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(-) Description

Title :  STRUCTURE OF A FAMILY 84 GLYCOSIDE HYDROLASE AND A FAMILY 32 CARBOHYDRATE-BINDING MODULE IN TANDEM FROM CLOSTRIDIUM PERFRINGENS.
 
Authors :  E. Ficko-Blean, K. J. Gregg, J. J. Adams, J. H. Hehemann, S. J. Smith, M. Czjzek, A. B. Boraston
Date :  02 Oct 08  (Deposition) - 27 Jan 09  (Release) - 14 Apr 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.30
Chains :  Asym./Biol. Unit :  A
Keywords :  Family 32 Carbohydrate Binding Module, Glycosidase, Clostridium Perfringens, Gh84, Gh84C, Cbm32, Hydrolase, Coiled Coil, Family 84 Glycoside Hydrolase, Carbohydrate Binding Module (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Ficko-Blean, K. J. Gregg, J. J. Adams, J. H. Hehemann, S. J. Smith, M. Czjzek, A. B. Boraston
Portrait Of An Enzyme: A Complete Structural Analysis Of A Multi-Modular Beta-N- Acetylglucosaminidase From Clostridium Perfringens
J. Biol. Chem. V. 284 9876 2009
PubMed-ID: 19193644  |  Reference-DOI: 10.1074/JBC.M808954200

(-) Compounds

Molecule 1 - O-GLCNACASE NAGJ
    Atcc: 13124
    Chains: A
    EC Number: 3.2.1.52
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Fragment: RESIDUES 31-767
    Organism Scientific: CLOSTRIDIUM PERFRINGENS
    Organism Taxid: 1502
    Synonym: BETA-HEXOSAMINIDASE, HEXOSAMINIDASE B, GH84, N-ACETYL-BETA-GLUCOSAMINIDASE, BETA-N-ACETYLHEXOSAMINIDASE, FAMILY 84 GLYCOSIDE HYDROLASE, FAMILY 32 CARBOHYDRATE BINDING MODULE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric/Biological Unit (1, 3)
No.NameCountTypeFull Name
1CA3Ligand/IonCALCIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:557 , ALA A:597 , SER A:600 , ALA A:602 , VAL A:603BINDING SITE FOR RESIDUE CA A1768
2AC2SOFTWAREGLU A:73 , GLU A:108 , ASP A:111BINDING SITE FOR RESIDUE CA A1769
3AC3SOFTWAREPHE A:647 , ASP A:652 , THR A:655 , ALA A:761 , GLU A:762BINDING SITE FOR RESIDUE CA A1770

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2V5D)

(-) Cis Peptide Bonds  (14, 14)

Asymmetric/Biological Unit
No.Residues
1Asn A:47 -Pro A:48
2Ala A:216 -Pro A:217
3Pro A:217 -Lys A:218
4Asp A:268 -Ala A:269
5Ala A:269 -Gly A:270
6Ser A:342 -Asn A:343
7Asn A:343 -Gly A:344
8Tyr A:397 -Pro A:398
9Leu A:621 -Thr A:622
10Pro A:626 -Arg A:627
11Arg A:627 -Thr A:628
12Thr A:628 -Val A:629
13Ser A:663 -Pro A:664
14Gly A:668 -Pro A:669

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2V5D)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2V5D)

(-) Exons   (0, 0)

(no "Exon" information available for 2V5D)

(-) 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:722
 aligned with OGA_CLOP1 | Q0TR53 from UniProtKB/Swiss-Prot  Length:1001

