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(-) Description

Title :  CRYSTAL STRUCTURE OF PASTEURELLA MULTOCIDA N-ACETYL-D-NEURAMINIC ACID LYASE
 
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./Biol. Unit :  A,B,C,D
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, C, D
    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
    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

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 21)

Asymmetric/Biological Unit (2, 21)
No.NameCountTypeFull Name
1EDO14Ligand/Ion1,2-ETHANEDIOL
2PO47Ligand/IonPHOSPHATE ION

(-) Sites  (21, 21)

Asymmetric Unit (21, 21)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:180 , PRO A:181 , ASN A:182 , HIS A:183 , HOH A:721BINDING SITE FOR RESIDUE PO4 A 301
02AC2SOFTWAREHIS A:120 , ASP A:123 , HOH A:469BINDING SITE FOR RESIDUE PO4 A 302
03AC3SOFTWAREALA A:10 , GLY A:46 , SER A:47 , THR A:48 , TYR A:136 , LYS A:164 , HOH A:526BINDING SITE FOR RESIDUE EDO A 303
04AC4SOFTWAREASP A:190 , GLU A:191 , HOH A:461 , HOH A:662 , HOH A:723BINDING SITE FOR RESIDUE EDO A 304
05AC5SOFTWAREPRO A:158 , LEU A:161 , ASN A:182 , HOH A:636BINDING SITE FOR RESIDUE EDO A 305
06AC6SOFTWAREPHE A:165 , ALA A:167 , PHE A:170 , GLY A:188 , PHE A:189BINDING SITE FOR RESIDUE EDO A 306
07AC7SOFTWAREALA B:179 , TYR B:180 , PRO B:181 , ASN B:182 , HIS B:183 , HOH B:700BINDING SITE FOR RESIDUE PO4 B 301
08AC8SOFTWAREHIS B:120 , ASP B:123 , HOH B:687 , HOH B:696BINDING SITE FOR RESIDUE PO4 B 302
09AC9SOFTWAREALA B:10 , GLY B:46 , SER B:47 , THR B:48 , TYR B:136 , LYS B:164 , HOH B:458BINDING SITE FOR RESIDUE EDO B 303
10BC1SOFTWAREASP B:190 , GLU B:191 , HOH B:522 , HOH B:561 , HOH B:628BINDING SITE FOR RESIDUE EDO B 304
11BC2SOFTWAREPHE B:165 , ALA B:167 , PHE B:170 , ALA B:187 , GLY B:188 , PHE B:189 , ALA B:196BINDING SITE FOR RESIDUE EDO B 305
12BC3SOFTWARELEU B:161 , ASN B:182 , HOH B:711BINDING SITE FOR RESIDUE EDO B 306
13BC4SOFTWARETYR C:180 , PRO C:181 , ASN C:182 , HIS C:183BINDING SITE FOR RESIDUE PO4 C 301
14BC5SOFTWAREALA C:10 , TYR C:43 , GLY C:46 , SER C:47 , THR C:48 , TYR C:136 , LYS C:164 , HOH C:439 , HOH C:613 , HOH C:655BINDING SITE FOR RESIDUE EDO C 302
15BC6SOFTWAREASP C:190 , GLU C:191 , HOH C:578 , HOH C:632BINDING SITE FOR RESIDUE EDO C 303
16BC7SOFTWAREASN C:248 , LYS C:280 , PHE C:283BINDING SITE FOR RESIDUE EDO C 304
17BC8SOFTWAREHIS C:120 , ASP C:123 , HOH C:465 , HOH C:644BINDING SITE FOR RESIDUE EDO C 305
18BC9SOFTWARETYR D:180 , PRO D:181 , ASN D:182 , HIS D:183 , HOH D:624 , HOH D:662BINDING SITE FOR RESIDUE PO4 D 301
19CC1SOFTWARELYS D:119 , HIS D:120 , ASP D:123 , HOH D:648BINDING SITE FOR RESIDUE PO4 D 302
20CC2SOFTWAREALA D:10 , GLY D:46 , SER D:47 , THR D:48 , TYR D:136 , LYS D:164 , HOH D:449BINDING SITE FOR RESIDUE EDO D 303
21CC3SOFTWAREASP D:190 , GLU D:191 , HOH D:498 , HOH D:611 , HOH D:635BINDING SITE FOR RESIDUE EDO D 304

