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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 :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Hydrolase, N-Acetylhexosaminides, Chitin Degradation (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  (2, 34)

Asymmetric Unit (2, 34)
No.NameCountTypeFull Name
1EDO32Ligand/Ion1,2-ETHANEDIOL
2GC22Ligand/Ion6-ACETAMIDO-6-DEOXY-CASTANOSPERMINE
Biological Unit 1 (2, 18)
No.NameCountTypeFull Name
1EDO17Ligand/Ion1,2-ETHANEDIOL
2GC21Ligand/Ion6-ACETAMIDO-6-DEOXY-CASTANOSPERMINE
Biological Unit 2 (2, 16)
No.NameCountTypeFull Name
1EDO15Ligand/Ion1,2-ETHANEDIOL
2GC21Ligand/Ion6-ACETAMIDO-6-DEOXY-CASTANOSPERMINE

(-) Sites  (34, 34)

Asymmetric Unit (34, 34)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:333 , GLN A:334 , TRP A:349 , THR A:354 , GLU A:358 , HOH A:2434 , HOH A:2540BINDING SITE FOR RESIDUE EDO A1495
02AC2SOFTWAREASP A:214 , LYS B:388 , ASP B:389 , THR B:390 , PRO B:391 , HOH B:2579 , HOH B:2580BINDING SITE FOR RESIDUE EDO B1495
03AC3SOFTWAREARG A:40 , ASP A:44 , HOH A:2090BINDING SITE FOR RESIDUE EDO A1496
04AC4SOFTWAREARG A:71 , ASP B:274 , ARG B:317 , EDO B:1497 , HOH B:2413BINDING SITE FOR RESIDUE EDO B1496
05AC5SOFTWAREVAL A:271 , ARG A:317 , HOH A:2541BINDING SITE FOR RESIDUE EDO A1497
06AC6SOFTWAREARG A:69 , ARG A:71 , HOH A:2059 , ASP B:274 , TYR B:277 , ASP B:278 , ARG B:317 , EDO B:1496BINDING SITE FOR RESIDUE EDO B1497
07AC7SOFTWAREASN B:240 , PRO B:256 , PRO B:257 , HOH B:2347 , HOH B:2581BINDING SITE FOR RESIDUE EDO B1498
08AC8SOFTWARETHR A:268 , LEU A:269 , CYS A:270 , VAL A:271 , PRO A:307 , ASP A:310 , HOH A:2359BINDING SITE FOR RESIDUE EDO A1498
09AC9SOFTWAREASP A:352 , LYS A:359 , TYR A:413 , PRO A:415 , HOH A:2415 , HOH A:2542BINDING SITE FOR RESIDUE EDO A1499
10BC1SOFTWAREASP B:352 , LYS B:359 , TYR B:413 , PRO B:415 , HOH B:2441BINDING SITE FOR RESIDUE EDO B1499
11BC2SOFTWAREALA A:366 , HOH A:2490 , SER B:355 , ASP B:356 , ALA B:357 , EDO B:1503 , HOH B:2582 , HOH B:2583 , HOH B:2584BINDING SITE FOR RESIDUE EDO B1500
12BC3SOFTWAREGLU A:420 , HOH A:2483 , HOH A:2484 , GLU B:358 , GLN B:361 , HOH B:2585BINDING SITE FOR RESIDUE EDO B1501
13BC4SOFTWAREARG A:138 , HOH A:2218 , HOH A:2486 , HOH A:2543 , HOH A:2544BINDING SITE FOR RESIDUE EDO A1500
14BC5SOFTWARETYR B:23 , THR B:26 , GLY B:28 , THR B:29 , GLY B:67 , EDO B:1507 , HOH B:2041 , HOH B:2149BINDING SITE FOR RESIDUE EDO B1502
15BC6SOFTWAREASP A:188 , SER A:189 , PRO A:191 , HIS B:30 , GLY B:64 , HIS B:65BINDING SITE FOR RESIDUE EDO A1501
16BC7SOFTWAREASP A:85 , SER A:86 , GLY A:131 , HOH A:2035 , HOH A:2546BINDING SITE FOR RESIDUE EDO A1502
17BC8SOFTWAREARG A:367 , GLY A:369 , SER B:355 , ASP B:356 , EDO B:1500 , HOH B:2442 , HOH B:2457BINDING SITE FOR RESIDUE EDO B1503
18BC9SOFTWAREASN A:240 , PRO A:257 , LEU A:258 , TYR A:259 , HOH A:2343 , HOH A:2547BINDING SITE FOR RESIDUE EDO A1503
19CC1SOFTWARELYS B:468 , PRO B:489 , GLN B:490 , VAL B:491 , PRO B:492 , HOH B:2586BINDING SITE FOR RESIDUE EDO B1504
20CC2SOFTWAREARG B:403 , HOH B:2553 , HOH B:2555BINDING SITE FOR RESIDUE EDO B1505
21CC3SOFTWARESER B:86 , GLU B:89 , GLY B:131 , THR B:132BINDING SITE FOR RESIDUE EDO B1506
22CC4SOFTWAREHIS B:65 , EDO B:1502 , HOH B:2147 , HOH B:2587 , HOH B:2588 , HOH B:2589BINDING SITE FOR RESIDUE EDO B1507
23CC5SOFTWAREPHE A:152 , GLU A:157 , SER A:435 , ASP A:436 , PRO A:437 , HOH A:2228 , HOH A:2236 , HOH A:2548 , HOH A:2549BINDING SITE FOR RESIDUE EDO A1504
24CC6SOFTWAREGLU A:80 , LYS A:172 , ARG A:294 , HOH A:2253 , HOH A:2374 , HOH A:2550BINDING SITE FOR RESIDUE EDO A1505
25CC7SOFTWAREARG A:138 , ALA A:140 , HOH A:2136BINDING SITE FOR RESIDUE EDO A1506
26CC8SOFTWAREHIS B:333 , GLN B:334 , TRP B:349 , THR B:354 , GLU B:358 , HOH B:2428 , HOH B:2460BINDING SITE FOR RESIDUE EDO B1508
27CC9SOFTWAREPRO A:137 , ARG A:138 , PRO A:458 , HOH A:2206 , HOH A:2209 , HOH A:2505 , HOH A:2543 , HOH A:2551BINDING SITE FOR RESIDUE EDO A1507
28DC1SOFTWAREGLY A:87 , GLY A:90 , VAL A:91 , THR A:92 , HOH A:2150BINDING SITE FOR RESIDUE EDO A1508
29DC2SOFTWAREVAL A:42 , SER A:224 , HIS A:226 , HOH A:2068 , HOH A:2309 , HOH A:2552BINDING SITE FOR RESIDUE EDO A1509
30DC3SOFTWAREPRO A:410 , ALA A:411 , ALA A:412 , TYR A:413 , LEU A:414 , ALA A:417 , VAL A:422 , HOH A:2553BINDING SITE FOR RESIDUE EDO A1510
31DC4SOFTWAREARG B:353 , HOH B:2591 , HOH B:2592BINDING SITE FOR RESIDUE EDO B1509
32DC5SOFTWAREARG B:150 , VAL B:264 , ASP B:301 , GLU B:302 , TRP B:332 , TRP B:349 , TYR B:381 , TRP B:396 , TRP B:430 , GLU B:432 , HOH B:2269 , HOH B:2356 , HOH B:2479 , HOH B:2593BINDING SITE FOR RESIDUE GC2 B1510
33DC6SOFTWAREARG A:150 , VAL A:264 , ASP A:301 , GLU A:302 , TRP A:332 , TRP A:349 , TYR A:381 , TRP A:396 , TRP A:430 , GLU A:432 , HOH A:2257 , HOH A:2349 , HOH A:2448 , HOH A:2554BINDING SITE FOR RESIDUE GC2 A1511
34DC7SOFTWAREARG A:24 , THR A:26 , ARG A:27 , TYR A:56 , HOH B:2202BINDING SITE FOR RESIDUE EDO A1512

