-4658.2010.07559.X

Molecule 1 - 3-PHYTASE
	Chains	:	A, B
	EC Number	:	3.1.3.8
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET22B
	Expression System Strain	:	C41(DE3)
	Expression System Taxid	:	562
	Fragment	:	RESIDUES 29-421
	Mutation	:	YES
	Organism Scientific	:	KLEBSIELLA PNEUMONIAE
	Organism Taxid	:	573
	Strain	:	ASR1

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 6)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL
2	MG	1	Ligand/Ion	MAGNESIUM ION
3	NA	3	Ligand/Ion	SODIUM ION

Biological Unit 1 (1, 4)

No.	Name	Count	Type	Full Name
1	GOL	4	Ligand/Ion	GLYCEROL
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	NA	-1	Ligand/Ion	SODIUM ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG B:312 , HOH B:2106 , HOH B:2226 , HOH B:2228 , HOH B:2282	BINDING SITE FOR RESIDUE NA B1407
2	AC2	SOFTWARE	TRP A:49 , THR A:51 , HOH A:2050 , HOH A:2059 , HOH A:2062 , HOH A:2063	BINDING SITE FOR RESIDUE NA A1407
3	AC3	SOFTWARE	ARG B:76	BINDING SITE FOR RESIDUE NA B1408
4	AC4	SOFTWARE	HIS A:358 , HOH A:2337	BINDING SITE FOR RESIDUE MG A1408
5	AC5	SOFTWARE	TYR A:61 , ASP A:110 , HOH A:2137 , HIS B:59 , GLU B:220 , ASN B:221 , HOH B:2206 , HOH B:2375 , HOH B:2376	BINDING SITE FOR RESIDUE GOL B1409
6	AC6	SOFTWARE	HIS A:59 , GLU A:220 , ASN A:221 , LEU A:222 , HOH A:2222 , HOH A:2394 , HOH A:2395 , TYR B:61 , GLN B:106 , ASP B:110 , HOH B:2134	BINDING SITE FOR RESIDUE GOL A1409

Asymmetric Unit

No.	Residues
1	A:85	-	A:116
2	A:176	-	A:182
3	A:370	-	A:379
4	B:85	-	B:116
5	B:176	-	B:182
6	B:370	-	B:379

Asymmetric Unit

No.	Residues
1	Ser A:279	-	Pro A:280
2	Ser B:279	-	Pro B:280

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

(no "PROSITE Motif" information available for 2WNH)

(no "Exon" information available for 2WNH)

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:399
 aligned with Q84CN9_KLEPN | Q84CN9 from UniProtKB/TrEMBL  Length:421

    Alignment length:399
                                                                                                                                                                                                                                                                                                                                                                                                                                       421 
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       | 
         Q84CN9_KLEPN    24 SAAAADWQLEKVVELSRHGIRPPTAGNREAIEAATGRPWTEWTTHDGELTGHGYAAVVNKGREEGQHYRQLGLLQAGCPTAESIYVRASPLQRTRATAQALVDGAFPGCGVAIHYVNGDADPLFQTDKFAATQTDPARQLAAVKEKAGDLAQRRQALAPTIQLLKQAVCQADKPCPIFDTPWRVEQSKSGKTTISGLSVMANMVETLRLGWSENLPLSQLAWGKIAQASQITALLPLLTENYDLSNDVLYTAQKRGSVLLNAMLDGVKPEANPNVRWLLLVAHDTNIAMVRTLMNFSWQLPGYSRGNIPPGSSLVLERWRDAKSGERYLRVYFQAQGLDDLRRLQTPDAQHPMLRQEWRQPGCRQTDVGTLCPFQAAITALGQRIDRPSTPAVAMVLP-   -
               SCOP domains d2wnha_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeeeeee.........hhhhhhhhh..................hhhhhhh.....hhhhhh............eeeee..hhhhhhhhhhhhh.....................hhhhhhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.....hhhhhh...eee.....eee..hhhhhhhhhhhhh......hhhhhh.....hhhhhhh.hhhhhhhhhh...hhhhhhhh.hhhhhhhhh...........eeeeeehhhhhhhhhhhhh.................eeeeeeeee.....eeeeeeeee..hhhhhhh...........................eehhhhhhhh....hhhhh......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wnh A   8 DPPPRDWQLEKVVELSRHGIRPPTAGNREAIEAATGRPWTEWTTHDGELTGHGYAAVVNKGREEGQHYRQLGLLQAGCPTAESIYVRASPLQRTRATAQALVDGAFPGCGVAIHYANGDADPLFQTDKFAATQTDPARQLAAVKEKAGDLAQRRQALAPTIQLLKQAVCQADKPCPIFDTPWRVEQSKSGKTTISGLSVMANMVETLRLGWSENLPLSQLAWGKIAQASQITALLPLLTENYDLSNDVLYTAQKRGSVLLNAMLDGVKPEASPNVRWLLLVAHDTNIAMVRTLMNFSWQLPGYSRGNIPPGSSLVLERWRDAKSGERYLRVYFQAQGLDDLRRLQTPDAQHPMLRQEWRQPGCRQTDVGTLCPFQAAITALGQRIDRPSAPAVAMVLPK 406
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397

