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(-) Description

Title :  CRYSTAL STRUCTURE OF BARLEY BETA-D-GLUCAN GLUCOHYDROLASE ISOENZYME EXO1 IN COMPLEX WITH GLUCO-PHENYLIMIDAZOLE
 
Authors :  M. Hrmova, V. A. Streltsov, B. J. Smith, A. Vasella, J. N. Varghese, G. B.
Date :  02 May 05  (Deposition) - 20 Dec 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A
Keywords :  2-Domain Fold, Ligand-Protein Complex, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Hrmova, V. A. Streltsov, B. J. Smith, A. Vasella, J. N. Varghese, G. B. Fincher
Structural Rationale For Low-Nanomolar Binding Of Transitio State Mimics To A Family Gh3 Beta-D-Glucan Glucohydrolase From Barley.
Biochemistry V. 44 16529 2005
PubMed-ID: 16342944  |  Reference-DOI: 10.1021/BI0514818

(-) Compounds

Molecule 1 - BETA-D-GLUCAN EXOHYDROLASE ISOENZYME EXOI
    Chains: A
    EC Number: 3.2.1.58
    Fragment: RESIDUES 1-602
    Organism Scientific: HORDEUM VULGARE
    Organism Taxid: 4513
    Strain: CULTIVAR CLIPPER
    Synonym: BETA-D-GLUCAN GLUCOHYDROLASE ISOENZYME EXO1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (8, 19)

Asymmetric/Biological Unit (8, 19)
No.NameCountTypeFull Name
1BMA3Ligand/IonBETA-D-MANNOSE
2FUC2Ligand/IonALPHA-L-FUCOSE
3GOL2Ligand/IonGLYCEROL
4IDD1Ligand/Ion(5R,6R,7S,8S)-5-(HYDROXYMETHYL)-2-PHENYL-5,6,7,8-TETRAHYDROIMIDAZO[1,2-A]PYRIDINE-6,7,8-TRIOL
5MAN1Ligand/IonALPHA-D-MANNOSE
6NAG7Ligand/IonN-ACETYL-D-GLUCOSAMINE
7SO41Ligand/IonSULFATE ION
8XYP2Ligand/IonBETA-D-XYLOPYRANOSE

(-) Sites  (19, 19)

