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(-) Description

Title :  MUTANT STREPTOMYCES PLICATUS BETA-HEXOSAMINIDASE (D313A) IN COMPLEX WITH PRODUCT (GLCNAC)
 
Authors :  S. J. Williams, B. L. Mark, D. J. Vocadlo, M. N. G. James, S. G. Withers
Date :  11 Jun 02  (Deposition) - 11 Dec 02  (Release) - 16 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Substrate Assisted Catalysis, Family 20 Glycosidase, Beta- Hexosaminidase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. J. Williams, B. L. Mark, D. J. Vocadlo, M. N. James, S. G. Withers
Aspartate 313 In The Streptomyces Plicatus Hexosaminidase Plays A Critical Role In Substrate-Assisted Catalysis By Orienting The 2-Acetamido Group And Stabilizing The Transition State.
J. Biol. Chem. V. 277 40055 2002
PubMed-ID: 12171933  |  Reference-DOI: 10.1074/JBC.M206481200

(-) Compounds

Molecule 1 - BETA-N-ACETYLHEXOSAMINIDASE
    Chains: A
    EC Number: 3.2.1.52
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET3A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: STREPTOMYCES PLICATUS
    Organism Taxid: 1922
    Synonym: BETA-HEXOSAMINIDASE, SPHEX

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (1x): A
Biological Unit 2 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 7)

Asymmetric Unit (4, 7)
No.NameCountTypeFull Name
1CL3Ligand/IonCHLORIDE ION
2GOL2Ligand/IonGLYCEROL
3NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
4SO41Ligand/IonSULFATE ION
Biological Unit 1 (3, 4)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL2Ligand/IonGLYCEROL
3NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
4SO41Ligand/IonSULFATE ION
Biological Unit 2 (3, 8)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL4Ligand/IonGLYCEROL
3NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
4SO42Ligand/IonSULFATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:162 , HIS A:250 , ALA A:313 , GLU A:314 , TRP A:344 , TRP A:361 , TYR A:393 , ASP A:395 , LEU A:406 , TRP A:408 , TRP A:442 , GLU A:444 , HOH A:580 , HOH A:808BINDING SITE FOR RESIDUE NAG A 507
2AC2SOFTWARETYR A:271 , LYS A:275 , LEU A:406 , SER A:407 , TRP A:408BINDING SITE FOR RESIDUE CL A 508
3AC3SOFTWAREASP A:175 , ARG A:176 , ARG A:179 , HOH A:639BINDING SITE FOR RESIDUE CL A 509
4AC4SOFTWARELYS A:275 , VAL A:276BINDING SITE FOR RESIDUE CL A 510
5AC5SOFTWAREARG A:150 , ALA A:423 , HOH A:622 , HOH A:766BINDING SITE FOR RESIDUE SO4 A 511
6AC6SOFTWAREPHE A:278 , SER A:317 , HIS A:345 , GLN A:346 , TRP A:361 , GLU A:370 , TRP A:408 , HOH A:734BINDING SITE FOR RESIDUE GOL A 512
7AC7SOFTWAREASP A:264 , VAL A:266 , ARG A:365 , ALA A:409 , HOH A:585 , HOH A:609 , HOH A:612 , HOH A:670BINDING SITE FOR RESIDUE GOL A 513

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:263 -A:282

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Ile A:22 -Pro A:23
2Gly A:136 -Pro A:137
3Met A:247 -Pro A:248
4Phe A:457 -Pro A:458

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1M03)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1M03)

(-) Exons   (0, 0)

(no "Exon" information available for 1M03)

(-) 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:499
 aligned with O85361_STRPL | O85361 from UniProtKB/TrEMBL  Length:506

