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(-) Description

Title :  PH 2.5 ACID PHOSPHATASE FROM ASPERGILLUS NIGER
 
Authors :  D. Kostrewa, M. Wyss, A. D'Arcy, A. P. G. M. Van Loon
Date :  15 Apr 99  (Deposition) - 19 Apr 00  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Phosphomonoesterase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Kostrewa, M. Wyss, A. D'Arcy, A. P. Van Loon
Crystal Structure Of Aspergillus Niger Ph 2. 5 Acid Phosphatase At 2. 4 A Resolution.
J. Mol. Biol. V. 288 965 1999
PubMed-ID: 10329192  |  Reference-DOI: 10.1006/JMBI.1999.2736

(-) Compounds

Molecule 1 - PROTEIN (PH 2.5 ACID PHOSPHATASE)
    Chains: A, B
    EC Number: 3.1.3.8
    Organism Scientific: ASPERGILLUS NIGER
    Organism Taxid: 5061
    Other Details: N-GLYCOSYLATED AT A 172, A 296, A439, B 172, B 296 AND B 439
    Strain: NW205

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 33)

Asymmetric Unit (5, 33)
No.NameCountTypeFull Name
1BMA2Ligand/IonBETA-D-MANNOSE
2GOL6Ligand/IonGLYCEROL
3MAN6Ligand/IonALPHA-D-MANNOSE
4NAG8Ligand/IonN-ACETYL-D-GLUCOSAMINE
5SO411Ligand/IonSULFATE ION
Biological Unit 1 (5, 66)
No.NameCountTypeFull Name
1BMA4Ligand/IonBETA-D-MANNOSE
2GOL12Ligand/IonGLYCEROL
3MAN12Ligand/IonALPHA-D-MANNOSE
4NAG16Ligand/IonN-ACETYL-D-GLUCOSAMINE
5SO422Ligand/IonSULFATE ION

(-) Sites  (33, 33)

