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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 P1211)
 
Authors :  J. P. Bacik, B. L. Mark
Date :  05 Sep 12  (Deposition) - 19 Dec 12  (Release) - 08 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
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 - GLYCOSIDE HYDROLASE NAGZ
    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, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1MUB2Ligand/IonN-ACETYLMURAMIC ACID
2NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1MUB1Ligand/IonN-ACETYLMURAMIC ACID
2NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1MUB1Ligand/IonN-ACETYLMURAMIC ACID
2NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:92 , ASP A:123 , ARG A:131 , ARG A:191 , LYS A:221 , HIS A:222 , HIS A:226 , MET A:267 , ASN A:318 , MUB A:702 , HOH A:1226BINDING SITE FOR RESIDUE NAG A 701
2AC2SOFTWAREARG A:131 , ASN A:318 , MET A:322 , NAG A:701 , HOH A:1210BINDING SITE FOR RESIDUE MUB A 702
3AC3SOFTWAREPHE B:92 , ASP B:123 , ARG B:191 , LYS B:221 , HIS B:222 , HIS B:226 , MET B:267 , ASN B:318 , MUB B:702BINDING SITE FOR RESIDUE NAG B 701
4AC4SOFTWAREARG B:131 , MET B:322 , NAG B:701 , HOH B:1246 , HOH B:1290 , HOH B:1377BINDING SITE FOR RESIDUE MUB B 702

(-) SS Bonds  (0, 0)

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

(-) 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 4GYK)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4GYK)

(-) 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:616
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhee....ee........ee....hhhhhhhhhhhh..eee.hhhhh.hhhhhhhhhhhhhhh......eeee.................hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee...............hhhhh...hhhhhhhhhhhhhhhhhhh..eeeeeee...................hhhhhhhh.hhhhhhhhhh...eeee...........eee......eee.hhhhhhhhhh...........eee.....hhhhhhhhhhhhhhhhhhhhh...ee......hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhh.hhhhhhhhhhhhhhhheeeee.hhh.........eeeeee.hhhhhhhhhhhhhhhhhh......eeeeee......hhhhhhhhhhh.eeeeee........ee..ee........hhhhhhhhhhhhhhhhh...eeeee..hhhhhhhh....eeee......ee..ee..hhhhhhhhhhh............ee.......eee.............. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gyk A  27 SASKRAIDANQIVNRMSLDEKLGQMLMPDFRNWQKEGESSPQALTKMNDEVASLVKKYQFGGIILFAENVKTTKQTVQLTDDYQKASPKIPLMLSIDQEGGIVTRLGEGTNFPGNMALGAARSRINAYQTGSIIGKELSALGINTDFSPVVDINNNPDNPVIGVRSFSSNRELTSRLGLYTMKGLQRQDIASALKHFPGHGDTDVDSHYGLPLVSHGQERLREVELYPFQKAIDAGADMVMTAHVQFPAFDDTTYKSKLDGSDILVPATLSKKVMTGLLRQEMGFNGVIVTNALNMKAIADHFGQEEAVVMAVKAGVDIALMPASVTSLKEEQKFARVIQALKEAVKNGDIPEQQINNSVERIISLKIKRGMYPARNSDSTKEKIAKAKKIVGSKQHLKAEKKLAEKAVTVLKNEQHTLPFKPKKGSRILIVAPYEEQTASIEQTIHDLIKRKKIKPVSLSKMNFASQVFKTEHEKQVKEADYIITGSYVVKNDPVVNDGVIDDTISDSSKWATVFPRAVMKAALQHNKPFVLMSLRNPYDAANFEEAKALIAVYGFKGYANGRYLQPNIPAGVMAIFGQAKPKGTLPVDIPSVTKPGNTLYPLGYGLNIKTGRPL 642
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636      


Chain B from PDB  Type:PROTEIN  Length:609
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhee....ee........ee....hhhhhhhhhhhh..eee.hhhhh.hhhhhhhhhhhhhhhh.....eeee.................hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee...............hhhhh...hhhhhhhhhhhhhhhhhhh..eeeeeee...................hhhhhhhhhhhhhhhhhhh...eeee...........eee......eee.hhhhhhhhhh...........eee.....hhhhhhhhhhhhhhhhhhhhh...ee......hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhh.hhhhhhhhhhhhhhhheeeee.hhh.........eeeeee.hhhhhhhhhhhhhhhhhh......eeeeee......hhhhhhhhhhh.eeeeee........ee..ee........hhhhhhhhhhhhhhhhh...eeeee..hhhhhhhh....eeee......ee..ee..hhhhhhhhhhh............ee.......eee.............. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gyk B  34 DANQIVNRMSLDEKLGQMLMPDFRNWQKEGESSPQALTKMNDEVASLVKKYQFGGIILFAENVKTTKQTVQLTDDYQKASPKIPLMLSIDQEGGIVTRLGEGTNFPGNMALGAARSRINAYQTGSIIGKELSALGINTDFSPVVDINNNPDNPVIGVRSFSSNRELTSRLGLYTMKGLQRQDIASALKHFPGHGDTDVDSHYGLPLVSHGQERLREVELYPFQKAIDAGADMVMTAHVQFPAFDDTTYKSKLDGSDILVPATLSKKVMTGLLRQEMGFNGVIVTNALNMKAIADHFGQEEAVVMAVKAGVDIALMPASVTSLKEEQKFARVIQALKEAVKNGDIPEQQINNSVERIISLKIKRGMYPARNSDSTKEKIAKAKKIVGSKQHLKAEKKLAEKAVTVLKNEQHTLPFKPKKGSRILIVAPYEEQTASIEQTIHDLIKRKKIKPVSLSKMNFASQVFKTEHEKQVKEADYIITGSYVVKNDPVVNDGVIDDTISDSSKWATVFPRAVMKAALQHNKPFVLMSLRNPYDAANFEEAKALIAVYGFKGYANGRYLQPNIPAGVMAIFGQAKPKGTLPVDIPSVTKPGNTLYPLGYGLNIKTGRPL 642
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633
   Legend:   → Mismatch (orange background)
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  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 4GYK)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (14, 14)

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 Related Entries

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UniProtKB/Swiss-Prot
        NAGZ_BACSU | P40406: 3bmx 3lk6 3nvd 4gyj

(-) Related Entries Specified in the PDB File

4gyj