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(-) Description

Title :  CRYSTAL STRUCTURE OF SALMONELLA TYPHIMURIUM FAMILY 3 GLYCOSIDE HYDROLASE (NAGZ) BOUND TO GLCNAC
 
Authors :  J. P. Bacik, B. L. Mark
Date :  30 Aug 12  (Deposition) - 19 Dec 12  (Release) - 16 Jan 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.35
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Tim-Barrel, Hydrolase (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 - BETA-HEXOSAMINIDASE
    Chains: A, B
    EC Number: 3.2.1.52
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: NAGZ, STM1209
    Organism Scientific: SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM
    Organism Taxid: 99287
    Strain: LT2 / SGSC1412 / ATCC 700720
    Synonym: BETA-N-ACETYLHEXOSAMINIDASE, N-ACETYL-BETA-GLUCOSAMINIDASE

 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  (3, 5)

Asymmetric Unit (3, 5)
No.NameCountTypeFull Name
1MES1Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
2NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
3NDG2Ligand/Ion2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1MES-1Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
2NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
3NDG1Ligand/Ion2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
Biological Unit 2 (3, 3)
No.NameCountTypeFull Name
1MES1Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
2NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
3NDG1Ligand/Ion2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:30 , ASP A:62 , ARG A:133 , LYS A:163 , HIS A:164 , MET A:210 , ASP A:248 , HOH A:580 , HOH A:618BINDING SITE FOR RESIDUE NDG A 401
2AC2SOFTWAREILE A:30 , ASP A:62 , ARG A:133 , LYS A:163 , HIS A:164 , MET A:210 , ASP A:248 , HOH A:580BINDING SITE FOR RESIDUE NAG A 402
3AC3SOFTWAREILE B:30 , ASP B:62 , ARG B:133 , LYS B:163 , HIS B:164 , MET B:210 , ASP B:248 , HOH B:577 , HOH B:605BINDING SITE FOR RESIDUE NDG B 401
4AC4SOFTWAREARG A:311 , ARG A:312 , ASP A:316 , HOH A:573 , HOH A:899 , SER B:310 , ARG B:312 , HOH B:528 , HOH B:953BINDING SITE FOR RESIDUE MES B 403
5AC5SOFTWAREILE B:30 , ASP B:62 , ARG B:133 , LYS B:163 , HIS B:164 , MET B:210 , ASP B:248 , HOH B:577 , HOH B:865BINDING SITE FOR RESIDUE NAG B 402

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Ala A:118 -Pro A:119
2Lys A:163 -His A:164
3Phe A:165 -Pro A:166
4Ala B:118 -Pro B:119
5Lys B:163 -His B:164
6Phe B:165 -Pro B:166

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4GVF)

(-) 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:340
                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains d4gvfa_ A: automated matches                                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee.......hhhhhhhhh...eeeeeehhhhh.hhhhhhhhhhhhhhhh....eeee.eee..ee............hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....ee.............hhhhh...hhhhhhhhhhhhhhhhhhhh...eeeee...................hhhhhhhhhhhhhhhhhhh....eeee...........hhhhhhhhhh...........eeeeee.hhh.hhhhhhhhhhhhhhhhhh..eeee..hhhhhhhhhhhh....hhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gvf A   1 MGPVMLNVEGCELDAEEREILAHPLVGGLILFTRNYHDPEQLRELVRQIRAASRNHLVVAVDQEGGRVQRFREGFTRLPAAQSFFALHGLEEGGRLAQEAGWLMASEMIAMDIDISFAPVLDVGHISAAIGERSYHADPAKALAMATRFIDGMHDAGMKTTGKHFPGHGAVTADSHKETPCDPRPETDIRGKDMSVFRTLISENKLDAIMPAHVIYRAIDPRPASGSPYWLKTVLRQELGFDGVIFSDDLSMEGAAIMGSYAERAQASLDAGCDMILVCNNRKGAVSVLDNLSPIKAERVTRLYHKGSFSRRELMDSARWKTASAQLNQLHERWQEEKAG 340
                                    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


Chain B from PDB  Type:PROTEIN  Length:328
                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains d4gvfb_ B: automated matches                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee.......hhhhhhhhh...eeeeeehhhhh.hhhhhhhhhhhhhhhh....eeee.eee..ee............hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....ee.............hhhhh...hhhhhhhhhhhhhhhhhhhh...eeeee..............hhhhhhhhhhhhhhhhhhh....eeee...........hhhhhhhhhh...........eeeeee...hhhhhhhhhhhh..eeee..hhhhhhhhhhhh....hhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gvf B   1 MGPVMLNVEGCELDAEEREILAHPLVGGLILFTRNYHDPEQLRELVRQIRAASRNHLVVAVDQEGGRVQRFREGFTRLPAAQSFFALHGLEEGGRLAQEAGWLMASEMIAMDIDISFAPVLDVGHISAAIGERSYHADPAKALAMATRFIDGMHDAGMKTTGKHFPGHGAVTETPCDPRPETDIRGKDMSVFRTLISENKLDAIMPAHVIYRAIDPRPASGSPYWLKTVLRQELGFDGVIFSDDLSSYAERAQASLDAGCDMILVCNNRKGAVSVLDNLSPIKAERVTRLYHKGSFSRRELMDSARWKTASAQLNQLHERWQEEKAGH 341
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170 ||    185       195       205       215       225       235       245     ||263       273       283       293       303       313       323       333        
                                                                                                                                                                                                     172|                                                                      251|                                                                                 
                                                                                                                                                                                                      178                                                                       260
   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  (1, 2)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (14, 14)

Asymmetric Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Ala A:118 - Pro A:119   [ RasMol ]  
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    Lys A:163 - His A:164   [ RasMol ]  
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 Related Entries

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        NAGZ_SALTY | Q8ZQ06: 4gvg 4gvh 4gvi 4hzm

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