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(-) Description

Title :  CRYSTAL STRUCTURE OF EXO-1,3-BETA GLUCANSE FROM SACCHAROMYCES CEREVISIAE
 
Authors :  A. D. Ferguson
Date :  11 May 01  (Deposition) - 02 Oct 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Hydrolase, Glucan Degradation, Hydrolyase, Glycosidase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. C. Taylor, A. D. Ferguson, J. J. M. Bergeron, D. Y. Thomas
The Er Protein Folding Sensor Udp-Glucose Glycoprotein:Glucosyltransferase Modifies Substrates Distant To Local Changes In Glycoprotein Conformation.
Nat. Struct. Mol. Biol. V. 11 128 2004
PubMed-ID: 14730348  |  Reference-DOI: 10.1038/NSMB715

(-) Compounds

Molecule 1 - GLUCAN 1,3-BETA-GLUCOSIDASE I/II
    Chains: A, B
    EC Number: 3.2.1.58
    Engineered: YES
    Expression System: SACCHAROMYCES CEREVISIAE
    Expression System Taxid: 4932
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Other Details: TWO MAN9GLCNAC GLYCAN CHAINS ARE LOCATED AT RESIDUES N165 AND N325
    Synonym: EXO-1,3-BETA GLUCANASE I/II

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 34)

Asymmetric Unit (5, 34)
No.NameCountTypeFull Name
1BMA8Ligand/IonBETA-D-MANNOSE
2GOL9Ligand/IonGLYCEROL
3MAN9Ligand/IonALPHA-D-MANNOSE
4NAG7Ligand/IonN-ACETYL-D-GLUCOSAMINE
5NDG1Ligand/Ion2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
Biological Unit 1 (4, 19)
No.NameCountTypeFull Name
1BMA6Ligand/IonBETA-D-MANNOSE
2GOL4Ligand/IonGLYCEROL
3MAN5Ligand/IonALPHA-D-MANNOSE
4NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
5NDG-1Ligand/Ion2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
Biological Unit 2 (5, 15)
No.NameCountTypeFull Name
1BMA2Ligand/IonBETA-D-MANNOSE
2GOL5Ligand/IonGLYCEROL
3MAN4Ligand/IonALPHA-D-MANNOSE
4NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE
5NDG1Ligand/Ion2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE

(-) Sites  (34, 34)

