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(-) Description

Title :  CRYSTAL STRUCTURE OF SALMONELLA TYPHIMURIUM FAMILY 3 GLYCOSIDE HYDROLASE (NAGZ)
 
Authors :  J. P. Bacik, B. L. Mark
Date :  30 Aug 12  (Deposition) - 19 Dec 12  (Release) - 19 Dec 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
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  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1MES2Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1MES1Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1MES1Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:32 , THR A:33 , ARG A:34 , ARG A:70 , MET A:252 , ASN A:280 , HOH A:7317BINDING SITE FOR RESIDUE MES A 7001
2AC2SOFTWAREARG A:311 , ARG A:312 , ASP A:316 , HOH A:7427 , SER B:310 , HOH B:7196 , HOH B:7289 , HOH B:7385BINDING SITE FOR RESIDUE MES B 7001

(-) SS Bonds  (0, 0)

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

(-) 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 4GVG)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4GVG)

(-) 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:331
                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains d4gvga_ 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....hhhhhhhhhhhhh..eee...hhhhhhhhhhhh....hhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gvg A   1 MGPVMLNVEGCELDAEEREILAHPLVGGLILFTRNYHDPEQLRELVRQIRAASRNHLVVAVDQEGGRVQRFREGFTRLPAAQSFFALHGLEEGGRLAQEAGWLMASEMIAMDIDISFAPVLDVGHISAAIGERSYHADPAKALAMATRFIDGMHDAGMKTTGKHFPGHGAVTHKETPCDPRPETDIRGKDMSVFRTLISENKLDAIMPAHVIYRAIDPRPASGSPYWLKTVLRQELGFDGVIFSDDLSMGSYAERAQASLDAGCDMILVCNNRKGAVSVLDNLSPIKAERVTRLYHKGSFSRRELMDSARWKTASAQLNQLHERWQEEKAG 340
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170 ||    183       193       203       213       223       233       243       259       269       279       289       299       309       319       329       339 
                                                                                                                                                                                                     172|                                                                         252|                                                                                 
                                                                                                                                                                                                      176                                                                          259                                                                                 


Chain B from PDB  Type:PROTEIN  Length:330
                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains d4gvgb_ 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....hhhhhhhhhhhhh..eee...hhhhhhhhhhhh....hhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4gvg B   1 MGPVMLNVEGCELDAEEREILAHPLVGGLILFTRNYHDPEQLRELVRQIRAASRNHLVVAVDQEGGRVQRFREGFTRLPAAQSFFALHGLEEGGRLAQEAGWLMASEMIAMDIDISFAPVLDVGHISAAIGERSYHADPAKALAMATRFIDGMHDAGMKTTGKHFPGHGAVTETPCDPRPETDIRGKDMSVFRTLISENKLDAIMPAHVIYRAIDPRPASGSPYWLKTVLRQELGFDGVIFSDDLSMGSYAERAQASLDAGCDMILVCNNRKGAVSVLDNLSPIKAERVTRLYHKGSFSRRELMDSARWKTASAQLNQLHERWQEEKAGH 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      |261       271       281       291       301       311       321       331       341
                                                                                                                                                                                                     172|                                                                       252|                                                                                  
                                                                                                                                                                                                      178                                                                        259
   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  (1, 2)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (14, 14)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        NAGZ_SALTY | Q8ZQ06: 4gvf 4gvh 4gvi 4hzm

(-) Related Entries Specified in the PDB File

4gvf 4gvh 4gvi