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(-) Description

Title :  CRYSTAL STRUCTURE OF MUTANT (D318N) BACILLUS SUBTILIS FAMILY 3 GLYCOSIDE HYDROLASE (NAGZ) IN COMPLEX WITH GLCNAC-MURNAC (SPACE GROUP P1)
 
Authors :  J. P. Bacik, B. L. Mark
Date :  05 Sep 12  (Deposition) - 19 Dec 12  (Release) - 28 Jan 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Tim-Barrel, Hydrolase, Hydrolase-Substrate Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. P. Bacik, G. E. Whitworth, K. A. Stubbs, D. J. Vocadlo, B. L. Mark
Active Site Plasticity Within The Glycoside Hydrolase Nagz Underlies A Dynamic Mechanism Of Substrate Distortion.
Chem. Biol. V. 19 1471 2012
PubMed-ID: 23177201  |  Reference-DOI: 10.1016/J.CHEMBIOL.2012.09.016

(-) Compounds

Molecule 1 - UNCHARACTERIZED LIPOPROTEIN YBBD
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 18-642
    Gene: BSU01660, NAGZ, YBBD, YZBA
    Mutation: YES
    Organism Scientific: BACILLUS SUBTILIS SUBSP. SUBTILIS
    Organism Taxid: 224308
    Strain: 168
    Synonym: ORF1

 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, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1MUB4Ligand/IonN-ACETYLMURAMIC ACID
2NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1MUB2Ligand/IonN-ACETYLMURAMIC ACID
2NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1MUB2Ligand/IonN-ACETYLMURAMIC ACID
2NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:90 , PHE A:92 , ASP A:123 , VAL A:187 , ARG A:191 , LYS A:221 , HIS A:222 , SER A:233 , HIS A:234 , MET A:267 , ASN A:318 , ALA A:319 , MET A:322 , MUB A:702 , MUB A:703BINDING SITE FOR RESIDUE NAG A 701
2AC2SOFTWAREARG A:57 , ARG A:131 , HIS A:234 , ALA A:319 , ASN A:321 , MET A:322 , NAG A:701 , MUB A:703 , SER B:65BINDING SITE FOR RESIDUE MUB A 702
3AC3SOFTWAREARG A:57 , PHE A:92 , ARG A:131 , ARG A:191 , ASN A:321 , NAG A:701 , MUB A:702 , HOH A:815 , HOH A:992 , HOH A:1366 , SER B:65 , SER B:66 , HOH B:1189BINDING SITE FOR RESIDUE MUB A 703
4AC4SOFTWAREHIS B:234 , NAG B:702 , MUB B:703BINDING SITE FOR RESIDUE MUB B 701
5AC5SOFTWAREILE B:90 , PHE B:92 , ASP B:123 , ARG B:191 , LYS B:221 , HIS B:222 , SER B:233 , HIS B:234 , MET B:267 , ASN B:318 , ALA B:319 , MET B:322 , MUB B:701 , MUB B:703BINDING SITE FOR RESIDUE NAG B 702
6AC6SOFTWARESER A:65 , SER A:66 , ARG B:57 , PHE B:92 , VAL B:129 , ARG B:131 , ARG B:191 , HIS B:234 , ALA B:319 , ASN B:321 , MET B:322 , MUB B:701 , NAG B:702 , HOH B:1111 , HOH B:1135 , HOH B:1264BINDING SITE FOR RESIDUE MUB B 703

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4GYJ)

(-) Cis Peptide Bonds  (10, 10)

Asymmetric Unit
No.Residues
1Ser A:174 -Pro A:175
2Lys A:221 -His A:222
3Phe A:223 -Pro A:224
4Tyr A:399 -Pro A:400
5Leu A:445 -Pro A:446
6Ser B:174 -Pro B:175
7Lys B:221 -His B:222
8Phe B:223 -Pro B:224
9Tyr B:399 -Pro B:400
10Leu B:445 -Pro B:446

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4GYJ)

