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(-) Description

Title :  BETA-N-ACETYLHEXOSAMINIDASE MUTANT E540D COMPLEXED WITH DI-N ACETYL-D-GLUCOSAMINE (CHITOBIASE)
 
Authors :  G. Prag, Y. Papanikolau, G. Tavlas, C. E. Vorgias, K. Petratos, A. B. Oppenheim
Date :  17 Mar 00  (Deposition) - 20 Sep 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Glycosyl Hydrolase, Beta-N-Acetylhexosaminidase, Chitinolysin, A/B(Tim)-Barrel, Site Directed Mutagenesis, Proton Donor, X-Ray Diffraction, Co-Crystal Structure (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Prag, Y. Papanikolau, G. Tavlas, C. E. Vorgias, K. Petratos, A. B. Oppenheim
Structures Of Chitobiase Mutants Complexed With The Substrate Di-N-Acetyl-D-Glucosamine: The Catalytic Role Of The Conserved Acidic Pair, Aspartate 539 And Glutamate 540.
J. Mol. Biol. V. 300 611 2000
PubMed-ID: 10884356  |  Reference-DOI: 10.1006/JMBI.2000.3906
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BETA-N-ACETYLHEXOSAMINIDASE
    Chains: A
    EC Number: 3.2.1.52
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Cellular Location: PERIPLASM
    Expression System Plasmid: PKK177-3
    Expression System Strain: A5039
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: MATURE PROTEIN, PERIPLASMATIC TARGETING SEQUENCE RESIDUES 1-27 CLEAVED OFF DURING MATURATION
    Mutation: YES
    Organism Scientific: SERRATIA MARCESCENS
    Organism Taxid: 615
    Other Details: COMPLEXED WITH DINAG
    Strain: A9270
    Synonym: N-ACETYL-BETA-D-GLUCOSAMINIDASE, CHITOBIASE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
1CBS1Ligand/IonDI(N-ACETYL-D-GLUCOSAMINE)
2SO44Ligand/IonSULFATE ION
Biological Unit 1 (2, 10)
No.NameCountTypeFull Name
1CBS2Ligand/IonDI(N-ACETYL-D-GLUCOSAMINE)
2SO48Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:349 , HIS A:452 , ASP A:539 , TRP A:616 , TRP A:639 , TYR A:669 , ASP A:671 , PHE A:672 , TYR A:683 , TRP A:685 , TRP A:737 , GLU A:739 , HOH A:2093 , HOH A:2095 , HOH A:2230 , HOH A:2447 , HOH A:2544 , HOH A:2657 , HOH A:2728BINDING SITE FOR RESIDUE CBS A 1001
2AC2SOFTWARETHR A:109 , ARG A:454 , PHE A:496 , ASN A:497 , ARG A:498 , GLN A:499 , HOH A:2780BINDING SITE FOR RESIDUE SO4 A 2001
3AC3SOFTWARELYS A:532 , ARG A:633 , ARG A:825 , HOH A:2615BINDING SITE FOR RESIDUE SO4 A 2003
4AC4SOFTWAREHIS A:107 , ARG A:545BINDING SITE FOR RESIDUE SO4 A 2004
5AC5SOFTWARELYS A:104 , THR A:118 , ALA A:119 , HOH A:2189 , HOH A:2506BINDING SITE FOR RESIDUE SO4 A 2002

(-) SS Bonds  (3, 3)

Asymmetric Unit
No.Residues
1A:56 -A:66
2A:400 -A:408
3A:505 -A:578

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Val A:218 -Pro A:219
2Met A:449 -Pro A:450
3Phe A:752 -Pro A:753

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1C7T)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1C7T)

(-) Exons   (0, 0)

(no "Exon" information available for 1C7T)

(-) 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:858
 aligned with CHB_SERMA | Q54468 from UniProtKB/Swiss-Prot  Length:885

