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Asym./Biol. Unit (Jmol Viewer)

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Title :   CRYSTAL STRUCTURE OF RED KIDNEY BEAN PURPLE ACID PHOSPHATASE WITH BOUND SULFATE

Authors :   L. W. Guddat, G. Schenk, L. R. Gahan, T. W. Elliot, E. Leung

Date :   27 Jun 07 (Deposition) - 14 Oct 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

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

Keywords :   Binuclear Metal Centre, Substrate Analog, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   G. Schenk, T. W. Elliott, E. Leung, L. E. Carrington, N. Mitic, L. R. Gahan, L. W. Guddat
Crystal Structures Of A Purple Acid Phosphatase, Representing Different Steps Of This Enzyme'S Catalytic Cycle.
Bmc Struct. Biol. V. 8 6 2008
PubMed-ID: 18234116 | Reference-DOI: 10.1186/1472-6807-8-6

Molecule 1 - PURPLE ACID PHOSPHATASE
	Chains	:	A, B
	EC Number	:	3.1.3.2
	Organism Common	:	KIDNEY BEAN
	Organism Scientific	:	PHASEOLUS VULGARIS
	Organism Taxid	:	3885

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (5, 16)

No.	Name	Count	Type	Full Name
1	FE	2	Ligand/Ion	FE (III) ION
2	NAG	6	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
3	NDG	2	Ligand/Ion	2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
4	SO4	4	Ligand/Ion	SULFATE ION
5	ZN	2	Ligand/Ion	ZINC ION

Asymmetric Unit (16, 16)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASN A:81 , ASN A:173 , HOH A:548 , HOH A:557 , TYR B:24 , ASP B:50	BINDING SITE FOR RESIDUE NDG A 450
02	AC2	SOFTWARE	ASP A:16 , ASN A:143 , SER A:147 , ARG A:188 , HOH A:566	BINDING SITE FOR RESIDUE NAG A 451
03	AC3	SOFTWARE	LYS A:395 , ASN A:396 , THR A:398 , HIS A:399 , HOH A:461 , HOH A:550 , HOH A:568	BINDING SITE FOR RESIDUE NAG A 452
04	AC4	SOFTWARE	GLU A:51 , ARG A:108 , ASN A:109 , HOH A:530 , HOH A:635	BINDING SITE FOR RESIDUE NDG A 453
05	AC5	SOFTWARE	TYR A:24 , GLU A:51 , ASN B:81 , ASN B:173 , HOH B:464 , HOH B:550	BINDING SITE FOR RESIDUE NAG B 450
06	AC6	SOFTWARE	ASP B:16 , ASN B:143 , SER B:147 , HOH B:539 , HOH B:642	BINDING SITE FOR RESIDUE NAG B 451
07	AC7	SOFTWARE	ASN B:396 , HIS B:399 , HOH B:462 , HOH B:475	BINDING SITE FOR RESIDUE NAG B 452
08	AC8	SOFTWARE	GLU B:51 , ARG B:108 , ASN B:109 , HOH B:482	BINDING SITE FOR RESIDUE NAG B 453
09	AC9	SOFTWARE	ASP A:135 , ASP A:164 , TYR A:167 , HIS A:325 , ZN A:434 , HOH A:454	BINDING SITE FOR RESIDUE FE A 433
10	BC1	SOFTWARE	ASP A:135 , ASP A:164 , ASN A:201 , HIS A:286 , HIS A:323 , FE A:433 , HOH A:454	BINDING SITE FOR RESIDUE ZN A 434
11	BC2	SOFTWARE	ASN A:201 , HIS A:202 , HIS A:295 , HIS A:296 , HIS A:323 , HIS A:325 , HOH A:454	BINDING SITE FOR RESIDUE SO4 A 435
12	BC3	SOFTWARE	ARG A:258 , TYR A:263 , LYS A:267 , HOH A:499 , HOH A:608	BINDING SITE FOR RESIDUE SO4 A 437
13	BC4	SOFTWARE	ASP B:135 , ASP B:164 , TYR B:167 , HIS B:325 , ZN B:434 , HOH B:454	BINDING SITE FOR RESIDUE FE B 433
14	BC5	SOFTWARE	ASP B:135 , ASP B:164 , ASN B:201 , HIS B:286 , HIS B:323 , FE B:433 , SO4 B:435 , HOH B:454	BINDING SITE FOR RESIDUE ZN B 434
15	BC6	SOFTWARE	ASN B:201 , HIS B:202 , HIS B:295 , HIS B:296 , ZN B:434 , HOH B:454	BINDING SITE FOR RESIDUE SO4 B 435
16	BC7	SOFTWARE	ARG B:258 , TYR B:263 , LYS B:267	BINDING SITE FOR RESIDUE SO4 B 437

