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(-) Description

Title :  CRYSTAL STRUCTURE OF PASTEURELLA MULTOCIDA N-ACETYL-D-NEURAMINIC ACID LYASE K164 MUTANT COMPLEXED WITH N-GLYCOLYLNEURAMINIC 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 :  1.85
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  (2, 10)

Asymmetric Unit (2, 10)
No.NameCountTypeFull Name
1ME28Ligand/Ion1-ETHOXY-2-(2-METHOXYETHOXY)ETHANE
2NGF2Ligand/Ion3,5-DIDEOXY-5-[(HYDROXYACETYL)AMINO]-D-GLYCERO-D-GALACTO-NON-2-ULOSONIC ACID
Biological Unit 1 (2, 20)
No.NameCountTypeFull Name
1ME216Ligand/Ion1-ETHOXY-2-(2-METHOXYETHOXY)ETHANE
2NGF4Ligand/Ion3,5-DIDEOXY-5-[(HYDROXYACETYL)AMINO]-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 , PHE A:140 , THR A:166 , GLY A:188 , PHE A:189 , ASP A:190 , GLU A:191 , GLY A:206 , SER A:207 , LEU A:250 , TYR A:251 , HOH A:833BINDING SITE FOR RESIDUE NGF A 501
02AC2SOFTWARELYS A:112 , PHE A:140 , LEU A:141 , GLY A:143 , HOH A:779 , HOH A:790 , HOH A:892 , LYS B:112 , PHE B:140 , GLY B:143BINDING SITE FOR RESIDUE ME2 A 502
03AC3SOFTWARETHR A:129 , GLY A:130 , LYS A:159 , HOH A:841BINDING SITE FOR RESIDUE ME2 A 503
04AC4SOFTWAREHIS A:120 , GLU A:275 , SER A:278 , HOH A:740BINDING SITE FOR RESIDUE ME2 A 504
05AC5SOFTWAREVAL A:148 , TYR A:171 , LEU A:172 , ARG A:175 , GLU A:243 , HOH A:621 , HOH A:649BINDING SITE FOR RESIDUE ME2 A 505
06AC6SOFTWARELEU A:246 , ALA A:247 , LYS A:280BINDING SITE FOR RESIDUE ME2 A 506
07AC7SOFTWAREALA B:10 , TYR B:43 , 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 , GLY B:206 , SER B:207 , LEU B:250 , TYR B:251 , HOH B:799BINDING SITE FOR RESIDUE NGF B 501
08AC8SOFTWAREILE B:146 , GLY B:147 , VAL B:148 , TYR B:171 , GLU B:243 , HOH B:663 , HOH B:926BINDING SITE FOR RESIDUE ME2 B 502
09AC9SOFTWAREASN B:248 , SER B:277 , GLU B:279 , LYS B:280 , PHE B:283BINDING SITE FOR RESIDUE ME2 B 503
10BC1SOFTWAREASP B:240 , PHE B:283 , GLU B:286 , LEU B:287 , LYS B:290 , TYR B:291 , HOH B:770BINDING SITE FOR RESIDUE ME2 B 504

(-) SS Bonds  (0, 0)

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

(-) 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 4IMG)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4IMG)

(-) 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:293
                                                                                                                                                                                                                                                                                                                                     
               SCOP domains d4imga_ A: automated matches                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee...........hhhhhhhhhhhhhhh....eeee.hhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhhhh..eeeeehhhhhh...hhhhhhhhhh...eeeeee...hhhhhhhhhhhh...eeee.hhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4img A   1 MKNLKGIFSALLVSFNADGSINEKGLRQIVRYNIDKMKVDGLYVGGSTGENFMLSTEEKKEIFRIAKDEAKDEIALIAQVGSVNLQEAIELGKYATELGYDSLSAVTPFYYKFSFPEIKHYYDSIIEATGNYMIVYSIPFLTGVNIGVEQFGELYKNPKVLGVAFTAGDFYLLERLKKAYPNHLIWAGFDEMMLPAASLGVDGAIGSTFNVNGVRARQIFELTQAGKLKEALEIQHVTNDLIEGILANGLYLTIKELLKLDGVEAGYCREPMTKELSSEKVAFAKELKAKYLS 293
                                    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   


Chain B from PDB  Type:PROTEIN  Length:293
                                                                                                                                                                                                                                                                                                                                     
               SCOP domains d4imgb_ B: automated matches                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee...........hhhhhhhhhhhhhhh....eeee.hhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhhhh..eeeeehhhhhh...hhhhhhhhhh...eeeeee...hhhhhhhhhhhh...eeee.hhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4img B   1 MKNLKGIFSALLVSFNADGSINEKGLRQIVRYNIDKMKVDGLYVGGSTGENFMLSTEEKKEIFRIAKDEAKDEIALIAQVGSVNLQEAIELGKYATELGYDSLSAVTPFYYKFSFPEIKHYYDSIIEATGNYMIVYSIPFLTGVNIGVEQFGELYKNPKVLGVAFTAGDFYLLERLKKAYPNHLIWAGFDEMMLPAASLGVDGAIGSTFNVNGVRARQIFELTQAGKLKEALEIQHVTNDLIEGILANGLYLTIKELLKLDGVEAGYCREPMTKELSSEKVAFAKELKAKYLS 293
                                    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
   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 4IMG)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)

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4imc 4imd 4ime 4imf