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(-) Description

Title :  STRUCTURE AND ACTIVITY OF THE GH20 BETA-N-ACETYLHEXOSAMINIDASE FROM STREPTOMYCES COELICOLOR A3(2)
 
Authors :  N. Nguyen Thi, W. A. Offen, G. J. Davies, N. Doucet
Date :  20 Sep 13  (Deposition) - 12 Mar 14  (Release) - 09 Apr 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Nguyen Thi, W. A. Offen, F. Shareck, G. J. Davies, N. Doucet
Structure And Activity Of The Streptomyces Coelicolor A3(2) Beta-N-Acetylhexosaminidase Provides Further Insight Into Gh20 Family Catalysis And Inhibition.
Biochemistry V. 53 1789 2014
PubMed-ID: 24559145  |  Reference-DOI: 10.1021/BI401697J

(-) Compounds

Molecule 1 - BETA-N-ACETYLHEXOSAMINIDASE
    Chains: A, B
    EC Number: 3.2.1.52
    Engineered: YES
    Expression System: STREPTOMYCES LIVIDANS
    Expression System Strain: 10-164
    Expression System Taxid: 1916
    Fragment: RESIDUES 42-535
    Organism Scientific: STREPTOMYCES COELICOLOR
    Organism Taxid: 1902
    Strain: A(3)2

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 22)

Asymmetric Unit (1, 22)
No.NameCountTypeFull Name
1EDO22Ligand/Ion1,2-ETHANEDIOL
Biological Unit 1 (1, 9)
No.NameCountTypeFull Name
1EDO9Ligand/Ion1,2-ETHANEDIOL
Biological Unit 2 (1, 13)
No.NameCountTypeFull Name
1EDO13Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (22, 22)

Asymmetric Unit (22, 22)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:301 , TRP A:332 , TRP A:349 , TYR A:381BINDING SITE FOR RESIDUE EDO A1495
02AC2SOFTWAREARG A:150 , TYR A:381 , ASP A:383 , LEU A:394 , TRP A:396 , GLU A:432 , HOH A:2177BINDING SITE FOR RESIDUE EDO A1496
03AC3SOFTWAREHIS A:226 , LEU A:227 , HOH A:2204 , HOH A:2250 , HOH A:2289BINDING SITE FOR RESIDUE EDO A1497
04AC4SOFTWAREGLU A:80 , ASN A:171 , LYS A:172 , ARG A:294 , HOH A:2292 , HOH A:2431BINDING SITE FOR RESIDUE EDO A1498
05AC5SOFTWAREGLU A:216 , ALA A:289 , LEU A:290 , THR A:291 , PRO A:292 , HOH A:2286BINDING SITE FOR RESIDUE EDO A1499
06AC6SOFTWAREGLU A:217 , ARG A:220 , HOH A:2241 , HOH A:2244BINDING SITE FOR RESIDUE EDO A1500
07AC7SOFTWAREASP A:156 , GLU A:157 , ARG A:160 , HOH A:2071 , HOH A:2187BINDING SITE FOR RESIDUE EDO A1501
08AC8SOFTWAREASN A:240 , PRO A:257 , LEU A:258 , TYR A:259 , HOH A:2267BINDING SITE FOR RESIDUE EDO A1502
09AC9SOFTWAREARG A:138 , TYR A:139 , VAL A:422 , ALA B:1 , GLU B:2 , HOH B:2002 , HOH B:2005BINDING SITE FOR RESIDUE EDO A1503
10BC1SOFTWAREVAL B:271 , TYR B:277 , ALA B:313 , ARG B:317BINDING SITE FOR RESIDUE EDO B1495
11BC2SOFTWAREGLU B:80 , ALA B:140 , LYS B:172 , ARG B:294 , HOH B:2464BINDING SITE FOR RESIDUE EDO B1496
12BC3SOFTWAREASP B:352 , LYS B:359 , TYR B:413 , PRO B:415 , HOH B:2355BINDING SITE FOR RESIDUE EDO B1497
13BC4SOFTWAREHIS B:226 , GLU B:228 , HOH B:2217 , HOH B:2266 , HOH B:2267 , HOH B:2465BINDING SITE FOR RESIDUE EDO B1498
14BC5SOFTWAREARG B:150 , TYR B:381 , ASP B:383 , TRP B:396 , TRP B:430 , GLU B:432 , HOH B:2190BINDING SITE FOR RESIDUE EDO B1499
15BC6SOFTWAREARG B:220 , TYR B:221 , SER B:224 , ARG B:225 , HOH B:2208 , HOH B:2466BINDING SITE FOR RESIDUE EDO B1500
16BC7SOFTWAREARG B:403 , HOH B:2447 , HOH B:2467BINDING SITE FOR RESIDUE EDO B1501
17BC8SOFTWAREPRO B:13 , ALA B:14 , SER B:15 , VAL B:16 , HOH B:2016 , HOH B:2023 , HOH B:2027BINDING SITE FOR RESIDUE EDO B1502
18BC9SOFTWAREASP B:156 , ARG B:160 , ASP B:163 , TYR B:221BINDING SITE FOR RESIDUE EDO B1503
19CC1SOFTWARESER B:224 , HOH B:2061 , HOH B:2268 , HOH B:2466BINDING SITE FOR RESIDUE EDO B1504
20CC2SOFTWAREASN B:240 , PRO B:257 , TYR B:259 , HOH B:2297 , HOH B:2470BINDING SITE FOR RESIDUE EDO B1505
21CC3SOFTWAREALA B:303 , HIS B:304BINDING SITE FOR RESIDUE EDO B1506
22CC4SOFTWAREVAL B:264 , TRP B:396BINDING SITE FOR RESIDUE EDO B1507