Asymmetric/Biological Unit

No.	Residues
1	A:345	-	B:345

Asymmetric/Biological Unit

No.	Residues
1	Gln A:374	-	Pro A:375
2	Gln B:374	-	Pro B:375

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

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

(no "Exon" information available for 2QFR)

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:424
 aligned with PPAF_PHAVU | P80366 from UniProtKB/Swiss-Prot  Length:459

    Alignment length:424
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455    
           PPAF_PHAVU    36 RDMPLDSDVFRVPPGYNAPQQVHITQGDLVGRAMIISWVTMDEPGSSAVRYWSEKNGRKRIAKGKMSTYRFFNYSSGFIHHTTIRKLKYNTKYYYEVGLRNTTRRFSFITPPQTGLDVPYTFGLIGDLGQSFDSNTTLSHYELSPKKGQTVLFVGDLSYADRYPNHDNVRWDTWGRFTERSVAYQPWIWTAGNHEIEFAPEINETEPFKPFSYRYHVPYEASQSTSPFWYSIKRASAHIIVLSSYSAYGRGTPQYTWLKKELRKVKRSETPWLIVLMHSPLYNSYNHHFMEGEAMRTKFEAWFVKYKVDVVFAGHVHAYERSERVSNIAYKITNGLCTPVKDQSAPVYITIGDAGNYGVIDSNMIQPQPEYSAFREASFGHGMFDIKNRTHAHFSWNRNQDGVAVEADSVWFFNRHWYPVDDST 459
               SCOP domains d2qfra1 A:9-120 automated matches                                                                               d2qfra2 A:121-432 automated matches                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains -----------------2qfrA01 A:26-122 Purple acid phosphatase, domain1                                                2qfrA02 A:123-432  [code=3.60.21.10, no name defined]                                                                                                                                                                                                                                                                  CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhh........eeeeeee.......eeeeeee.......eeeeee......eeee.eee..........eeeeeee.......eeeeee......eeeeee..........eeeeee.....hhhhhhhhhhhhhh.....eeee.....hhhhhhhhhhhhhhhhhhhhhhhhh...eee..hhhhh..hhhhh....hhhhhhhh..hhhhhh......eeeee..eeeee..........hhhhhhhhhhhhh.......eeeee...............hhhhhhhhhhhhhhh...eeee.....eeee..ee.............ee.....eeeee....................eeeee...eeeeeee....eeeeeeee.........eeeeee........... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qfr A   9 RDMPLDSDVFRVPPGYNAPQQVHITQGDLVGRAMIISWVTMDEPGSSAVRYWSEKNGRKRIAKGKMSTYRFFNYSSGFIHHTTIRKLKYNTKYYYEVGLRNTTRRFSFITPPQTGLDVPYTFGLIGDLGQSFDSNTTLSHYELSPKKGQTVLFVGDLSYADRYPNHDNVRWDTWGRFTERSVAYQPWIWTAGNHEIEFAPEINETEPFKPFSYRYHVPYEASQSTSPFWYSIKRASAHIIVLSSYSAYGRGTPQYTWLKKELRKVKRSETPWLIVLMHSPLYNSYNHHFMEGEAMRTKFEAWFVKYKVDVVFAGHVHAYERSERVSNIAYKITNGLCTPVKDQSAPVYITIGDAGNYGVIDSNMIQPQPEYSAFREASFGHGMFDIKNRTHAHFSWNRNQDGVAVEADSVWFFNRHWYPVDDST 432
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428

Chain B from PDB  Type:PROTEIN  Length:424
 aligned with PPAF_PHAVU | P80366 from UniProtKB/Swiss-Prot  Length:459