(-) 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:618
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhh.hhhhhhhhhee....ee........ee....hhhhhhhhhhhh..eee.hhhhh.hhhhhhhhhhhhhhhh.....eeee.................hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee...............hhhhh...hhhhhhhhhhhhhhhhhhh..eeeeeee...................hhhhhhhh.hhhhhhhhhh...eeee...........eee......eee.hhhhhhhhhh...........eee.....hhhhhh..hhhhhhhhhhhhh...ee......hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhh.hhhhhhhhhhhhhhhheeeee.hhh.........eeeeee.hhhhhhhhhhhhhhhhhh......eeeeee......hhhhhhhhhhh.eeeeee........ee..ee.....hhhhhhhhhhhhhhhhhhhh...eeeee..hhhhhhhh....eeee......ee..ee..hhhhhhhhhhh............ee.......eee.............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4gyj A  25 EASASKRAIDANQIVNRMSLDEKLGQMLMPDFRNWQKEGESSPQALTKMNDEVASLVKKYQFGGIILFAENVKTTKQTVQLTDDYQKASPKIPLMLSIDQEGGIVTRLGEGTNFPGNMALGAARSRINAYQTGSIIGKELSALGINTDFSPVVDINNNPDNPVIGVRSFSSNRELTSRLGLYTMKGLQRQDIASALKHFPGHGDTDVDSHYGLPLVSHGQERLREVELYPFQKAIDAGADMVMTAHVQFPAFDDTTYKSKLDGSDILVPATLSKKVMTGLLRQEMGFNGVIVTNALNMKAIADHFGQEEAVVMAVKAGVDIALMPASVTSLKEEQKFARVIQALKEAVKNGDIPEQQINNSVERIISLKIKRGMYPARNSDSTKEKIAKAKKIVGSKQHLKAEKKLAEKAVTVLKNEQHTLPFKPKKGSRILIVAPYEEQTASIEQTIHDLIKRKKIKPVSLSKMNFASQVFKTEHEKQVKEADYIITGSYVVKNDPVVNDGVIDDTISDSSKWATVFPRAVMKAALQHNKPFVLMSLRNPYDAANFEEAKALIAVYGFKGYANGRYLQPNIPAGVMAIFGQAKPKGTLPVDIPSVTKPGNTLYPLGYGLNIKTGRPL 642
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634        


Chain B from PDB  Type:PROTEIN  Length:617
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh.hhhhhhhhhee....ee........ee....hhhhhhhhhhhh..eee.hhhhh.hhhhhhhhhhhhhhhh.....eeee.................hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee...............hhhhh...hhhhhhhhhhhhhhhhhhh..eeeeeee...................hhhhhhhh.hhhhhhhhhh...eeee...........eee......eee.hhhhhhhhhh...........eee.....hhhhhh..hhhhhhhhhhhhh...ee......hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhh.hhhhhhhhhhhhhhhheeeee.hhh.........eeeeee.hhhhhhhhhhhhhhhhhh......eeeeee......hhhhhhhhhhh.eeeeee........ee..ee.....hhhhhhhhhhhhhhhhhhhh...eeeee..hhhhhhhh....eeee......ee..ee..hhhhhhhhhhh............ee.......eee.............. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gyj B  26 ASASKRAIDANQIVNRMSLDEKLGQMLMPDFRNWQKEGESSPQALTKMNDEVASLVKKYQFGGIILFAENVKTTKQTVQLTDDYQKASPKIPLMLSIDQEGGIVTRLGEGTNFPGNMALGAARSRINAYQTGSIIGKELSALGINTDFSPVVDINNNPDNPVIGVRSFSSNRELTSRLGLYTMKGLQRQDIASALKHFPGHGDTDVDSHYGLPLVSHGQERLREVELYPFQKAIDAGADMVMTAHVQFPAFDDTTYKSKLDGSDILVPATLSKKVMTGLLRQEMGFNGVIVTNALNMKAIADHFGQEEAVVMAVKAGVDIALMPASVTSLKEEQKFARVIQALKEAVKNGDIPEQQINNSVERIISLKIKRGMYPARNSDSTKEKIAKAKKIVGSKQHLKAEKKLAEKAVTVLKNEQHTLPFKPKKGSRILIVAPYEEQTASIEQTIHDLIKRKKIKPVSLSKMNFASQVFKTEHEKQVKEADYIITGSYVVKNDPVVNDGVIDDTISDSSKWATVFPRAVMKAALQHNKPFVLMSLRNPYDAANFEEAKALIAVYGFKGYANGRYLQPNIPAGVMAIFGQAKPKGTLPVDIPSVTKPGNTLYPLGYGLNIKTGRPL 642
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635
   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  (0, 0)

(no "SCOP Domain" information available for 4GYJ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (14, 14)

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 Related Entries

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        NAGZ_BACSU | P40406: 3bmx 3lk6 3nvd 4gyk

(-) Related Entries Specified in the PDB File

4gyk