    Alignment length:858
                                    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       507       517       527       537       547       557       567       577       587       597       607       617       627       637       647       657       667       677       687       697       707       717       727       737       747       757       767       777       787       797       807       817       827       837       847       857       867       877        
            CHB_SERMA    28 DQQLVDQLSQLKLNVKMLDNRAGENGVDCAALGADWASCNRVLFTLSNDGQAIDGKDWVIYFHSPRQTLRVDNDQFKIAHLTGDLYKLEPTAKFSGFPAGKAVEIPVVAEYWQLFRNDFLPRWYATSGDAKPKMLANTDTENLDQFVAPFTGDQWKRTKDDKNILMTPASRFVSNADLQTLPAGALRGKIVPTPMQVKVHAQDADLRKGVALDLSTLVKPAADVVSQRFALLGVPVQTNGYPIKTDIQPGKFKGAMAVSGAYELKIGKKEAQVIGFDQAGVFYGLQSILSLVPSDGSGKIATLDASDAPRFPYRGIFLDVARNFHKKDAVLRLLDQMAAYKLNKFHFHLSDDEGWRIEIPGLPELTEVGGQRCHDLSETTCLLPQYGQGPDVYGGFFSRQDYIDIIKYAQARQIEVIPEIDMPAHARAAVVSMEARYKKLHAAGKEQEANEFRLVDPTDTSNTTSVQFFNRQSYLNPCLDSSQRFVDKVIGEIAQMHKEAGQPIKTWHFGGDEAKNIRLGAGYTDKAKPEPGKGIIDQSNEDKPWAKSQVCQTMIKEGKVADMEHLPSYFGQEVSKLVKAHGIDRMQAWQDGLKDAESSKAFATSRVGVNFWDTLYWGGFDSVNDWANKGYEVVVSNPDYVYMDFPYEVNPDERGYYWGTRFSDERKVFSFAPDNMPQNAETSVDRDGNHFNAKSDKPWPGAYGLSAQLWSETQRTDPQMEYMIFPRALSVAERSWHRAGWEQDYRAGREYKGGETHFVDTQALEKDWLRFANILGQRELAKLDKGGVAYRLPVPGARVAAGKLEANIALPGLGIEYSTDGGKQWQRYDAKAKPAVSGEVQVRSVSPDGKRYSRAEKV 885
               SCOP domains d1c7ta2 A:28-200 Bacterial chitobiase, n-terminal domain                                                                                                                     d1c7ta4 A:201-337 Bacterial chitobiase, Domain 2                                                                                         d1c7ta3 A:338-780 Bacterial chitobiase (beta-N-acetylhexosaminidase)                                                                                                                                                                                                                                                                                                                                                                                       d1c7ta1 A:781-885 Bacterial chitobiase (N-acetyl-beta-glucoseaminidase), C-terminal domain                SCOP domains
               CATH domains 1c7tA01 A:28-169  [code=2.60.40.290, no name defined]                                                                                         ---------------------------------------1c7tA02 A:209-335 Chitobiase, domain 2                                                                                         1c7tA03 A:336-819 Glycosidases                                                                                                                                                                                                                                                                                                                                                                                                                                                                      1c7tA04 A:820-885  [code=2.60.40.320, no name defined]             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhh.eeeeeeee.hhhhh...hhhhhhhhh.eeeeeeeeee..........eeeee....eeee....eeeee....eeeeee..........eeeeeeeeee....hhhhh....eee......ee.hhhh..hhhhh....................hhhhhhhhhh.....hhhhh.........eeeeeeeeee....eee.....hhhhhhhhhhhhhhh........eeeeeee.hhhhhhhhh....eeeee....eeeee.hhhhhhhhhhhhhhhh......eeeeeeeee.....eeeeeee......hhhhhhhhhhhhhhh...eeeee..............hhhhhh..ee....................ee...hhhhhhhhhhhhhhh..eeeeeeee...hhhhhhhhhhhhhhhhhh.hhhhhhhh.................hhhhh....hhhhhhhhhhhhhhhhhhhhhh......eeee.....hhhhh..eee........eee...........hhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...eeeee.hhhh...hhhhh...eeeeee..hhhhhhhhhhhhhhhh..eeee.hhhhhh.....................hhhhhhhh...hhhhhhhhh........ee..........eeeeee......hhhhhhhhhhhhhhhhhhhhhh.............ee.......hhhhhhhhhhhhhhhhhhhhhhhhhhh.........eeeee..eeeee......eeeee.......ee.hhhhh.......eeeee..........ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1c7t A  28 DQQLVDQLSQLKLNVKMLDNRAGENGVDCAALGADWASCNRVLFTLSNDGQAIDGKDWVIYFHSPRQTLRVDNDQFKIAHLTGDLYKLEPTAKFSGFPAGKAVEIPVVAEYWQLFRNDFLPRWYATSGDAKPKMLANTDTENLDQFVAPFTGDQWKRTKDDKNILMTPASRFVSNADLQTLPAGALRGKIVPTPMQVKVHAQDADLRKGVALDLSTLVKPAADVVSQRFALLGVPVQTNGYPIKTDIQPGKFKGAMAVSGAYELKIGKKEAQVIGFDQAGVFYGLQSILSLVPSDGSGKIATLDASDAPRFPYRGIFLDVARNFHKKDAVLRLLDQMAAYKLNKFHFHLSDDEGWRIEIPGLPELTEVGGQRCHDLSETTCLLPQYGQGPDVYGGFFSRQDYIDIIKYAQARQIEVIPEIDMPAHARAAVVSMEARYKKLHAAGKEQEANEFRLVDQTDTSNTTSVQFFNRQSYLNPCLDSSQRFVDKVIGEIAQMHKEAGQPIKTWHFGGDDAKNIRLGAGYTDKAKPEPGKGIIDQSNEDKPWAKSQVCQTMIKEGKVADMEHLPSYFGQEVSKLVKAHGIDRMQAWQDGLKDAESSKAFATSRVGVNFWDTLYWGGFDSVNDWANKGYEVVVSNPDYVYMDFPYEVNPDERGYYWGTRFSDERKVFSFAPDNMPQNAETSVDRDGNHFNAKSDKPWPGAYGLSAQLWSETQRTDPQMEYMIFPRALSVAERSWHRAGWEQDYRAGREYKGGETHFVDTQALEKDWLRFANILGQRELAKLDKGGVAYRLPVPGARVAGGKLEANIALPGLGIEYSTDGGKQWQRYDAKAKPAVSGEVQVRSVSPDGKRYSRAEKV 885
                                    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       507       517       527       537       547       557       567       577       587       597       607       617       627       637       647       657       667       677       687       697       707       717       727       737       747       757       767       777       787       797       807       817       827       837       847       857       867       877
   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  (4, 4)

Asymmetric Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (4, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1C7T)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A   (CHB_SERMA | Q54468)
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: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.
    GO:0004553    hydrolase activity, hydrolyzing O-glycosyl compounds    Catalysis of the hydrolysis of any O-glycosyl bond.
    GO:0030247    polysaccharide binding    Interacting selectively and non-covalently with any polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.
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:0006032    chitin catabolic process    The chemical reactions and pathways resulting in the breakdown of chitin, a linear polysaccharide consisting of beta-(1->4)-linked N-acetyl-D-glucosamine 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.
    GO:0000272    polysaccharide catabolic process    The chemical reactions and pathways resulting in the breakdown of a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.
cellular component
    GO:0042597    periplasmic space    The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

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  1c7t
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  3.2.1.52
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 Related Entries

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

UniProtKB/Swiss-Prot
        CHB_SERMA | Q54468: 1c7s 1qba 1qbb

(-) Related Entries Specified in the PDB File

1c7s BETA-N-ACETYLHEXOSAMINIDASE MUTANT D539A
1qba
1qbb
1qbc