    Alignment length:424
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455    
           PPAF_PHAVU    36 RDMPLDSDVFRVPPGYNAPQQVHITQGDLVGRAMIISWVTMDEPGSSAVRYWSEKNGRKRIAKGKMSTYRFFNYSSGFIHHTTIRKLKYNTKYYYEVGLRNTTRRFSFITPPQTGLDVPYTFGLIGDLGQSFDSNTTLSHYELSPKKGQTVLFVGDLSYADRYPNHDNVRWDTWGRFTERSVAYQPWIWTAGNHEIEFAPEINETEPFKPFSYRYHVPYEASQSTSPFWYSIKRASAHIIVLSSYSAYGRGTPQYTWLKKELRKVKRSETPWLIVLMHSPLYNSYNHHFMEGEAMRTKFEAWFVKYKVDVVFAGHVHAYERSERVSNIAYKITNGLCTPVKDQSAPVYITIGDAGNYGVIDSNMIQPQPEYSAFREASFGHGMFDIKNRTHAHFSWNRNQDGVAVEADSVWFFNRHWYPVDDST 459
               SCOP domains d2qfrb1 B:9-120 automated matches                                                                               d2qfrb2 B:121-432 automated matches                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains -----------------2qfrB01 B:26-122 Purple acid phosphatase, domain1                                                2qfrB02 B:123-432  [code=3.60.21.10, no name defined]                                                                                                                                                                                                                                                                  CATH domains
           Pfam domains (1) --------------------------------------------------------------------------------------------Metallophos-2qfrB01 B:101-300                                                                                                                                                                           ------------------------Metallophos_C-2qfrB03 B:325-391                                    ----------------------------------------- Pfam domains (1)
           Pfam domains (2) --------------------------------------------------------------------------------------------Metallophos-2qfrB02 B:101-300                                                                                                                                                                           ------------------------Metallophos_C-2qfrB04 B:325-391                                    ----------------------------------------- Pfam domains (2)
         Sec.struct. author ......hhhhh........eeeeeee.......eeeeeee.......eeeeee......eeee.eee..........eeeeeee.......eeeeee......eeeeee..........eeeeee.....hhhhhhhhhhhhhh.....eeee.....hhhhhhhhhhhhhhhhhhhhhhhhh...ee...hhhhhh.hhhhh....hhhhhhhh..hhhhhh......eeeee..eeeee..........hhhhhhhhhhhhh.......eeeee...............hhhhhhhhhhhhhhh...eeee.....eeee..ee.............ee.....eeeee....................eeeee...eeeeeee....eeeeeeee.........eeeeee........... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qfr B   9 RDMPLDSDVFRVPPGYNAPQQVHITQGDLVGRAMIISWVTMDEPGSSAVRYWSEKNGRKRIAKGKMSTYRFFNYSSGFIHHTTIRKLKYNTKYYYEVGLRNTTRRFSFITPPQTGLDVPYTFGLIGDLGQSFDSNTTLSHYELSPKKGQTVLFVGDLSYADRYPNHDNVRWDTWGRFTERSVAYQPWIWTAGNHEIEFAPEINETEPFKPFSYRYHVPYEASQSTSPFWYSIKRASAHIIVLSSYSAYGRGTPQYTWLKKELRKVKRSETPWLIVLMHSPLYNSYNHHFMEGEAMRTKFEAWFVKYKVDVVFAGHVHAYERSERVSNIAYKITNGLCTPVKDQSAPVYITIGDAGNYGVIDSNMIQPQPEYSAFREASFGHGMFDIKNRTHAHFSWNRNQDGVAVEADSVWFFNRHWYPVDDST 432
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428

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(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 4-Layer Sandwich (459)

Topology: Purple Acid Phosphatase; chain A, domain 2 (87)

Homologous Superfamily: [code=3.60.21.10, no name defined] (83)

Kidney bean (Phaseolus vulgaris) (2)

1a	2qfrA02	A:123-432
1b	2qfrB02	B:123-432

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: Purple acid phosphatase, domain1 (6)

Kidney bean (Phaseolus vulgaris) (2)

2a	2qfrA01	A:26-122
2b	2qfrB01	B:26-122

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (PPAF_PHAVU | P80366)

molecular function
	GO:0003993	acid phosphatase activity	Catalysis of the reaction: an orthophosphoric monoester + H2O = an alcohol + phosphate, with an acid pH optimum.
	GO:0008199	ferric iron binding	Interacting selectively and non-covalently with ferric iron, Fe(III).
	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:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
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/Biological Unit
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	Cis Peptide Bonds
		Gln A:374 - Pro A:375	[ RasMol ]
		Gln B:374 - Pro B:375	[ RasMol ]

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	2qfr
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	3.1.3.2
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	PPAF_PHAVU \| P80366	:	1kbp 2qfp 3kbp 4dhl 4dsy 4dt2 4kbp 4kkz

2qfp	FLUORIDE COMPLEX
3kbp	FREE ENZYME
4kbp	PHOSPHATE COMPLEX

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 16)

Sites (16, 16)

SS Bonds (1, 1)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

Sequences/Alignments

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SCOP Domains (2, 4)

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Gene Ontology (7, 7)

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