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(-) Description

Title :  CATALYTIC DOMAIN OF GLUCOAMYLASE FROM ASPERGILLUS NIGER COMPLEXED WITH TRIS AND GLYCEROL
 
Authors :  J. Lee, M. Paetzel
Date :  30 Sep 08  (Deposition) - 13 Oct 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase, Glycoprotein, Glycosidase, Polysaccharide Degradation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Lee, M. Paetzel
Structure Of The Catalytic Domain Of Glucoamylase From Aspergillus Niger.
Acta Crystallogr. , Sect. F V. 67 188 2011
PubMed-ID: 21301084  |  Reference-DOI: 10.1107/S1744309110049390

(-) Compounds

Molecule 1 - GLUCOAMYLASE
    Chains: A
    EC Number: 3.2.1.3
    Fragment: CATALYTIC DOMAIN (RESIDUES 25-494)
    Organism Scientific: ASPERGILLUS NIGER
    Organism Taxid: 5061
    Other Details: PREPARED BY SUBTILISIN C-TERMINAL CLEAVAGE, COMPLEXED WITH TRIS AND GLYCEROL
    Other Details - Source: GENE GLAA
    Synonym: GLUCAN 1,4-ALPHA-GLUCOSIDASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 21)

Asymmetric/Biological Unit (5, 21)
No.NameCountTypeFull Name
1BMA2Ligand/IonBETA-D-MANNOSE
2GOL1Ligand/IonGLYCEROL
3MAN13Ligand/IonALPHA-D-MANNOSE
4NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
5TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

(-) Sites  (21, 21)

Asymmetric Unit (21, 21)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:195 , THR A:197 , TYR A:247 , NAG A:502 , HOH A:1047 , HOH A:1085 , HOH A:1105 , HOH A:1148 , HOH A:1185BINDING SITE FOR RESIDUE NAG A 501
02AC2SOFTWARECYS A:473 , NAG A:501 , BMA A:503 , HOH A:1223 , HOH A:1373BINDING SITE FOR RESIDUE NAG A 502
03AC3SOFTWARENAG A:502 , MAN A:504 , HOH A:1383BINDING SITE FOR RESIDUE BMA A 503
04AC4SOFTWARESER A:250 , TRP A:252 , PHE A:261 , BMA A:503 , HOH A:1351BINDING SITE FOR RESIDUE MAN A 504
05AC5SOFTWAREVAL A:37 , TRP A:52 , ASN A:419 , SER A:421 , ASP A:438 , NAG A:552 , HOH A:1290BINDING SITE FOR RESIDUE NAG A 551
06AC6SOFTWAREARG A:437 , NAG A:551 , BMA A:553 , MAN A:571 , MAN A:572 , HOH A:1107 , HOH A:1171 , HOH A:1179 , HOH A:1290 , HOH A:1377BINDING SITE FOR RESIDUE NAG A 552
07AC7SOFTWARENAG A:552 , MAN A:554 , MAN A:571 , HOH A:1256 , HOH A:1331BINDING SITE FOR RESIDUE BMA A 553
08AC8SOFTWAREBMA A:553 , MAN A:555 , HOH A:1340BINDING SITE FOR RESIDUE MAN A 554
09AC9SOFTWAREVAL A:53 , SER A:54 , PRO A:65 , PHE A:73 , MAN A:554 , MAN A:556 , HOH A:1161 , HOH A:1340BINDING SITE FOR RESIDUE MAN A 555
10BC1SOFTWAREMAN A:555BINDING SITE FOR RESIDUE MAN A 556
11BC2SOFTWARENAG A:552 , BMA A:553 , MAN A:572 , HOH A:1240BINDING SITE FOR RESIDUE MAN A 571
12BC3SOFTWARESER A:66 , ASN A:69 , SER A:435 , ARG A:437 , NAG A:552 , MAN A:571 , HOH A:1146 , HOH A:1229BINDING SITE FOR RESIDUE MAN A 572
13BC4SOFTWAREASP A:287 , GLU A:463 , THR A:464 , SER A:465 , ALA A:466 , SER A:467 , SER A:468 , HOH A:1221 , HOH A:1232BINDING SITE FOR RESIDUE MAN A 600
14BC5SOFTWARESER A:468 , PRO A:470BINDING SITE FOR RESIDUE MAN A 601
15BC6SOFTWARETHR A:476 , SER A:477 , MAN A:603 , HOH A:1296BINDING SITE FOR RESIDUE MAN A 602
16BC7SOFTWARESER A:477 , MAN A:602 , HOH A:1079 , HOH A:1272BINDING SITE FOR RESIDUE MAN A 603
17BC8SOFTWAREARG A:184 , ASP A:369 , SER A:483 , SER A:484 , MAN A:606 , HOH A:1238 , HOH A:1258 , HOH A:1300 , HOH A:1338BINDING SITE FOR RESIDUE MAN A 604
18BC9SOFTWAREALA A:110 , ILE A:111 , GLY A:114 , SER A:484 , VAL A:485 , HOH A:1167BINDING SITE FOR RESIDUE MAN A 605
19CC1SOFTWAREASP A:369 , VAL A:370 , SER A:484 , THR A:486 , MAN A:604 , HOH A:1300BINDING SITE FOR RESIDUE MAN A 606
20CC2SOFTWARETRP A:76 , ARG A:78 , ASP A:79 , LEU A:201 , GLU A:203 , GOL A:801BINDING SITE FOR RESIDUE TRS A 701
21CC3SOFTWARETYR A:72 , SER A:97 , TRP A:202 , GLU A:203 , GLU A:204 , ARG A:329 , TRS A:701 , HOH A:1420BINDING SITE FOR RESIDUE GOL A 801