Asymmetric Unit (33, 33)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:296 , ALA A:297 , THR A:300 , LEU A:432 , TRP A:436 , GOL A:703 , HOH A:928 , HOH A:1110BINDING SITE FOR RESIDUE NAG A 596
02AC2SOFTWAREASN A:180 , ASN A:437 , ASN A:439 , HOH A:898 , HOH A:1075 , THR B:441 , NAG B:739BINDING SITE FOR RESIDUE NAG A 739
03AC3SOFTWAREGLY A:143 , ASN A:172 , ASN A:176 , PRO A:450 , ILE A:451 , NAG A:473 , HOH A:827 , HOH A:967 , HOH A:988 , GOL B:706BINDING SITE FOR RESIDUE NAG A 472
04AC4SOFTWARECYS A:109 , ILE A:451 , CYS A:453 , NAG A:472 , BMA A:474 , HOH A:967 , HOH A:1031BINDING SITE FOR RESIDUE NAG A 473
05AC5SOFTWARENAG A:473 , MAN A:475 , MAN A:478 , HOH A:963BINDING SITE FOR RESIDUE BMA A 474
06AC6SOFTWAREBMA A:474 , MAN A:476 , HOH A:1076 , NAG B:596BINDING SITE FOR RESIDUE MAN A 475
07AC7SOFTWAREMAN A:475 , MAN A:477 , ASN B:412 , NAG B:596BINDING SITE FOR RESIDUE MAN A 476
08AC8SOFTWAREMAN A:476 , ASN B:412 , LYS B:413 , SO4 B:811BINDING SITE FOR RESIDUE MAN A 477
09AC9SOFTWAREBMA A:474BINDING SITE FOR RESIDUE MAN A 478
10BC1SOFTWAREMAN A:475 , MAN A:476 , ASN B:296 , THR B:300 , TYR B:431 , LEU B:432 , TRP B:436 , HOH B:938BINDING SITE FOR RESIDUE NAG B 596
11BC2SOFTWARETHR A:441 , NAG A:739 , HOH A:1060 , HOH A:1082 , ASN B:180 , ASN B:437 , ASN B:439 , HOH B:908 , HOH B:1102 , HOH B:1127BINDING SITE FOR RESIDUE NAG B 739
12BC3SOFTWARETYR B:110 , GLY B:143 , ASN B:172 , ASN B:176 , PRO B:450 , ILE B:451 , NAG B:473 , HOH B:839 , HOH B:976 , HOH B:997 , HOH B:1062BINDING SITE FOR RESIDUE NAG B 472
13BC4SOFTWARECYS B:109 , TYR B:110 , ILE B:451 , CYS B:453 , NAG B:472 , BMA B:474 , HOH B:972 , HOH B:976 , HOH B:1039BINDING SITE FOR RESIDUE NAG B 473
14BC5SOFTWARECYS B:453 , NAG B:473 , MAN B:475 , MAN B:478 , HOH B:972 , HOH B:1067BINDING SITE FOR RESIDUE BMA B 474
15BC6SOFTWAREBMA B:474BINDING SITE FOR RESIDUE MAN B 475
16BC7SOFTWAREBMA B:474BINDING SITE FOR RESIDUE MAN B 478
17BC8SOFTWAREGLY A:305 , PRO A:306 , LYS A:307 , ARG A:365 , HOH A:870 , HOH A:930 , HOH A:1021BINDING SITE FOR RESIDUE SO4 A 801
18BC9SOFTWAREARG A:66 , PRO A:68 , SER A:69 , ALA A:72 , PHE A:246 , HOH A:1106BINDING SITE FOR RESIDUE SO4 A 802
19CC1SOFTWAREPRO A:334 , ASN A:335 , ASN A:347 , PRO A:348 , HOH A:907 , HOH A:1010 , ASN B:335BINDING SITE FOR RESIDUE SO4 A 803
20CC2SOFTWARESER A:69 , PRO A:70 , SER A:71 , HOH A:1121BINDING SITE FOR RESIDUE SO4 A 804
21CC3SOFTWAREPRO A:48 , GLU A:53 , VAL A:54 , HIS A:139 , HOH A:864 , HOH A:1022BINDING SITE FOR RESIDUE SO4 A 805
22CC4SOFTWAREGLY B:305 , PRO B:306 , LYS B:307 , ARG B:365 , HOH B:880 , HOH B:940 , HOH B:1029BINDING SITE FOR RESIDUE SO4 B 806
23CC5SOFTWAREARG B:66 , PRO B:68 , SER B:69 , ALA B:72 , HOH B:1051BINDING SITE FOR RESIDUE SO4 B 807
24CC6SOFTWAREASN A:335 , PRO B:334 , ASN B:335 , ASN B:347 , PRO B:348 , HOH B:917 , HOH B:1018BINDING SITE FOR RESIDUE SO4 B 808
25CC7SOFTWARESER B:69 , PRO B:70 , SER B:71 , HOH B:949BINDING SITE FOR RESIDUE SO4 B 809
26CC8SOFTWAREPRO B:48 , CYS B:52 , GLU B:53 , VAL B:54 , HIS B:139 , HOH B:1030BINDING SITE FOR RESIDUE SO4 B 810
27CC9SOFTWAREMAN A:477 , SER B:409 , ASN B:412 , HOH B:918BINDING SITE FOR RESIDUE SO4 B 811
28DC1SOFTWARETYR A:154 , GLU A:184 , HIS A:318 , HOH A:902BINDING SITE FOR RESIDUE GOL A 701
29DC2SOFTWAREGLU A:159 , GLU A:166 , GLY A:170 , ARG A:447 , HOH A:976BINDING SITE FOR RESIDUE GOL A 702
30DC3SOFTWAREGLN A:304 , TYR A:431 , TRP A:436 , ASN A:437 , NAG A:596BINDING SITE FOR RESIDUE GOL A 703
31DC4SOFTWARETYR B:154 , GLU B:184 , HIS B:318 , HOH B:912BINDING SITE FOR RESIDUE GOL B 704
32DC5SOFTWARELEU B:123 , GLU B:159 , GLU B:166 , GLY B:170 , ARG B:447BINDING SITE FOR RESIDUE GOL B 705
33DC6SOFTWAREGLU A:144 , ASN A:176 , NAG A:472 , HOH A:1092BINDING SITE FOR RESIDUE GOL B 706

(-) SS Bonds  (10, 10)

Asymmetric Unit
No.Residues
1A:52 -A:368
2A:109 -A:453
3A:197 -A:422
4A:206 -A:279
5A:394 -A:402
6B:52 -B:368
7B:109 -B:453
8B:197 -B:422
9B:206 -B:279
10B:394 -B:402

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1QFX)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1QFX)

(-) PROSITE Motifs  (2, 4)