(-) 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 4C7F)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4C7F)

(-) Exons   (0, 0)

(no "Exon" information available for 4C7F)

(-) 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: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 d4c7fa1 A:1-138 automated matches                                                                                                         d4c7fa2 A:139-494 automated matches                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeee....eee....eeee..hhhhhhhhhhhhhhhhhhhh....ee.....eeeeee.........eeeeee..eeeeee.hhhhhhhhhhhhhhhhhhhhhh.......eee..eeeee.....eeeeeee......hhhhhhhhhhhhhh....eeeee..............hhhhhh....hhhhh.....hhhhhhhhhhhhhhh..eeeee......hhhhhhhhhhhh......................hhhhhhhhhhhhhhhhhh....eee.........hhhhhhhhhhhhhhhhhhh..eeeee.hhhhh......eeee......hhhhhhhhhhhhhh..eeee..........................hhhhhhh..........hhh.eeeeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4c7f A   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    


Chain B 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 d4c7fb1 B:2-138 automated matches                                                                                                        d4c7fb2 B:139-494 automated matches                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeee....ee......ee...hhhhhhhhhhhhhhhhhhhh....ee......eeeee.........eeeeee..eeeeee.hhhhhhhhhhhhhhhhhhhhhh........ee..eeeee.....eeeeeee......hhhhhhhhhhhhhh....eeeee..............hhhhhh....hhhhh.....hhhhhhhhhhhhhhh..eeeee......hhhhhhhhhhhh......................hhhhhhhhhhhhhhhhhh....eee.........hhhhhhhhhhhhhhhhhhh..eeeee.hhhhh......eeee......hhhhhhhhhhhhhh..eeee..........................hhhhhhh.hhhhh....hhh.eeeeeeee......hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4c7f B   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
   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, 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 4C7F)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4C7F)

(-) 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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  4c7f
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  Q9L068_STRCO | Q9L068
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  3.2.1.52
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  Q9L068_STRCO | Q9L068
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q9L068_STRCO | Q9L068: 4c7d 4c7g

(-) Related Entries Specified in the PDB File

4c7d 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)