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1A:234 -A:237
2A:246 -A:473
3A:286 -A:294

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Gly A:47 -Ala A:48
2Asn A:69 -Pro A:70
3Arg A:146 -Pro A:147
4Phe A:261 -Asp A:262

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLUCOAMYLASEPS00820 Glucoamylase active site region signature.AMYG_ASPNG197-207  1A:197-207

(-) Exons   (0, 0)

(no "Exon" information available for 3EQA)

(-) 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
(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:458
 aligned with AMYG_ASPNG | P69328 from UniProtKB/Swiss-Prot  Length:640

    Alignment length:458
                                    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       469       479        
           AMYG_ASPNG    30 WLSNEATVARTAILNNIGADGAWVSGADSGIVVASPSTDNPDYFYTWTRDSGLVLKTLVDLFRNGDTSLLSTIENYISAQAIVQGISNPSGDLSSGAGLGEPKFNVDETAYTGSWGRPQRDGPALRATAMIGFGQWLLDNGYTSTATDIVWPLVRNDLSYVAQYWNQTGYDLWEEVNGSSFFTIAVQHRALVEGSAFATAVGSSCSWCDSQAPEILCYLQSFWTGSFILANFDSSRSGKDANTLLGSIHTFDPEAACDDSTFQPCSPRALANHKEVVDSFRSIYTLNDGLSDSEAVAVGRYPEDTYYNGNPWFLCTLAAAEQLYDALYQWDKQGSLEVTDVSLDFFKALYSDAATGTYSSSSSTYSSIVDAVKTFADGFVSIVETHAASNGSMSEQYDKSDGEQLSARDLTWSYAALLTANNRRNSVVPASWGETSASSVPGTCAATSAIGTYSSVTV 487
               SCOP domains d3eqaa_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhh.............................eehhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh...........hhhhhh.eee...ee.........hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh...ee......eeeehhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.......ee.......hhhhhhhhhhh.......hhhhh...hhhhhhhhhhhhhh....hhhhh................hhhhh..hhhhhhhhhhhhhhhhhhhhhhheeee...hhhhhhhhh.....eeee..hhhhhhhhhhhhhhhhhhhhhhhhhh........ee......ee....hhhhhhhhhhhhhhhh.......hhhhh..................... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------GLUCOAMYLAS---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3eqa A  30 WLSNEATVARTAILNNIGADGAWVSGADSGIVVASPSTDNPDYFYTWTRDSGLVLKTLVDLFRNGDTSLLSTIENYISAQAIVQGISNPSGDLSSGAGLGEPKFNVDETAYTGSWGRPQRDGPALRATAMIGFGQWLLDNGYTSTATDIVWPLVRNDLSYVAQYWNQTGYDLWEEVNGSSFFTIAVQHRALVEGSAFATAVGSSCSWCDSQAPEILCYLQSFWTGSFILANFDSSRSGKDANTLLGSIHTFDPEAACDDSTFQPCSPRALANHKEVVDSFRSIYTLNDGLSDSEAVAVGRYPEDTYYNGNPWFLCTLAAAEQLYDALYQWDKQGSLEVTDVSLDFFKALYSDAATGTYSSSSSTYSSIVDAVKTFADGFVSIVETHAASNGSMSEQYDKSDGEQLSARDLTWSYAALLTANNRRNSVVPASWGETSASSVPGTCAATSAIGTYSSVTV 487
                                    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       469       479
   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, 1)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3EQA)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (AMYG_ASPNG | P69328)
molecular function
    GO:0030246    carbohydrate binding    Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0004339    glucan 1,4-alpha-glucosidase activity    Catalysis of the hydrolysis of terminal (1->4)-linked alpha-D-glucose residues successively from non-reducing ends of the chains with release of beta-D-glucose.
    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:0016798    hydrolase activity, acting on glycosyl bonds    Catalysis of the hydrolysis of any glycosyl bond.
    GO:2001070    starch binding    Interacting selectively and non-covalently with starch.
biological process
    GO:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0000272    polysaccharide catabolic process    The chemical reactions and pathways resulting in the breakdown of a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.
    GO:0005976    polysaccharide metabolic process    The chemical reactions and pathways involving a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.
cellular component
    GO:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        AMYG_ASPNG | P69328: 1ac0 1acz 1kul 1kum

(-) Related Entries Specified in the PDB File

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