    Alignment length:499
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497         
         O85361_STRPL     8 DRKAPVRPTPLDRVIPAPASVDPGGAPYRITRGTHIRVDDSREARRVGDYLADLLRPATGYRLPVTAHGHGGIRLRLAGGPYGDEGYRLDSGPAGVTITARKAAGLFHGVQTLRQLLPPAVEKDSAQPGPWLVAGGTIEDTPRYAWRSAMLDVSRHFFGVDEVKRYIDRVARYKYNKLHLHLSDDQGWRIAIDSWPRLATYGGSTEVGGGPGGYYTKAEYKEIVRYAASRHLEVVPEIDMPGHTNAALASYAELNCDGVAPPLYTGTKVGFSSLCVDKDVTYDFVDDVIGELAALTPGRYLHIGGDEAHSTPKADFVAFMKRVQPIVAKYGKTVVGWHQLAGAEPVEGALVQYWGLDRTGDAEKAEVAEAARNGTGLILSPADRTYLDMKYTKDTPLGLSWAGYVEVQRSYDWDPAGYLPGAPADAVRGVEAPLWTETLSDPDQLDYMAFPRLPGVAELGWSPASTHDWDTYKVRLAAQAPYWEAAGIDFYRSPQVPWT 506
               SCOP domains d1m03a2 A:8-150 beta-N-acetylhexosaminidase, N-terminal domain                                                                                 d1m03a1 A:151-506 beta-N-acetylhexosaminidase                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 1m03A02 A:8-148 Chitobiase, domain 2                                                                                                         -1m03A01 A:150-470 Glycosidases                                                                                                                                                                                                                                                                                                   ------------------------------------ CATH domains
               Pfam domains -----------------------------------------------------------------------------------------------------------------------------------------------Glyco_hydro_20-1m03A01 A:151-471                                                                                                                                                                                                                                                                                                 ----------------------------------- Pfam domains
         Sec.struct. author ...................eeee....eee.....ee...hhhhhhhhhhhhhhhhhhhh....ee......eeeee.........eeeeee..eeeeee.hhhhhhhhhhhhhhhhhhhhhh.......eee..eeeee.....eeeeeee......hhhhhhhhhhhhhh....eeeee.ee..ee.......hhhhhh..............hhhhhhhhhhhhhhh..eeeee......hhhhhhhhhhhh......................hhhhhhhhhhhhhhhhhh....eee.........hhhhhhhhhhhhhhhhhhh..eeeee.hhhhh......eeee......hhhhhhhhhhhhhh..eeee..........................hhhhhhh.hhhhh....hhh.eeeeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1m03 A   8 DRKAPVRPTPLDRVIPAPASVDPGGAPYRITRGTHIRVDDSREARRVGDYLADLLRPATGYRLPVTAHGHGGIRLRLAGGPYGDEGYRLDSGPAGVTITARKAAGLFHGVQTLRQLLPPAVEKDSAQPGPWLVAGGTIEDTPRYAWRSAMLDVSRHFFGVDEVKRYIDRVARYKYNKLHLHLSDDQGWRIAIDSWPRLATYGGSTEVGGGPGGYYTKAEYKEIVRYAASRHLEVVPEIDMPGHTNAALASYAELNCDGVAPPLYTGTKVGFSSLCVDKDVTYDFVDDVIGELAALTPGRYLHIGGAEAHSTPKADFVAFMKRVQPIVAKYGKTVVGWHQLAGAEPVEGALVQYWGLDRTGDAEKAEVAEAARNGTGLILSPADRTYLDMKYTKDTPLGLSWAGYVEVQRSYDWDPAGYLPGAPADAVRGVEAPLWTETLSDPDQLDYMAFPRLPGVAELGWSPASTHDWDTYKVRLAAQAPYWEAAGIDFYRSPQVPWT 506
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497
   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 Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: Glyco_hydro_tim (488)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A   (O85361_STRPL | O85361)
molecular function
    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: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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  1m03
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 Related Entries

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

UniProtKB/TrEMBL
        O85361_STRPL | O85361: 1hp4 1hp5 1jak 1m01 1m04 5fcz 5fd0

(-) Related Entries Specified in the PDB File

1hp5 STREPTOMYCES PLICATUS [BETA]-N-ACETYLHEXOSAMINIDASE COMPLEXED WITH INTERMEDIATE ANALOUGE NAG-THIAZOLINE
1jak STREPTOMYCES PLICATUS [BETA]-N-ACETYLHEXOSAMINIDASE IN COMPLEX WITH (2R,3R,4S,5R)-2-ACETAMIDO-3,4-DIHYDROXY-5- HYDROXYMETHYL-PIPERIDINIUM CHLORIDE (IFG)
1m01 WILDTYPE STREPTOMYCES PLICATUS BETA-HEXOSAMINIDASE IN COMPLEX WITH PRODUCT (GLCNAC)
1m04 MUTANT STREPTOMYCES PLICATUS BETA-HEXOSAMINIDASE (D313N) IN COMPLEX WITH PRODUCT (GLCNAC)