Asymmetric Unit (19, 19)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:220 , ASN A:221 , NAG A:2212 , HOH A:6365 , HOH A:6417 , HOH A:6518 , HOH A:6626 , HOH A:6653 , HOH A:6795BINDING SITE FOR RESIDUE NAG A 2211
02AC2SOFTWARETHR A:294 , NAG A:2211 , BMA A:2213 , HOH A:6626 , HOH A:6653BINDING SITE FOR RESIDUE NAG A 2212
03AC3SOFTWARENAG A:2212 , HOH A:6888BINDING SITE FOR RESIDUE BMA A 2213
04AC4SOFTWAREASN A:496 , ASN A:498 , THR A:500 , NAG A:4982 , FUC A:4984 , HOH A:6415 , HOH A:6562 , HOH A:6662 , HOH A:6698BINDING SITE FOR RESIDUE NAG A 4981
05AC5SOFTWARELYS A:493 , NAG A:4981 , BMA A:4983 , FUC A:4984 , MAN A:4985 , XYP A:4987 , HOH A:6576 , HOH A:6662 , HOH A:6693 , HOH A:6710BINDING SITE FOR RESIDUE NAG A 4982
06AC6SOFTWARENAG A:4982 , MAN A:4985 , XYP A:4987 , HOH A:6902BINDING SITE FOR RESIDUE BMA A 4983
07AC7SOFTWARENAG A:4981 , NAG A:4982 , MAN A:4985 , HOH A:6662 , HOH A:6699 , HOH A:6766BINDING SITE FOR RESIDUE FUC A 4984
08AC8SOFTWAREHIS A:487 , NAG A:4982 , BMA A:4983 , FUC A:4984 , NAG A:4986 , HOH A:6158 , HOH A:6317 , HOH A:6409 , HOH A:6576BINDING SITE FOR RESIDUE MAN A 4985
09AC9SOFTWARETYR A:425 , HIS A:487 , GLU A:503 , MAN A:4985 , HOH A:6310 , HOH A:6384 , HOH A:6528 , HOH A:6766 , HOH A:6914BINDING SITE FOR RESIDUE NAG A 4986
10BC1SOFTWARELYS A:493 , NAG A:4982 , BMA A:4983 , HOH A:6641 , HOH A:6710BINDING SITE FOR RESIDUE XYP A 4987
11BC2SOFTWARETHR A:598 , ASN A:600 , NAG A:6002 , FUC A:6004 , HOH A:6104 , HOH A:6197 , HOH A:6237 , HOH A:6649BINDING SITE FOR RESIDUE NAG A 6001
12BC3SOFTWARENAG A:6001 , BMA A:6003 , FUC A:6004 , XYP A:6005 , HOH A:6595BINDING SITE FOR RESIDUE NAG A 6002
13BC4SOFTWARENAG A:6002 , XYP A:6005 , HOH A:6586 , HOH A:6738 , HOH A:6927BINDING SITE FOR RESIDUE BMA A 6003
14BC5SOFTWARENAG A:6001 , NAG A:6002BINDING SITE FOR RESIDUE FUC A 6004
15BC6SOFTWARETHR A:118 , ARG A:119 , ASP A:120 , ARG A:566 , NAG A:6002 , BMA A:6003 , HOH A:6304 , HOH A:6504 , HOH A:6722 , HOH A:6738 , HOH A:6927BINDING SITE FOR RESIDUE XYP A 6005
16BC7SOFTWAREPRO A:338 , MET A:339 , SER A:340 , HOH A:6444 , HOH A:6757BINDING SITE FOR RESIDUE SO4 A 3001
17BC8SOFTWAREASP 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 , TRP A:430 , GLU A:491 , GOL A:2001 , HOH A:6735BINDING SITE FOR RESIDUE IDD A 1001
18BC9SOFTWAREGLY A:56 , GLY A:57 , TRP A:434 , IDD A:1001 , HOH A:6171 , HOH A:6180 , HOH A:6734 , HOH A:6735BINDING SITE FOR RESIDUE GOL A 2001
19CC1SOFTWAREARG A:119 , ARG A:566 , LEU A:593 , HOH A:6834 , HOH A:6849 , HOH A:6865 , HOH A:6918BINDING SITE FOR RESIDUE GOL A 2002

(-) 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 1X38)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1X38)

(-) Exons   (0, 0)

(no "Exon" information available for 1X38)

(-) 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 d1x38a1 A:1-388 Beta-D-glucan exohydrolase, N-terminal domain                                                                                                                                                                                                                                                                                                                                       d1x38a2 A:389-602 Beta-D-glucan exohydrolase, C-terminal domain                                                                                                                                                        SCOP domains
               CATH domains 1x38A01 A:1-373  [code=3.20.20.300, no name defined]                                                                                                                                                                                                                                                                                                                                 1x38A02 A:374-602  [code=3.40.50.1700, no name defined]                                                                                                                                                                               CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh...hhhhhhhhhhh..hhhhhhhhheeee.hhhhhhhhhhh...eeee..........hhhhhhhhhhhhhhhhhh.......eeee................hhhhhhhh.hhhhhhhhhhhhhhhhhhh...ee..............hhhhh...hhhhhhhh.hhhhhhhh.....................eeeee.hhhhhhhhh...ee..hhhhhhhhhhhhhhhhhhh...eeee...ee..ee...hhhhhh...........eee.....hhhhh.....hhhhhhhhhhhhh...ee...hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh........hhhhhhhh.hhhhhhhhhhhhhhhheeeee.................eeeee.....hhhhhhh.................hhhhhhhhhh....eeeee...hhhhhhhh....eeeeee....hhhhhh.........hhhhhhhhhh...eeeeee......hhhhhhhh.eeeeee.....hhhhhhhhh...............hhhhh........................ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1x38 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)
  - → 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  (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 1X38)

(-) 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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  1x38
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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 1j8v 1lq2 1x39 3wlh 3wli 3wlj 3wlk 3wll 3wlm 3wln 3wlo 3wlp 3wlq 3wlr 3wls 3wlt

(-) Related Entries Specified in the PDB File

1lq2 THE SAME PROTEIN AT 2.70 A
1x39 THE SAME PROTEIN AT 1.80 A