Asymmetric Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HIS_ACID_PHOSPHAT_1PS00616 Histidine acid phosphatases phosphohistidine signature.PHYB_ASPAW73-87
 		  2A:54-68
B:54-68
2HIS_ACID_PHOSPHAT_2PS00778 Histidine acid phosphatases active site signature.PHYB_ASPAW331-347
 		  2A:312-328
B:312-328
Biological Unit 1 (2, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HIS_ACID_PHOSPHAT_1PS00616 Histidine acid phosphatases phosphohistidine signature.PHYB_ASPAW73-87
 		  4A:54-68
B:54-68
2HIS_ACID_PHOSPHAT_2PS00778 Histidine acid phosphatases active site signature.PHYB_ASPAW331-347
 		  4A:312-328
B:312-328

(-) Exons   (0, 0)

(no "Exon" information available for 1QFX)

(-) Sequences/Alignments

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:441
 aligned with PHYB_ASPAW | P34755 from UniProtKB/Swiss-Prot  Length:479

    Alignment length:447
                                    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       422       432       442       452       462       472       
           PHYB_ASPAW    33 KQFSQEFRDGYSILKHYGGNGPYSERVSYGIARDPPTSCEVDQVIMVKRHGERYPSPSAGKDIEEALAKVYSINTTEYKGDLAFLNDWTYYVPNECYYNAETTSGPYAGLLDAYNHGNDYKARYGHLWNGETVVPFFSSGYGRVIETARKFGEGFFGYNYSTNAALNIISESEVMGADSLTPTCDTDNDQTTCDNLTYQLPQFKVAAARLNSQNPGMNLTASDVYNLMVMASFELNARPFSNWINAFTQDEWVSFGYVEDLNYYYCAGPGDKNMAAVGAVYANASLTLLNQGPKEAGSLFFNFAHDTNITPILAALGVLIPNEDLPLDRVAFGNPYSIGNIVPMGGHLTIERLSCQATALSDEGTYVRLVLNEAVLPFNDCTSGPGYSCPLANYTSILNKNLPDYTTTCNVSASYPQYLSFWWNYNTTTELNYRSSPIACQEGDAMD 479
               SCOP domains d1qfxa_ A: Phytase (myo-inositol-hexakisphosphate-3-phosphohydrolase)                                                                                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains ----------------------1qfxA02                     ---------------------------------------------------------1qfxA02 A:36-63,A:121-198,A:285-331,A:356-460 Phosphoglycerate mutase-like    --------------------------------------------------------------------------------------1qfxA02 A:36-63,A:121-198,A:285-331,A:356-460  ------------------------1qfxA02 A:36-63,A:121-198,A:285-331,A:356-460 Phosphoglycerate mutase-like                                CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhh.hhh.......................eeeeeeeeeee.......hhhhhhhhhhhhhhh..--....hhhhhhhh.......hhh...........hhhhhhhhhhhhhhhhhhh......eeeeee..hhhhhhhhhhhhhhhhhhhhhheeeeee...hhh...........----..........hhhhhhhhhhhhh.......hhhhhhhhhhhhhh.........hhh..hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh.hhhh..eeeeee.hhhhhhhhhhh.....................hhh......eeeeeeeee........eeeeeeee..eee........hhh...hhhhhhhhhhh...hhhh....................................... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------HIS_ACID_PHOSPH---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------HIS_ACID_PHOSPHAT------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qfx A  14 KQFSQEFRDGYSILKHYGGNGPYSERVSYGIARDPPTSCEVDQVIMVKRHGERYPSPSAGKDIEEALAKVYSI--TEYKGDLAFLNDWTYYVPNECYYNAETTSGPYAGLLDAYNHGNDYKARYGHLWNGETVVPFFSSGYGRVIETARKFGEGFFGYNYSTNAALNIISESEVMGADSLTPTCDT----TTCDNLTYQLPQFKVAAARLNSQNPGMNLTASDVYNLMVMASFELNARPFSNWINAFTQDEWVSFGYVEDLNYYYCAGPGDKNMAAVGAVYANASLTLLNQGPKEAGSLFFNFAHDTNITPILAALGVLIPNEDLPLDRVAFGNPYSIGNIVPMGGHLTIERLSCQATALSDEGTYVRLVLNEAVLPFNDCTSGPGYSCPLANYTSILNKNLPDYTTTCNVSASYPQYLSFWWNYNTTTELNYRSSPIACQEGDAMD 460
                                    23        33        43        53        63        73        83  |  |  93       103       113       123       133       143       153       163       173       183       193     |   -|      213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       
                                                                                                   86 89                                                                                                           199  204                                                                                                                                                                                                                                                                


Chain B from PDB  Type:PROTEIN  Length:443
 aligned with PHYB_ASPAW | P34755 from UniProtKB/Swiss-Prot  Length:479