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:251 -A:270
2B:251 -B:270

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Ile A:10 -Pro A:11
2Gly A:124 -Pro A:125
3Met A:235 -Pro A:236
4Phe A:445 -Pro A:446
5Ile B:10 -Pro B:11
6Gly B:124 -Pro B:125
7Met B:235 -Pro B:236
8Phe B:445 -Pro B:446

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4C7D)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4C7D)

(-) Exons   (0, 0)

(no "Exon" information available for 4C7D)

(-) 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:493
 aligned with Q9L068_STRCO | Q9L068 from UniProtKB/TrEMBL  Length:535

    Alignment length:493
                                    52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532   
         Q9L068_STRCO    43 EPTPLDRVIPAPASVEPGGAPYRITRGTHIRVDDSREARRVGDYLADLLRPATGYRLPVTSHGHGGIRLRLAEGPYGDEGYRLDSGREGVTITARKAAGLFHGVQTLRQLLPAAVEKDSAQPGPWLVAGGTIEDTPRYAWRSAMLDVSRHFFSVDEVKRYIDRVALYKYNKLHLHISDDQGWRLAIDSWPRLATYGGSTEVGGGPGGHYTKADYEEIVRYAASRHLEVVPEIDMPGHTNAALASYAELNCDGVAPPLYTGTKVGFSTLCVDKDVTYDFVDDVLGELAALTPGRYLHIGGDEAHSTPQADFVAFMKRVQPIVAKYGKTVVGWHQLAGAEPVEGALVQYWGLDRTSDAEKAQVAAAARNGTGLILSPADRTYLDMKYTKDTPLGLSWAGYVEVRRSYDWDPAAYLPGAPAEAVRGVEAPLWTETLSDPDQLDFMAFPRLPGVAELGWSPASTHDWDTYKVRLAGQAPHWEAMGIDYYRSPQVPWT 535
               SCOP domains d4c7da1 A:2-138 automated matches                                                                                                        d4c7da2 A:139-494 automated matches                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeee....ee......eee..hhhhhhhhhhhhhhhhhhhh....ee.....eeeeee.........eeeeee..eeeeee.hhhhhhhhhhhhhhhhhhhhhh........ee..eeeee.....eeeeeee......hhhhhhhhhhhhhh....eeeee.ee..ee.......hhhhhh....hhhhh.....hhhhhhhhhhhhhhh..eeeeeeee...hhhhhhhhhhhh.......................hhhhhhhhhhhhhhhhh....eeeee.......hhhhhhhhhhhhhhhhhhh..eeeee.hhhhh......eeee......hhhhhhhhhhhhhh..eeee..........................hhhhhhh.hhhhh....hhh.eeeeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4c7d A   2 EPTPLDRVIPAPASVEPGGAPYRITRGTHIRVDDSREARRVGDYLADLLRPATGYRLPVTSHGHGGIRLRLAEGPYGDEGYRLDSGREGVTITARKAAGLFHGVQTLRQLLPAAVEKDSAQPGPWLVAGGTIEDTPRYAWRSAMLDVSRHFFSVDEVKRYIDRVALYKYNKLHLHISDDQGWRLAIDSWPRLATYGGSTEVGGGPGGHYTKADYEEIVRYAASRHLEVVPEIDMPGHTNAALASYAELNCDGVAPPLYTGTKVGFSTLCVDKDVTYDFVDDVLGELAALTPGRYLHIGGDEAHSTPQADFVAFMKRVQPIVAKYGKTVVGWHQLAGAEPVEGALVQYWGLDRTSDAEKAQVAAAARNGTGLILSPADRTYLDMKYTKDTPLGLSWAGYVEVRRSYDWDPAAYLPGAPAEAVRGVEAPLWTETLSDPDQLDFMAFPRLPGVAELGWSPASTHDWDTYKVRLAGQAPHWEAMGIDYYRSPQVPWT 494
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491   