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Glu A:270 -Pro A:271
2Glu B:270 -Pro B:271
3Glu C:270 -Pro C:271
4Glu D:270 -Pro D:271

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4IMC)

(-) Sequences/Alignments

Asymmetric/Biological 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 d4imca_ 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
                 4imc A   2 KNLKGIFSALLVSFNADGSINEKGLRQIVRYNIDKMKVDGLYVGGSTGENFMLSTEEKKEIFRIAKDEAKDEIALIAQVGSVNLQEAIELGKYATELGYDSLSAVTPFYYKFSFPEIKHYYDSIIEATGNYMIVYSIPFLTGVNIGVEQFGELYKNPKVLGVKFTAGDFYLLERLKKAYPNHLIWAGFDEMMLPAASLGVDGAIGSTFNVNGVRARQIFELTQAGKLKEALEIQHVTNDLIEGILANGLYLTIKELLKLDGVEAGYCREPMTKELSSEKVAFAKELKAKYLS 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 d4imcb_ 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...hhhhhhhhh....eeeeee...hhhhhhhhhhhh...eeee.hhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4imc B   2 KNLKGIFSALLVSFNADGSINEKGLRQIVRYNIDKMKVDGLYVGGSTGENFMLSTEEKKEIFRIAKDEAKDEIALIAQVGSVNLQEAIELGKYATELGYDSLSAVTPFYYKFSFPEIKHYYDSIIEATGNYMIVYSIPFLTGVNIGVEQFGELYKNPKVLGVKFTAGDFYLLERLKKAYPNHLIWAGFDEMMLPAASLGVDGAIGSTFNVNGVRARQIFELTQAGKLKEALEIQHVTNDLIEGILANGLYLTIKELLKLDGVEAGYCREPMTKELSSEKVAFAKELKAKYLS 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 C from PDB  Type:PROTEIN  Length:292
                                                                                                                                                                                                                                                                                                                                    
               SCOP domains d4imcc_ C: 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.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4imc C   2 KNLKGIFSALLVSFNADGSINEKGLRQIVRYNIDKMKVDGLYVGGSTGENFMLSTEEKKEIFRIAKDEAKDEIALIAQVGSVNLQEAIELGKYATELGYDSLSAVTPFYYKFSFPEIKHYYDSIIEATGNYMIVYSIPFLTGVNIGVEQFGELYKNPKVLGVKFTAGDFYLLERLKKAYPNHLIWAGFDEMMLPAASLGVDGAIGSTFNVNGVRARQIFELTQAGKLKEALEIQHVTNDLIEGILANGLYLTIKELLKLDGVEAGYCREPMTKELSSEKVAFAKELKAKYLS 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 D from PDB  Type:PROTEIN  Length:292
                                                                                                                                                                                                                                                                                                                                    
               SCOP domains d4imcd_ D: 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
                 4imc D   2 KNLKGIFSALLVSFNADGSINEKGLRQIVRYNIDKMKVDGLYVGGSTGENFMLSTEEKKEIFRIAKDEAKDEIALIAQVGSVNLQEAIELGKYATELGYDSLSAVTPFYYKFSFPEIKHYYDSIIEATGNYMIVYSIPFLTGVNIGVEQFGELYKNPKVLGVKFTAGDFYLLERLKKAYPNHLIWAGFDEMMLPAASLGVDGAIGSTFNVNGVRARQIFELTQAGKLKEALEIQHVTNDLIEGILANGLYLTIKELLKLDGVEAGYCREPMTKELSSEKVAFAKELKAKYLS 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)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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, 4)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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        NANA_PASMU | Q9CKB0: 4imd 4ime 4imf 4img

(-) Related Entries Specified in the PDB File

4imd 4ime 4imf 4img