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(-) Description

Title :  CRYSTAL STRUCTURE OF BARLEY BETA-D-GLUCAN GLUCOHYDROLASE ISOENZYME EXO1 IN COMPLEX WITH 4'-NITROPHENYL 3I-THIOLAMINARITRIOSIDE
 
Authors :  M. Hrmova, R. De Gori, B. J. Smith, J. K. Fairweather, H. Driguez, J. N. V G. B. Fincher
Date :  22 May 01  (Deposition) - 12 Jun 02  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A
Keywords :  2-Domain Fold, Ligand-Protein Complex, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Hrmova, R. De Gori, B. J. Smith, J. K. Fairweather, H. Driguez, J. N. Varghese, G. B. Fincher
Structural Basis For Broad Substrate Specificity In Higher Plant Beta-D-Glucan Glucohydrolases.
Plant Cell V. 14 1033 2002
PubMed-ID: 12034895  |  Reference-DOI: 10.1105/TPC.010442

(-) Compounds

Molecule 1 - BETA-D-GLUCAN GLUCOHYDROLASE ISOENZYME EXO1
    Chains: A
    EC Number: 3.2.1.58
    Organism Scientific: HORDEUM VULGARE
    Organism Taxid: 4513
    Strain: CULTIVAR CLIPPER
    Synonym: BETA-D-GLUCAN EXOHYDROLASE ISOENZYME EXOI

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 12)

Asymmetric/Biological Unit (5, 12)
No.NameCountTypeFull Name
1BMA2Ligand/IonBETA-D-MANNOSE
2FUC1Ligand/IonALPHA-L-FUCOSE
3LAM1Ligand/Ion4'-NITROPHENYL-S-(BETA-D-GLUCOPYRANOSYL)-(1-3)-(3-THIO-BETA-D-GLUCOPYRANOSYL)-(1-3)-BETA-D-GLUCOPYRANOSIDE
4MAN1Ligand/IonALPHA-D-MANNOSE
5NAG7Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:220 , ASN A:221 , ASN A:222 , NAG A:611 , HOH A:822 , HOH A:927BINDING SITE FOR RESIDUE NAG A 610
02AC2SOFTWARETHR A:294 , NAG A:610 , BMA A:612BINDING SITE FOR RESIDUE NAG A 611
03AC3SOFTWARENAG A:611BINDING SITE FOR RESIDUE BMA A 612
04AC4SOFTWAREASN A:496 , ASN A:498 , THR A:500 , NAG A:614 , FUC A:616 , HOH A:806BINDING SITE FOR RESIDUE NAG A 613
05AC5SOFTWARENAG A:613 , BMA A:615 , FUC A:616 , MAN A:617BINDING SITE FOR RESIDUE NAG A 614
06AC6SOFTWARENAG A:614 , MAN A:617BINDING SITE FOR RESIDUE BMA A 615
07AC7SOFTWARENAG A:613 , NAG A:614 , MAN A:617 , HOH A:806BINDING SITE FOR RESIDUE FUC A 616
08AC8SOFTWAREHIS A:487 , NAG A:614 , BMA A:615 , FUC A:616 , NAG A:618 , HOH A:881BINDING SITE FOR RESIDUE MAN A 617
09AC9SOFTWARETYR A:425 , HIS A:487 , GLU A:503 , MAN A:617 , HOH A:841 , HOH A:906BINDING SITE FOR RESIDUE NAG A 618
10BC1SOFTWARETHR A:598 , ASN A:600 , NAG A:620 , HOH A:891BINDING SITE FOR RESIDUE NAG A 619
11BC2SOFTWARENAG A:619BINDING SITE FOR RESIDUE NAG A 620
12BC3SOFTWAREGLY A:56 , GLY A:57 , ASP A:95 , ARG A:158 , LYS A:206 , HIS A:207 , MET A:250 , TYR A:253 , ASP A:285 , TRP A:286 , ARG A:291 , MET A:316 , TRP A:434 , GLU A:491BINDING SITE FOR RESIDUE LAM A 621

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:151 -A:159
2A:513 -A:518

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1Ala A:145 -Pro A:146
2Lys A:206 -His A:207
3Phe A:208 -Val A:209
4Thr A:294 -Pro A:295
5Val A:317 -Pro A:318
6Leu A:404 -Pro A:405
7Glu A:503 -Pro A:504
8Leu A:578 -Pro A:579

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1J8V)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1J8V)

(-) Exons   (0, 0)

(no "Exon" information available for 1J8V)

(-) 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:602
 aligned with Q9XEI3_HORVV | Q9XEI3 from UniProtKB/TrEMBL  Length:630