Asymmetric Unit (34, 34)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:116 , GLY A:161 , TRP A:162 , ASN A:165 , NAG A:1454BINDING SITE FOR RESIDUE NAG A1453
02AC2SOFTWAREGLN A:158 , NAG A:1453 , BMA A:1455 , BMA A:1461BINDING SITE FOR RESIDUE NAG A1454
03AC3SOFTWARENAG A:1454 , BMA A:1456 , MAN A:1457 , BMA A:1461 , BMA A:1462BINDING SITE FOR RESIDUE BMA A1455
04AC4SOFTWAREBMA A:1455 , BMA A:1462BINDING SITE FOR RESIDUE BMA A1456
05AC5SOFTWAREBMA A:1455 , BMA A:1458 , MAN A:1459 , MAN A:1460 , BMA A:1461BINDING SITE FOR RESIDUE MAN A1457
06AC6SOFTWAREMAN A:1457 , MAN A:1459BINDING SITE FOR RESIDUE BMA A1458
07AC7SOFTWAREMAN A:1457 , BMA A:1458BINDING SITE FOR RESIDUE MAN A1459
08AC8SOFTWAREMAN A:1457 , BMA A:1461 , BMA A:1462BINDING SITE FOR RESIDUE MAN A1460
09AC9SOFTWARENAG A:1454 , BMA A:1455 , MAN A:1457 , MAN A:1460 , BMA A:1462BINDING SITE FOR RESIDUE BMA A1461
10BC1SOFTWAREBMA A:1455 , BMA A:1456 , MAN A:1460 , BMA A:1461BINDING SITE FOR RESIDUE BMA A1462
11BC2SOFTWAREASN A:275 , ASN A:325 , NAG A:1464BINDING SITE FOR RESIDUE NAG A1463
12BC3SOFTWAREASN A:275 , ASP A:278 , NAG A:1463 , MAN A:1465 , HOH A:2228BINDING SITE FOR RESIDUE NAG A1464
13BC4SOFTWAREASN A:275 , TYR A:276 , ASP A:279 , NAG A:1464 , MAN A:1466 , BMA A:1467BINDING SITE FOR RESIDUE MAN A1465
14BC5SOFTWARETYR A:276 , ASP A:279 , MAN A:1465BINDING SITE FOR RESIDUE MAN A1466
15BC6SOFTWAREPRO A:273 , MAN A:1465BINDING SITE FOR RESIDUE BMA A1467
16BC7SOFTWAREGLU B:116 , GLY B:161 , TRP B:162 , ASN B:165 , NAG B:1455BINDING SITE FOR RESIDUE NAG B1454
17BC8SOFTWAREGLN B:158 , NAG B:1454 , MAN B:1456BINDING SITE FOR RESIDUE NAG B1455
18BC9SOFTWAREALA A:379 , NAG B:1455 , MAN B:1457 , MAN B:1458 , MAN B:1461BINDING SITE FOR RESIDUE MAN B1456
19CC1SOFTWAREMAN B:1456 , MAN B:1461BINDING SITE FOR RESIDUE MAN B1457
20CC2SOFTWARETYR A:380 , MAN B:1456 , BMA B:1459 , BMA B:1460BINDING SITE FOR RESIDUE MAN B1458
21CC3SOFTWARETYR A:380 , SER B:154 , MAN B:1458 , BMA B:1460BINDING SITE FOR RESIDUE BMA B1459
22CC4SOFTWAREMAN B:1458 , BMA B:1459 , MAN B:1461BINDING SITE FOR RESIDUE BMA B1460
23CC5SOFTWAREMAN B:1456 , MAN B:1457 , BMA B:1460BINDING SITE FOR RESIDUE MAN B1461
24CC6SOFTWAREASN B:325 , NDG B:1463 , HOH B:2161BINDING SITE FOR RESIDUE NAG B1462
25CC7SOFTWARENAG B:1462BINDING SITE FOR RESIDUE NDG B1463
26CC8SOFTWARETRP A:288 , GLY A:289 , VAL A:290 , HIS A:328 , TRP A:329 , HOH A:2224 , HOH A:2225BINDING SITE FOR RESIDUE GOL A1449
27CC9SOFTWAREGLU A:65 , TYR A:67 , HIS A:175 , ASN A:186 , TRP A:409 , HOH A:2158BINDING SITE FOR RESIDUE GOL A1450
28DC1SOFTWAREASP A:45 , GLU A:283 , SER A:327 , HIS A:328 , ARG A:403 , HOH A:2226BINDING SITE FOR RESIDUE GOL A1451
29DC2SOFTWAREASN A:121 , GLN A:125 , TYR A:411 , GLN A:422 , HOH A:2227 , GLN B:117 , ASN B:121 , GOL B:1452BINDING SITE FOR RESIDUE GOL A1452
30DC3SOFTWAREGLU B:65 , TYR B:67 , HIS B:175 , ASN B:186 , TYR B:297 , GLU B:334 , TRP B:409 , HOH B:2166BINDING SITE FOR RESIDUE GOL B1449
31DC4SOFTWARETRP B:288 , GLY B:289 , VAL B:290 , HIS B:328 , TRP B:329 , HOH B:2004 , HOH B:2135BINDING SITE FOR RESIDUE GOL B1450
32DC5SOFTWARETHR A:435 , ARG A:437 , HOH A:2222 , ASP B:398 , GLU B:401 , THR B:435 , ARG B:437 , HOH B:2225BINDING SITE FOR RESIDUE GOL B1451
33DC6SOFTWAREGLN A:117 , ASN A:121 , GOL A:1452 , ASN B:121 , GLN B:125 , TYR B:411 , GLN B:422 , HOH B:2205 , HOH B:2226BINDING SITE FOR RESIDUE GOL B1452
34DC7SOFTWAREHOH B:2124 , HOH B:2174 , HOH B:2227BINDING SITE FOR RESIDUE GOL B1453

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:317 -A:443
2A:342 -A:372
3B:317 -B:443
4B:342 -B:372

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gln A:432 -Pro A:433
2Gln B:432 -Pro B:433

