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(-) Description

Title :  X-RAY CRYSTAL STRUCTURE OF N-ACETYLNEURAMINIC ACID LYASE IN COMPLEX WITH PYRUVATE, WITH THE PHENYLALANINE AT POSITION 190 REPLACED WITH THE NON-CANONICAL AMINO ACID DIHYDROXYPROPYLCYSTEINE.
 
Authors :  C. L. Windle, C. H. Trinh, A. R. Pearson, A. S. Nelson, A. Berry
Date :  25 Jul 16  (Deposition) - 22 Mar 17  (Release) - 29 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Aldolase, Non-Canonical Amino Acid, Tim Barrel, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. L. Windle, K. J. Simmons, J. R. Ault, C. H. Trinh, A. Nelson, A. R. Pearson, A. Berry
Extending Enzyme Molecular Recognition With An Expanded Amino Acid Alphabet.
Proc. Natl. Acad. Sci. V. 114 2610 2017 U. S. A.
PubMed-ID: 28196894  |  Reference-DOI: 10.1073/PNAS.1616816114

(-) Compounds

Molecule 1 - N-ACETYLNEURAMINATE LYASE
    Atcc: 25923
    Chains: A, B, C, D
    EC Number: 4.1.3.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Organ: NA
    Expression System Plasmid: PKK223-3
    Expression System Taxid: 469008
    Expression System Tissue: NA
    Expression System Vector Type: PLASMID
    Gene: NANA, SAOUHSC_00295
    Organism Scientific: STAPHYLOCOCCUS AUREUS (STRAIN NCTC 8325)
    Organism Taxid: 93061
    Synonym: NEU5AC LYASE,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  (3, 10)

Asymmetric/Biological Unit (3, 10)
No.NameCountTypeFull Name
1KPI4Mod. Amino Acid(2S)-2-AMINO-6-[(1-HYDROXY-1-OXO-PROPAN-2-YLIDENE)AMINO]HEXANOIC ACID
2P9S4Mod. Amino AcidDIHYDROXYPROPYLCYSTEINE
3PEG2Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:141 , GLY A:144 , ASP D:141 , LEU D:142 , GLY D:144binding site for residue PEG A 301
2AC2SOFTWAREASP B:141 , ASP C:141binding site for residue PEG B 301
3AC3SOFTWAREASP B:141 , TYR B:166 , THR B:167 , ALA B:168 , SER B:188 , ASP B:191 , GLU B:192 , MET B:193 , LEU B:194 , ILE B:206 , HOH B:401 , HOH B:402binding site for Di-peptide GLY B 189 and P9S B 190
4AC4SOFTWAREASP B:141 , THR B:167 , ALA B:168 , SER B:188 , GLY B:189 , GLU B:192 , MET B:193 , LEU B:194 , GLY B:207 , SER B:208 , THR B:209 , TYR B:210 , GLN B:236 , HOH B:401 , HOH B:402 , HOH B:440 , HOH B:457binding site for Di-peptide P9S B 190 and ASP B 191
5AC5SOFTWAREASP C:141 , TYR C:166 , THR C:167 , LEU C:187 , SER C:188 , ASP C:191 , GLU C:192 , MET C:193 , LEU C:194 , ILE C:206 , HOH C:303 , HOH C:324binding site for Di-peptide GLY C 189 and P9S C 190
6AC6SOFTWAREASP C:141 , SER C:188 , GLY C:189 , GLU C:192 , MET C:193 , LEU C:194 , GLY C:207 , SER C:208 , THR C:209 , TYR C:210 , GLN C:236 , HOH C:303 , HOH C:324 , HOH C:325 , HOH C:368 , HOH C:384binding site for Di-peptide P9S C 190 and ASP C 191
7AC7SOFTWAREASP D:141 , TYR D:166 , THR D:167 , ALA D:168 , SER D:188 , ASP D:191 , GLU D:192 , MET D:193 , LEU D:194 , ILE D:206 , HOH D:306binding site for Di-peptide GLY D 189 and P9S D 190
8AC8SOFTWAREASP D:141 , ALA D:168 , SER D:188 , GLY D:189 , GLU D:192 , MET D:193 , LEU D:194 , GLY D:207 , SER D:208 , THR D:209 , TYR D:210 , GLN D:236 , HOH D:306 , HOH D:343 , HOH D:372binding site for Di-peptide P9S D 190 and ASP D 191

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5LKY)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Arg A:271 -Pro A:272
2Arg B:271 -Pro B:272
3Arg C:271 -Pro C:272
4Arg D:271 -Pro D:272

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5LKY)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5LKY)

(-) Exons   (0, 0)

(no "Exon" information available for 5LKY)