    Alignment length:602
                                    35        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       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625  
         Q9XEI3_HORVV    26 DYVLYKDATKPVEDRVADLLGRMTLAEKIGQMTQIERLVATPDVLRDNFIGSLLSGGGSVPRKGATAKEWQDMVDGFQKACMSTRLGIPMIYGIDAVHGQNNVYGATIFPHNVGLGATRDPYLVKRIGEATALEVRATGIQYAFAPCIAVCRDPRWGRCYESYSEDRRIVQSMTELIPGLQGDVPKDFTSGMPFVAGKNKVAACAKHFVGDGGTVDGINENNTIINREGLMNIHMPAYKNAMDKGVSTVMISYSSWNGVKMHANQDLVTGYLKDTLKFKGFVISDWEGIDRITTPAGSDYSYSVKASILAGLDMIMVPNNYQQFISILTGHVNGGVIPMSRIDDAVTRILRVKFTMGLFENPYADPAMAEQLGKQEHRDLAREAARKSLVLLKNGKTSTDAPLLPLPKKAPKILVAGSHADNLGYQCGGWTIEWQGDTGRTTVGTTILEAVKAAVDPSTVVVFAENPDAEFVKSGGFSYAIVAVGEHPYTETKGDNLNLTIPEPGLSTVQAVCGGVRCATVLISGRPVVVQPLLAASDALVAAWLPGSEGQGVTDALFGDFGFTGRLPRTWFKSVDQLPMNVGDAHYDPLFRLGYGLTTNAT 627
               SCOP domains d1j8va1 A:1-388 Beta-D-glucan exohydrolase, N-terminal domain                                                                                                                                                                                                                                                                                                                                       d1j8va2 A:389-602 Beta-D-glucan exohydrolase, C-terminal domain                                                                                                                                                        SCOP domains
               CATH domains 1j8vA01 A:1-373  [code=3.20.20.300, no name defined]                                                                                                                                                                                                                                                                                                                                 1j8vA02 A:374-559  [code=3.40.50.1700, no name defined]                                                                                                                                   ------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh...hhhhhhhhhhh..hhhhhhhhheeee.hhhhhhhhhhh...eeee..........hhhhhhhhhhhhhhhhhh.......eeee................hhhhhhh..hhhhhhhhhhhhhhhhhh....ee..............hhhhh...hhhhhhhh.hhhhhhhh.....................eeeee.hhhhhhhhh...ee..hhhhhhhh.hhhhhhhhhh...eeee...ee..ee...hhhhhh...........eee.....hhhhh.....hhhhhhhhhhhhh...ee...hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh........hhhhhhhh.hhhhhhhhhhhhhhhheeeee.................eeeee.....hhhhhhh.................hhhhhhhhhh....eeeee...hhhhhhh.....eeeeee....hhhhhh.........hhhhhhhhhhhh.eeeeee......hhhhhhhh.eeeeee.....hhhhhhhhh...............hhhhh........................ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1j8v A   1 DYVLYKDATKPVEDRVADLLGRMTLAEKIGQMTQIERLVATPDVLRDNFIGSLLSGGGSVPRKGATAKEWQDMVDGFQKACMSTRLGIPMIYGIDAVHGQNNVYGATIFPHNVGLGATRDPYLVKRIGEATALEVRATGIQYAFAPCIAVCRDPRWGRCYESYSEDRRIVQSMTELIPGLQGDVPKDFTSGMPFVAGKNKVAACAKHFVGDGGTVDGINENNTIINREGLMNIHMPAYKNAMDKGVSTVMISYSSWNGVKMHANQDLVTGYLKDTLKFKGFVISDWEGIDRITTPAGSDYSYSVKASILAGLDMIMVPNKYQQFISILTGHVNGGVIPMSRIDDAVTRILRVKFTMGLFENPYADPAMAEQLGKQEHRDLAREAARKSLVLLKNGKTSTDAPLLPLPKKAPKILVAGSHADNLGYQCGGWTIEWQGDTGRTTVGTTILEAVKAAVDPSTVVVFAENPDAEFVKSGGFSYAIVAVGEHPYTETKGDNLNLTIPEPGLSTVQAVCGGVRCATVLISGRPVVVQPLLAASDALVAAWLPGSEGQGVTDALFGDFGFTGRLPRTWFKSVDQLPMNVGDAHYDPLFRLGYGLTTNAT 602
                                    10        20        30        40        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       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600
   Legend:   → Mismatch (orange background)
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  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  (2, 2)

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

(-) CATH Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1J8V)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q9XEI3_HORVV | Q9XEI3)
molecular function
    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: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.

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    Leu A:578 - Pro A:579   [ RasMol ]  
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  1j8v
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  3.2.1.58
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 Related Entries

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

UniProtKB/TrEMBL
        Q9XEI3_HORVV | Q9XEI3: 1ex1 1ieq 1iev 1iew 1iex 1lq2 1x38 1x39 3wlh 3wli 3wlj 3wlk 3wll 3wlm 3wln 3wlo 3wlp 3wlq 3wlr 3wls 3wlt

(-) Related Entries Specified in the PDB File

1ex1 THREE-DIMENSIONAL STRUCTURE OF BARLEY BETA-D-GLUCAN EXOHYDROLASE, A FAMILY 3 GLYCOSYL HYDROLASE
1ieq THE ENTRY CONTAINS THE SAME PROTEIN WITH BOUND GLUCOSE