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(-) Description

Title :  CRYSTAL STRUCTURE OF PASTEURELLA MULTOCIDA N-ACETYL-D-NEURAMINIC ACID LYASE K164 MUTANT COMPLEXED WITH N-ACETYLNEURAMINIC ACID
 
Authors :  A. J. Fisher, N. Huynh
Date :  02 Jan 13  (Deposition) - 06 Nov 13  (Release) - 11 Dec 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Tim Barrel, Schiff Base, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Huynh, A. Aye, Y. Li, H. Yu, H. Cao, V. K. Tiwari, D. W. Shin, X. Chen, A. J. Fisher
Structural Basis For Substrate Specificity And Mechanism Of N-Acetyl-D-Neuraminic Acid Lyase From Pasteurella Multocida
Biochemistry V. 52 8570 2013
PubMed-ID: 24152047  |  Reference-DOI: 10.1021/BI4011754

(-) Compounds

Molecule 1 - N-ACETYLNEURAMINATE LYASE
    Chains: A, B
    EC Number: 4.1.3.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET22B(+)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: NANA, PM1715
    Mutation: YES
    Organism Scientific: PASTEURELLA MULTOCIDA SUBSP. GALLICIDA
    Organism Taxid: 1169409
    Strain: P1059
    Synonym: N-ACETYLNEURAMINATE PYRUVATE-LYASE, N-ACETYLNEURAMINIC ACID ALDOLASE, SIALATE LYASE, SIALIC ACID ALDOLASE, SIALIC ACID LYASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 10)

Asymmetric Unit (4, 10)
No.NameCountTypeFull Name
1CL3Ligand/IonCHLORIDE ION
2IPA2Ligand/IonISOPROPYL ALCOHOL
3ME23Ligand/Ion1-ETHOXY-2-(2-METHOXYETHOXY)ETHANE
4SI32Ligand/Ion5-(ACETYLAMINO)-3,5-DIDEOXY-D-GLYCERO-D-GALACTO-NON-2-ULOSONIC ACID
Biological Unit 1 (3, 14)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2IPA4Ligand/IonISOPROPYL ALCOHOL
3ME26Ligand/Ion1-ETHOXY-2-(2-METHOXYETHOXY)ETHANE
4SI34Ligand/Ion5-(ACETYLAMINO)-3,5-DIDEOXY-D-GLYCERO-D-GALACTO-NON-2-ULOSONIC ACID

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREALA A:10 , GLY A:46 , SER A:47 , THR A:48 , TYR A:136 , ILE A:138 , THR A:166 , GLY A:188 , PHE A:189 , ASP A:190 , GLU A:191 , ILE A:205 , GLY A:206 , SER A:207 , LEU A:250 , TYR A:251 , HOH A:412BINDING SITE FOR RESIDUE SI3 A 301
02AC2SOFTWAREASP A:169 , TYR A:171 , GLU A:243 , HOH A:415BINDING SITE FOR RESIDUE ME2 A 302
03AC3SOFTWAREGLY A:168BINDING SITE FOR RESIDUE CL A 303
04AC4SOFTWAREHIS A:183BINDING SITE FOR RESIDUE CL A 304
05AC5SOFTWAREPHE A:113 , GLN A:150BINDING SITE FOR RESIDUE IPA A 305
06AC6SOFTWAREPRO A:158 , VAL A:160 , LEU A:161 , ASN A:182BINDING SITE FOR RESIDUE IPA A 306
07AC7SOFTWAREALA B:10 , GLY B:46 , SER B:47 , THR B:48 , TYR B:136 , ILE B:138 , THR B:166 , GLY B:188 , PHE B:189 , ASP B:190 , GLU B:191 , ILE B:205 , GLY B:206 , SER B:207 , LEU B:250 , TYR B:251 , HOH B:518BINDING SITE FOR RESIDUE SI3 B 301
08AC8SOFTWAREPRO A:139 , PHE A:140 , LEU A:141 , PRO B:139 , PHE B:140 , LEU B:141 , GLY B:143 , HOH B:527BINDING SITE FOR RESIDUE ME2 B 302
09AC9SOFTWARETYR B:171 , GLU B:243 , HOH B:418 , HOH B:448BINDING SITE FOR RESIDUE ME2 B 303
10BC1SOFTWARETYR B:180 , PRO B:181 , ASN B:182 , HIS B:183BINDING SITE FOR RESIDUE CL B 304

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Glu A:270 -Pro A:271
2Glu B:270 -Pro B:271

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4IMF)

(-) 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:292
                                                                                                                                                                                                                                                                                                                                    
               SCOP domains d4imfa_ A: automated matches                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee...........hhhhhhhhhhhhhhh....eeee.hhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhh..eeeee.......hhhhhhhhhhhhhhhhh..eeeeehhhhhh...hhhhhhhhh....eeeeee...hhhhhhhhhhhh...eeee.hhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4imf A   2 KNLKGIFSALLVSFNADGSINEKGLRQIVRYNIDKMKVDGLYVGGSTGENFMLSTEEKKEIFRIAKDEAKDEIALIAQVGSVNLQEAIELGKYATELGYDSLSAVTPFYYKFSFPEIKHYYDSIIEATGNYMIVYSIPFLTGVNIGVEQFGELYKNPKVLGVAFTAGDFYLLERLKKAYPNHLIWAGFDEMMLPAASLGVDGAIGSTFNVNGVRARQIFELTQAGKLKEALEIQHVTNDLIEGILANGLYLTIKELLKLDGVEAGYCREPMTKELSSEKVAFAKELKAKYLS 293
                                    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  


Chain B from PDB  Type:PROTEIN  Length:292
                                                                                                                                                                                                                                                                                                                                    
               SCOP domains d4imfb_ B: automated matches                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee...........hhhhhhhhhhhhhhh....eeee.hhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhh..eeeee.......hhhhhhhhhhhhhhhhh..eeeeehhhhhh...hhhhhhhhh....eeeeee...hhhhhhhhhhhh...eeee.hhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4imf B   2 KNLKGIFSALLVSFNADGSINEKGLRQIVRYNIDKMKVDGLYVGGSTGENFMLSTEEKKEIFRIAKDEAKDEIALIAQVGSVNLQEAIELGKYATELGYDSLSAVTPFYYKFSFPEIKHYYDSIIEATGNYMIVYSIPFLTGVNIGVEQFGELYKNPKVLGVAFTAGDFYLLERLKKAYPNHLIWAGFDEMMLPAASLGVDGAIGSTFNVNGVRARQIFELTQAGKLKEALEIQHVTNDLIEGILANGLYLTIKELLKLDGVEAGYCREPMTKELSSEKVAFAKELKAKYLS 293
                                    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
   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 4IMF)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Glu A:270 - Pro A:271   [ RasMol ]  
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