Chain B from PDB  Type:PROTEIN  Length:494
 aligned with Q9L068_STRCO | Q9L068 from UniProtKB/TrEMBL  Length:535

    Alignment length:494
                                    51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531    
         Q9L068_STRCO    42 AEPTPLDRVIPAPASVEPGGAPYRITRGTHIRVDDSREARRVGDYLADLLRPATGYRLPVTSHGHGGIRLRLAEGPYGDEGYRLDSGREGVTITARKAAGLFHGVQTLRQLLPAAVEKDSAQPGPWLVAGGTIEDTPRYAWRSAMLDVSRHFFSVDEVKRYIDRVALYKYNKLHLHISDDQGWRLAIDSWPRLATYGGSTEVGGGPGGHYTKADYEEIVRYAASRHLEVVPEIDMPGHTNAALASYAELNCDGVAPPLYTGTKVGFSTLCVDKDVTYDFVDDVLGELAALTPGRYLHIGGDEAHSTPQADFVAFMKRVQPIVAKYGKTVVGWHQLAGAEPVEGALVQYWGLDRTSDAEKAQVAAAARNGTGLILSPADRTYLDMKYTKDTPLGLSWAGYVEVRRSYDWDPAAYLPGAPAEAVRGVEAPLWTETLSDPDQLDFMAFPRLPGVAELGWSPASTHDWDTYKVRLAGQAPHWEAMGIDYYRSPQVPWT 535
               SCOP domains d4c7db1 B:1-138 automated matches                                                                                                         d4c7db2 B:139-494 automated matches                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeee....eee.....eee..hhhhhhhhhhhhhhhhhhhh....ee......eeeee.........eeeeee..eeeeee.hhhhhhhhhhhhhhhhhhhhhh.......eee..eeeee.....eeeeeee......hhhhhhhhhhhhhh....eeeee..............hhhhhh....hhhhh.....hhhhhhhhhhhhhhh..eeeeeeee...hhhhhhhhhhhh......................hhhhhhhhhhhhhhhhhh....eeeee.......hhhhhhhhhhhhhhhhhhh..eeeee.hhhhh......eeee......hhhhhhhhhhhhhh..eeee..........................hhhhhhh.hhhhh....hhh.eeeeeeee......hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4c7d B   1 AEPTPLDRVIPAPASVEPGGAPYRITRGTHIRVDDSREARRVGDYLADLLRPATGYRLPVTSHGHGGIRLRLAEGPYGDEGYRLDSGREGVTITARKAAGLFHGVQTLRQLLPAAVEKDSAQPGPWLVAGGTIEDTPRYAWRSAMLDVSRHFFSVDEVKRYIDRVALYKYNKLHLHISDDQGWRLAIDSWPRLATYGGSTEVGGGPGGHYTKADYEEIVRYAASRHLEVVPEIDMPGHTNAALASYAELNCDGVAPPLYTGTKVGFSTLCVDKDVTYDFVDDVLGELAALTPGRYLHIGGDEAHSTPQADFVAFMKRVQPIVAKYGKTVVGWHQLAGAEPVEGALVQYWGLDRTSDAEKAQVAAAARNGTGLILSPADRTYLDMKYTKDTPLGLSWAGYVEVRRSYDWDPAAYLPGAPAEAVRGVEAPLWTETLSDPDQLDFMAFPRLPGVAELGWSPASTHDWDTYKVRLAGQAPHWEAMGIDYYRSPQVPWT 494
                                    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
   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, 4)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4C7D)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4C7D)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q9L068_STRCO | Q9L068)
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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  4c7d
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  Q9L068_STRCO | Q9L068
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 Related Entries

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

UniProtKB/TrEMBL
        Q9L068_STRCO | Q9L068: 4c7f 4c7g

(-) Related Entries Specified in the PDB File

4c7f STRUCTURE AND ACTIVITY OF THE GH20 BETA-N- ACETYLHEXOSAMINIDASE FROM STREPTOMYCES COELICOLOR A3(2)
4c7g STRUCTURE AND ACTIVITY OF THE GH20 BETA-N- ACETYLHEXOSAMINIDASE FROM STREPTOMYCES COELICOLOR A3(2)