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1H4P)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLYCOSYL_HYDROL_F5PS00659 Glycosyl hydrolases family 5 signature.EXG1_YEAST225-234
 		  2A:225-234
B:225-234
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLYCOSYL_HYDROL_F5PS00659 Glycosyl hydrolases family 5 signature.EXG1_YEAST225-234
 		  1A:225-234
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLYCOSYL_HYDROL_F5PS00659 Glycosyl hydrolases family 5 signature.EXG1_YEAST225-234
 		  1-
B:225-234

(-) Exons   (1, 2)

Asymmetric Unit (1, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YLR300W1YLR300W.1XII:728957-7303031347EXG1_YEAST1-4484482A:41-448
B:41-448		408
408

(-) 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:408
 aligned with EXG1_YEAST | P23776 from UniProtKB/Swiss-Prot  Length:448

    Alignment length:408
                                    50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440        
           EXG1_YEAST    41 YYDYDHGSLGEPIRGVNIGGWLLLEPYITPSLFEAFRTNDDNDEGIPVDEYHFCQYLGKDLAKSRLQSHWSTFYQEQDFANIASQGFNLVRIPIGYWAFQTLDDDPYVSGLQESYLDQAIGWARNNSLKVWVDLHGAAGSQNGFDNSGLRDSYKFLEDSNLAVTTNVLNYILKKYSAEEYLDTVIGIELINEPLGPVLDMDKMKNDYLAPAYEYLRNNIKSDQVIIIHDAFQPYNYWDDFMTENDGYWGVTIDHHHYQVFASDQLERSIDEHIKVACEWGTGVLNESHWTVCGEFAAALTDCTKWLNSVGFGARYDGSWVNGDQTSSYIGSCANNDDIAYWSDERKENTRRYVEAQLDAFEMRGGWIIWCYKTESSLEWDAQRLMFNGLFPQPLTDRKYPNQCGTISN 448
               SCOP domains d1h4pa_ A: Exo-beta-(1,3)-glucanase                                                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1h4pA00 A:41-448 Glycosidases                                                                                                                                                                                                                                                                                                                                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ............eeeee...........hhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee.hhh...........hhhhhhhhhhhhhhhh..eeeeeeee.......hhhhh........hhhhhhhhhhhhhhhhhhh.hhhhhh.eeeee.....hhhhhhhhhhhhhhhhhhhhhhhhh......eeee......hhhhhh.hhhhh...eeeeeee....hhhhhh.hhhhhhhhhhhhhhhhh....eeeeeee.........................................hhhhhhhhhhhhhhhhhhhhhhhhh...eeee...........hhhhhhhh.............hhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GLYCOSYL_H---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:41-448 UniProt: 1-448 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                      Transcript 1
                 1h4p A  41 YYDYDHGSLGEPIRGVNIGGWLLLEPYITPSLFEAFRTNDDNDEGIPVDEYHFCQYLGKDLAKSRLQSHWSTFYQEQDFANIASQGFNLVRIPIGYWAFQILDDDPYVSGLQESYLDQAIGWARNNSLKVWVDLHGAAGSQNGFDNSGLRDSYKFLEDSNLAVTINVLNYILKKYSAEEYLDIVIGIELINEPLGPVLDMDKMKNDYLAPAYEYLRNNIKSDQVIIIHDAFQPYNYWDDFMTENDGYWGVTIDHHHYQVFASDQLERSIDEHIKVACEWGTGVLNESHWIVCGEFAAALTDCIKWLNSVGFGARYDGSWVNGDQTSSYIGSCANNDDIAYWSDERKENTRRYVEAQLDAFEMRGGWIIWCYKTESSLEWDAQRLMFNGLFPQPLTDRKYPNQCGTISN 448
                                    50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440        


Chain B from PDB  Type:PROTEIN  Length:408
 aligned with EXG1_YEAST | P23776 from UniProtKB/Swiss-Prot  Length:448