(-) 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:291
                                                                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee...........hhhhhhhhhhhhhhh....eeee.hhhhhhhhhhhhhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhhh..eeeee.......hhhhhhhhhhhhhhhhh..eeeeehhhhhh...hhhhhhhhhh...eeeeee...hhhhhhhhhhhh...eeee.hhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5lky A   3 KDLKGLYAALLVPFDENGQVNEQGLKQIAQNAIETEELDGLYVNGSSGENFLLNTEQKKQVFKVAKEAVGDKVKLIAQVGSLDLNEAIELGKYATELGYDALSAVTPFYYPFTFEEIRDYYFDIIEATQNNMIIYAIPDLTGVNISIEQFSELFNHEKIVGVkYTAPNFFLLERIRKAFPDKLILSGxDEMLVQATISGVDGAIGSTYNVNGRRARKIFDLARQGQIQEAYQLQHDSNDIIETVLSMGIYPTLKEILRHRGIDAGLPKRPFKPFNEAHRQTLDQLIAKYDL 293
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162  |    172       182       192       202       212       222       232       242       252       262       272       282       292 
                                                                                                                                                                                            165-KPI                  190-P9S                                                                                                   


Chain B from PDB  Type:PROTEIN  Length:290
                                                                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee...........hhhhhhhhhhhhhhh....eeee.hhhhhhhhhhhhhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhhhh..eeeeehhhhhh...hhhhhhhhhh...eeeeee...hhhhhhhhhhhh...eeee.hhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5lky B   4 DLKGLYAALLVPFDENGQVNEQGLKQIAQNAIETEELDGLYVNGSSGENFLLNTEQKKQVFKVAKEAVGDKVKLIAQVGSLDLNEAIELGKYATELGYDALSAVTPFYYPFTFEEIRDYYFDIIEATQNNMIIYAIPDLTGVNISIEQFSELFNHEKIVGVkYTAPNFFLLERIRKAFPDKLILSGxDEMLVQATISGVDGAIGSTYNVNGRRARKIFDLARQGQIQEAYQLQHDSNDIIETVLSMGIYPTLKEILRHRGIDAGLPKRPFKPFNEAHRQTLDQLIAKYDL 293
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163 |     173       183      |193       203       213       223       233       243       253       263       273       283       293
                                                                                                                                                                                           165-KPI                  190-P9S                                                                                                   


Chain C from PDB  Type:PROTEIN  Length:291
                                                                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee...........hhhhhhhhhhhhhhh....eeee.hhhhhhhhhhhhhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhhh..eeeee.......hhhhhhhhhhhhhhhhh..eeeeehhhhhh...hhhhhhhhhh...eeeeee...hhhhhhhhhhhh...eeee.hhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5lky C   3 KDLKGLYAALLVPFDENGQVNEQGLKQIAQNAIETEELDGLYVNGSSGENFLLNTEQKKQVFKVAKEAVGDKVKLIAQVGSLDLNEAIELGKYATELGYDALSAVTPFYYPFTFEEIRDYYFDIIEATQNNMIIYAIPDLTGVNISIEQFSELFNHEKIVGVkYTAPNFFLLERIRKAFPDKLILSGxDEMLVQATISGVDGAIGSTYNVNGRRARKIFDLARQGQIQEAYQLQHDSNDIIETVLSMGIYPTLKEILRHRGIDAGLPKRPFKPFNEAHRQTLDQLIAKYDL 293
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162  |    172       182       192       202       212       222       232       242       252       262       272       282       292 
                                                                                                                                                                                            165-KPI                  190-P9S                                                                                                   


Chain D from PDB  Type:PROTEIN  Length:291
                                                                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee...........hhhhhhhhhhhhhhh....eeee.hhhhhhhhhhhhhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhhh..eeeee.......hhhhhhhhhhhhhhhhh..eeeeehhhhhh...hhhhhhhhhh...eeeeee...hhhhhhhhhhhh...eeee.hhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5lky D   3 KDLKGLYAALLVPFDENGQVNEQGLKQIAQNAIETEELDGLYVNGSSGENFLLNTEQKKQVFKVAKEAVGDKVKLIAQVGSLDLNEAIELGKYATELGYDALSAVTPFYYPFTFEEIRDYYFDIIEATQNNMIIYAIPDLTGVNISIEQFSELFNHEKIVGVkYTAPNFFLLERIRKAFPDKLILSGxDEMLVQATISGVDGAIGSTYNVNGRRARKIFDLARQGQIQEAYQLQHDSNDIIETVLSMGIYPTLKEILRHRGIDAGLPKRPFKPFNEAHRQTLDQLIAKYDL 293
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162  |    172       182       192       202       212       222       232       242       252       262       272       282       292 
                                                                                                                                                                                            165-KPI                  190-P9S
   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  (0, 0)

(no "SCOP Domain" information available for 5LKY)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5LKY)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5LKY)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Arg A:271 - Pro A:272   [ RasMol ]  
    Arg B:271 - Pro B:272   [ RasMol ]  
    Arg C:271 - Pro C:272   [ RasMol ]  
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        NANA_STAA8 | Q2G160: 4ah7 4aho 4ahp 4ahq 4ama 5a8g 5kzd 5kze

(-) Related Entries Specified in the PDB File

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