Chain B from PDB  Type:PROTEIN  Length:400
 aligned with Q84CN9_KLEPN | Q84CN9 from UniProtKB/TrEMBL  Length:421

    Alignment length:400
                                                                                                                                                                                                                                                                                                                                                                                                                                        421 
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412        |-
         Q84CN9_KLEPN    23 HSAAAADWQLEKVVELSRHGIRPPTAGNREAIEAATGRPWTEWTTHDGELTGHGYAAVVNKGREEGQHYRQLGLLQAGCPTAESIYVRASPLQRTRATAQALVDGAFPGCGVAIHYVNGDADPLFQTDKFAATQTDPARQLAAVKEKAGDLAQRRQALAPTIQLLKQAVCQADKPCPIFDTPWRVEQSKSGKTTISGLSVMANMVETLRLGWSENLPLSQLAWGKIAQASQITALLPLLTENYDLSNDVLYTAQKRGSVLLNAMLDGVKPEANPNVRWLLLVAHDTNIAMVRTLMNFSWQLPGYSRGNIPPGSSLVLERWRDAKSGERYLRVYFQAQGLDDLRRLQTPDAQHPMLRQEWRQPGCRQTDVGTLCPFQAAITALGQRIDRPSTPAVAMVLP-   -
               SCOP domains d2wnhb_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------His_Phos_2-2wnhB01 B:15-341                                                                                                                                                                                                                                                                                                            ----------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) --------His_Phos_2-2wnhB02 B:15-341                                                                                                                                                                                                                                                                                                            ----------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author .......eeeeeeeeeee.........hhhhhhhhh..................hhhhhhh.....hhhhhh............eeeee..hhhhhhhhhhhhh.....................hhhhhhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.....hhhhhh...eee.....eee..hhhhhhhhhhhhh......hhhhh......hhhhhhh.hhhhhhhhhh...hhhhhhhh.hhhhhhhhh...........eeeeeehhhhhhhhhhhhh.................eeeeeeeee.....eeeeeeeee..hhhhhh............................eehhhhhhhh....hhhhh......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wnh B   7 SDPPPRDWQLEKVVELSRHGIRPPTAGNREAIEAATGRPWTEWTTHDGELTGHGYAAVVNKGREEGQHYRQLGLLQAGCPTAESIYVRASPLQRTRATAQALVDGAFPGCGVAIHYANGDADPLFQTDKFAATQTDPARQLAAVKEKAGDLAQRRQALAPTIQLLKQAVCQADKPCPIFDTPWRVEQSKSGKTTISGLSVMANMVETLRLGWSENLPLSQLAWGKIAQASQITALLPLLTENYDLSNDVLYTAQKRGSVLLNAMLDGVKPEASPNVRWLLLVAHDTNIAMVRTLMNFSWQLPGYSRGNIPPGSSLVLERWRDAKSGERYLRVYFQAQGLDDLRRLQTPDAQHPMLRQEWRQPGCRQTDVGTLCPFQAAITALGQRIDRPSAPAVAMVLPK 406
                                    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

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: automated matches (13)

Protein domain: automated matches (13)

Klebsiella pneumoniae [TaxId: 573] (3)

1a	d2wnha_	A:
1b	d2wnhb_	B:

(no "CATH Domain" information available for 2WNH)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: PGM (50)

Family: His_Phos_2 (19)

Klebsiella pneumoniae (3)

1a	His_Phos_2-2wnhB01	B:15-341
1b	His_Phos_2-2wnhB02	B:15-341

Asymmetric Unit(hide GO term definitions)

Chain A,B (Q84CN9_KLEPN | Q84CN9)

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.
biological process
	GO:0016311	dephosphorylation	The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.

Asymmetric Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		GOL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Ser A:279 - Pro A:280	[ RasMol ]
		Ser B:279 - Pro B:280	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	2wnh
		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
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	Q84CN9_KLEPN \| Q84CN9
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/TrEMBL

Access by Enzyme Classificator (EC Number)
	3.1.3.8
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	Q84CN9_KLEPN \| Q84CN9
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/TrEMBL
	Q84CN9_KLEPN \| Q84CN9	:	2wni 2wu0

2wni	CRYSTAL STRUCTURE ANALYSIS OF KLEBSIELLA SP ASR1 PHYTASE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 6)

Sites (6, 6)

SS Bonds (6, 6)

Cis Peptide Bonds (2, 2)

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, 2)

Gene Ontology (4, 4)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File