    Alignment length:408
                                    50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440        
           EXG1_YEAST    41 YYDYDHGSLGEPIRGVNIGGWLLLEPYITPSLFEAFRTNDDNDEGIPVDEYHFCQYLGKDLAKSRLQSHWSTFYQEQDFANIASQGFNLVRIPIGYWAFQTLDDDPYVSGLQESYLDQAIGWARNNSLKVWVDLHGAAGSQNGFDNSGLRDSYKFLEDSNLAVTTNVLNYILKKYSAEEYLDTVIGIELINEPLGPVLDMDKMKNDYLAPAYEYLRNNIKSDQVIIIHDAFQPYNYWDDFMTENDGYWGVTIDHHHYQVFASDQLERSIDEHIKVACEWGTGVLNESHWTVCGEFAAALTDCTKWLNSVGFGARYDGSWVNGDQTSSYIGSCANNDDIAYWSDERKENTRRYVEAQLDAFEMRGGWIIWCYKTESSLEWDAQRLMFNGLFPQPLTDRKYPNQCGTISN 448
               SCOP domains d1h4pb_ B: Exo-beta-(1,3)-glucanase                                                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1h4pB00 B:41-448 Glycosidases                                                                                                                                                                                                                                                                                                                                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ............eeeee...........hhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhh...eeeeeee.hhh...........hhhhhhhhhhhhhhhh..eeeeeeee.......hhhhh........hhhhhhhhhhhhhhhhhhh.hhhhhh.eeeee.....hhhhhhhhhhhhhhhhhhhhhhhhh......eeee.....................eeeeeee....hhhhhh.hhhhhhhhhhhhhhh......eeeeeee........................ee..ee...........hhhhhhhhhhhhhhhhhhhhhhhhh...eeee...........hhhhhhhh..................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GLYCOSYL_H---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:41-448 UniProt: 1-448 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                      Transcript 1
                 1h4p B  41 YYDYDHGSLGEPIRGVNIGGWLLLEPYITPSLFEAFRTNDDNDEGIPVDEYHFCQYLGKDLAKSRLQSHWSTFYQEQDFANIASQGFNLVRIPIGYWAFQILDDDPYVSGLQESYLDQAIGWARNNSLKVWVDLHGAAGSQNGFDNSGLRDSYKFLEDSNLAVTINVLNYILKKYSAEEYLDIVIGIELINEPLGPVLDMDKMKNDYLAPAYEYLRNNIKSDQVIIIHDAFQPYNYWDDFMTENDGYWGVTIDHHHYQVFASDQLERSIDEHIKVACEWGTGVLNESHWIVCGEFAAALTDCIKWLNSVGFGARYDGSWVNGDQTSSYIGSCANNDDIAYWSDERKENTRRYVEAQLDAFEMRGGWIIWCYKTESSLEWDAQRLMFNGLFPQPLTDRKYPNQCGTISN 448
                                    50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440
   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)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1H4P)

(-) Gene Ontology  (14, 14)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (EXG1_YEAST | P23776)
molecular function
    GO:0004338    glucan exo-1,3-beta-glucosidase activity    Catalysis of the successive hydrolysis of beta-D-glucose units from the non-reducing ends of (1->3)-beta-D-glucans, releasing alpha-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:0004553    hydrolase activity, hydrolyzing O-glycosyl compounds    Catalysis of the hydrolysis of any O-glycosyl bond.
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:0071555    cell wall organization    A process that results in the assembly, arrangement of constituent parts, or disassembly of the cell wall, the rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis.
    GO:0006073    cellular glucan metabolic process    The chemical reactions and pathways involving glucans, polysaccharides consisting only of glucose residues, occurring at the level of an individual cell.
    GO:0031505    fungal-type cell wall organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the fungal-type cell wall.
    GO:0009251    glucan catabolic process    The chemical reactions and pathways resulting in the breakdown of glucans, polysaccharides consisting only of glucose residues.
    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.
cellular component
    GO:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    GO:0005618    cell wall    The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, most prokaryotic cells and some protozoan parasites, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan; in protozoan parasites such as Giardia species, it's made of carbohydrates and proteins.
    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.
    GO:0009277    fungal-type cell wall    A rigid yet dynamic structure surrounding the plasma membrane that affords protection from stresses and contributes to cell morphogenesis, consisting of extensively cross-linked glycoproteins and carbohydrates. The glycoproteins may be modified with N- or O-linked carbohydrates, or glycosylphosphatidylinositol (GPI) anchors; the polysaccharides are primarily branched glucans, including beta-linked and alpha-linked glucans, and may also include chitin and other carbohydrate polymers, but not cellulose or pectin. Enzymes involved in cell wall biosynthesis are also found in the cell wall. Note that some forms of fungi develop a capsule outside of the cell wall under certain circumstances; this is considered a separate structure.

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  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
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  1h4p
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  3.2.1.58
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 Related Entries

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