    Alignment length:447
                                    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       422       432       442       452       462       472       
           PHYB_ASPAW    33 KQFSQEFRDGYSILKHYGGNGPYSERVSYGIARDPPTSCEVDQVIMVKRHGERYPSPSAGKDIEEALAKVYSINTTEYKGDLAFLNDWTYYVPNECYYNAETTSGPYAGLLDAYNHGNDYKARYGHLWNGETVVPFFSSGYGRVIETARKFGEGFFGYNYSTNAALNIISESEVMGADSLTPTCDTDNDQTTCDNLTYQLPQFKVAAARLNSQNPGMNLTASDVYNLMVMASFELNARPFSNWINAFTQDEWVSFGYVEDLNYYYCAGPGDKNMAAVGAVYANASLTLLNQGPKEAGSLFFNFAHDTNITPILAALGVLIPNEDLPLDRVAFGNPYSIGNIVPMGGHLTIERLSCQATALSDEGTYVRLVLNEAVLPFNDCTSGPGYSCPLANYTSILNKNLPDYTTTCNVSASYPQYLSFWWNYNTTTELNYRSSPIACQEGDAMD 479
               SCOP domains d1qfxb_ B: Phytase (myo-inositol-hexakisphosphate-3-phosphohydrolase)                                                                                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains ----------------------1qfxB02                     ---------------------------------------------------------1qfxB02 B:36-63,B:121-200,B:285-331,B:356-460 Phosphoglycerate mutase-like      ------------------------------------------------------------------------------------1qfxB02 B:36-63,B:121-200,B:285-331,B:356-460  ------------------------1qfxB02 B:36-63,B:121-200,B:285-331,B:356-460 Phosphoglycerate mutase-like                                CATH domains
           Pfam domains (1) ---------------------------------------His_Phos_2-1qfxB01 B:53-385                                                                                                                                                                                                                                                                                                                  --------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ---------------------------------------His_Phos_2-1qfxB02 B:53-385                                                                                                                                                                                                                                                                                                                  --------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ........hhh.hhh.......................eeeeeeeeeee.......hhhhhhhhhhhhhhh..--....hhhhhhhh.......hhh...........hhhhhhhhhhhhhhhhhhh......eeeeee..hhhhhhhhhhhhhhhhhhhhhheeeeee...hhh.............--..hhh.....hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh.....hhhhh..hhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.hhhh..eeeeee.hhhhhhhhhhh.....................hhh......eeeeeeeee........eeeeeeee..eee........hhh...hhhhhhhhhhh...hhhh....................................... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------HIS_ACID_PHOSPH---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------HIS_ACID_PHOSPHAT------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qfx B  14 KQFSQEFRDGYSILKHYGGNGPYSERVSYGIARDPPTSCEVDQVIMVKRHGERYPSPSAGKDIEEALAKVYSI--TEYKGDLAFLNDWTYYVPNECYYNAETTSGPYAGLLDAYNHGNDYKARYGHLWNGETVVPFFSSGYGRVIETARKFGEGFFGYNYSTNAALNIISESEVMGADSLTPTCDTDN--TTCDNLTYQLPQFKVAAARLNSQNPGMNLTASDVYNLMVMASFELNARPFSNWINAFTQDEWVSFGYVEDLNYYYCAGPGDKNMAAVGAVYANASLTLLNQGPKEAGSLFFNFAHDTNITPILAALGVLIPNEDLPLDRVAFGNPYSIGNIVPMGGHLTIERLSCQATALSDEGTYVRLVLNEAVLPFNDCTSGPGYSCPLANYTSILNKNLPDYTTTCNVSASYPQYLSFWWNYNTTTELNYRSSPIACQEGDAMD 460
                                    23        33        43        53        63        73        83  |  |  93       103       113       123       133       143       153       163       173       183       193       | -|      213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       
                                                                                                   86 89                                                                                                             201  |                                                                                                                                                                                                                                                                
                                                                                                                                                                                                                        204
   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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Architecture: 3-Layer(aba) Sandwich (12045)
(-)
Topology: Rossmann fold (7312)
(-)
Homologous Superfamily: Phosphoglycerate mutase-like (91)
(-)
Aspergillus niger. Organism_taxid: 5061. Strain: nw205 (1)
1a1qfxA02A:36-63,A:121-198,A:285-331,A:356-460
1b1qfxB02B:36-63,B:121-200,B:285-331,B:356-460

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: PGM (50)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (PHYB_ASPAW | P34755)
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.

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  1qfx
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  PHYB_ASPAW | P34755
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