    Alignment length:727
                                    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       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       
            OGA_CLOP1    41 VLVPNLNPTPENLEVVGDGFKITSSINLVGEEEADENAVNALREFLTANNIEINSENDPNSTTLIIGEVDDDIPELDEALNGTTAENLKEEGYALVSNDGKIAIEGKDGDGTFYGVQTFKQLVKESNIPEVNITDYPTVSARGIVEGFYGTPWTHQDRLDQIKFYGENKLNTYIYAPKDDPYHREKWREPYPESEMQRMQELINASAENKVDFVFGISPGIDIRFDGDAGEEDFNHLITKAESLYDMGVRSFAIYWDDIQDKSAAKHAQVLNRFNEEFVKAKGDVKPLITVPTEYDTGAMVSNGQPRAYTRIFAETVDPSIEVMWTGPGVVTNEIPLSDAQLISGIYNRNMAVWWNYPVTDYFKGKLALGPMHGLDKGLNQYVDFFTVNPMEHAELSKISIHTAADYSWNMDNYDYDKAWNRAIDMLYGDLAEDMKVFANHSTRMDNKTWAKSGREDAPELRAKMDELWNKLSSKEDASALIEELYGEFARMEEACNNLKANLPEVALEECSRQLDELITLAQGDKASLDMIVAQLNEDTEAYESAKEIAQNKLNTALSSFAVISEKVAQSFIQEALSFDLTLINPRTVKITASSEETSGENAPASFASDGDMNTFWHSKWSSPAHEGPHHLTLELDNVYEINKVKYAPRQDSKNGRITGYKVSVSLDGENFTEVKTGTLEDNAAIKFIEFDSVDAKYVRLDVTDSVSDQANGRGKFATAAEVNVHG 767
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----------------------------------------------------------------------------Glyco_hydro_20b-2v5dA03 A:118-177                           ----NAGidase-2v5dA02 A:182-482                                                                                                                                                                                                                                                                                   ---------------------------------------------------------------------------------------------------------------------------------------------------F5_F8_type_C-2v5dA01 A:630-763                                                                                                        ---- Pfam domains
         Sec.struct. author ...........eeee....ee...eeeee.....hhhhhhhhhhhhhhh..ee.........eeeeee....hhhhhhhhh...........eeeee...eeeeee.hhhhhhhhhhhhhhhh...ee..eeeee.....eeeee........hhhhhhhhhhhhhhh...eee.............-----..hhhhhhhhhhhhhhh..eeee...hhhhh......hhhhhhhhhhhhhhhhhhh..eeeee.......hhhhhhhhhhhhhhhhhhhhh.....eee....hhhhhh.....hhhhhhhhhhh....eeee..........hhhhhhhhhhhhh..eeeee...........................eeeeee........hhhhhhhhhhhhhh....hhhhhhhhhhhhhhh.hhhhhhhhhhh...ee.....ee....hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh............ee..........hhhhhhh......ee............eeeeeeeeeeeeeeeeee........eeeeeeeeee.........eeee.......eeeeeeeeeeeeeeeeeeeee...........ee.eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2v5d A  41 VLVPNLNPTPENLEVVGDGFKITSSINLVGEEEADENAVNALREFLTANNIEINSENDPNSTTLIIGEVDDDIPELDEALNGTTAENLKEEGYALVSNDGKIAIEGKDGDGTFYGVQTFKQLVKESNIPEVNITDYPTVSARGIVEGFYGTPWTHQDRLDQIKFYGENKLNTYIYAPKDDPYHREKW-----ESEMQRMQELINASAENKVDFVFGISPGIDIRFDGDAGEEDFNHLITKAESLYDMGVRSFAIYWDDIQDKSAAKHAQVLNRFNEEFVKAKGDVKPLITVPTEYDTGAMVSNGQPRAYTRIFAETVDPSIEVMWTGPGVVTNEIPLSDAQLISGIYNRNMAVWWNYPVTDYFKGKLALGPMHGLDKGLNQYVDFFTVNPMEHAELSKISIHTAADYSWNMDNYDYDKAWNRAIDMLYGDLAEDMKVFANHSTRMDNKTWAKSGREDAPELRAKMDELWNKLSSKEDASALIEELYGEFARMEEACNNLKANLPEVALEECSRQLDELITLAQGDKASLDMIVAQLNEDTEAYESAKEIAQNKLNTALSSFAVISEKVAQSFIQEALSFDLTLINPRTVKITASSEETSGENAPASFASDGDMNTFWHSKWSSPAHEGPHHLTLELDNVYEINKVKYAPRQDSKNGRITGYKVSVSLDGENFTEVKTGTLEDNAAIKFIEFDSVDAKYVRLDVTDSVSDQANGRGKFATAAEVNVHG 767
                                    50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220      |  -  |    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       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       
                                                                                                                                                                                                                    227   233
   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  (0, 0)

(no "SCOP Domain" information available for 2V5D)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2V5D)

(-) Pfam Domains  (3, 3)

Asymmetric/Biological Unit
(-)
Clan: GBD (153)
(-)
Clan: Glyco_hydro_tim (488)
(-)
Clan: no clan defined [family: Glyco_hydro_20b] (22)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (OGA_CLOP1 | Q0TR53)
molecular function
    GO:0016231    beta-N-acetylglucosaminidase activity    Catalysis of the hydrolysis of terminal non-reducing N-acetyl-D-glucosamine residues in N-acetyl-beta-D-glucosaminides.
    GO:0004563    beta-N-acetylhexosaminidase activity    Catalysis of the hydrolysis of terminal non-reducing N-acetyl-D-hexosamine residues in N-acetyl-beta-D-hexosaminides.
    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: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.
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:0006517    protein deglycosylation    The removal of sugar residues from a glycosylated protein.

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 Related Entries

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

UniProtKB/Swiss-Prot
        OGA_CLOP1 | Q0TR53: 2cbi 2cbj 2j1a 2j1e 2j62 2j7m 2jh2 2o4e 2ozn 2v5c 2vur 2w1n 2wb5 2x0y 2xpk 2ydq 2ydr 2yds 4zxl

(-) Related Entries Specified in the PDB File

2j62 STRUCTURE OF A BACTERIAL O-GLCNACASE IN COMPLEX WITH GLCNACSTATIN
2jh2 X-RAY CRYSTAL STRUCTURE OF A COHESIN-LIKE MODULE FROM CLOSTRIDIUM PERFRINGENS
2v5c FAMILY 84 GLYCOSIDE HYDROLASE FROM CLOSTRIDIUM PERFRINGENS, 2.1 ANGSTROM STRUCTURE
2vur CHEMICAL DISSECTION OF THE LINK BETWEEN STREPTOZOTOCIN, O-GLCNAC AND PANCREATIC CELL DEATH