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(-) Description

Title :  THE THREE-DIMENSIONAL STRUCTURE OF N-ACETYLNEURAMINATE LYASE FROM ESCHERICHIA COLI
 
Authors :  T. Izard, M. C. Lawrence, R. L. Malby, G. G. Lilley, P. M. Colman
Date :  28 Feb 94  (Deposition) - 15 Sep 95  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  1,2,3,4
Keywords :  Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Izard, M. C. Lawrence, R. L. Malby, G. G. Lilley, P. M. Colman
The Three-Dimensional Structure Of N-Acetylneuraminate Lyase From Escherichia Coli.
Structure V. 2 361 1994
PubMed-ID: 8081752  |  Reference-DOI: 10.1016/S0969-2126(00)00038-1
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - N-ACETYLNEURAMINATE LYASE
    Chains: 1, 2, 3, 4
    EC Number: 4.1.3.3
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : 1234

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1SO44Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA 1:11 , TYR 1:43 , GLY 1:46 , SER 1:47 , THR 1:48 , TYR 1:137 , LYS 1:165BINDING SITE FOR RESIDUE SO4 1 302
2AC2SOFTWAREALA 2:11 , TYR 2:43 , GLY 2:46 , SER 2:47 , THR 2:48 , TYR 2:137 , LYS 2:165BINDING SITE FOR RESIDUE SO4 2 304
3AC3SOFTWAREALA 3:11 , TYR 3:43 , GLY 3:46 , SER 3:47 , THR 3:48 , TYR 3:137 , LYS 3:165BINDING SITE FOR RESIDUE SO4 3 306
4AC4SOFTWAREALA 4:11 , TYR 4:43 , GLY 4:46 , SER 4:47 , THR 4:48 , TYR 4:137 , LYS 4:165BINDING SITE FOR RESIDUE SO4 4 308

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1NAL)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Lys 1:272 -Pro 1:273
2Lys 3:272 -Pro 3:273
3Lys 4:272 -Pro 4:273

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1NAL)

(-) PROSITE Motifs  (2, 8)

Asymmetric/Biological Unit (2, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DHDPS_1PS00665 Dihydrodipicolinate synthase signature 1.NANA_ECOLI41-58
 
 
 		  41:41-58
2:41-58
3:41-58
4:41-58
2DHDPS_2PS00666 Dihydrodipicolinate synthase signature 2.NANA_ECOLI137-167
 
 
 		  41:137-167
2:137-167
3:137-167
4:137-167

(-) Exons   (0, 0)

(no "Exon" information available for 1NAL)

(-) 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 1 from PDB  Type:PROTEIN  Length:291
 aligned with NANA_ECOLI | P0A6L4 from UniProtKB/Swiss-Prot  Length:297

    Alignment length:291
                                    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 
           NANA_ECOLI     4 NLRGVMAALLTPFDQQQALDKASLRRLVQFNIQQGIDGLYVGGSTGEAFVQSLSEREQVLEIVAEEAKGKIKLIAHVGCVSTAESQQLAASAKRYGFDAVSAVTPFYYPFSFEEHCDHYRAIIDSADGLPMVVYNIPALSGVKLTLDQINTLVTLPGVGALKQTSGDLYQMEQIRREHPDLVLYNGYDEIFASGLLAGADGGIGSTYNIMGWRYQGIVKALKEGDIQTAQKLQTECNKVIDLLIKTGVFRGLKTVLHYMDVVSVPLCRKPFGPVDEKYLPELKALAQQLMQ 294
               SCOP domains d1nal1_ 1: N-acetylneuraminate lyase                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 1nal100 1:4-294 Aldolase class I                                                                                                                                                                                                                                                                    CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee............hhhhhhhhhhhh.....eeee...........hhhhhhhhhhhhh......eeeee......hhhhhhhhhhhh....eeeee........hhhhhhhhhhhhhh.....eeeee..........hhhhhhh.....eeeeee....hhhhhhhhhh....eeee..hhhhhhhhhh...eeee..hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh....................hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------DHDPS_1           ------------------------------------------------------------------------------DHDPS_2  PDB: 1:137-167        ------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nal 1   4 NLRGVMAALLTPFDQQQALDKASLRRLVQFNIQQGIDGLYVGGSTGEAFVQSLSEREQVLEIVAEEGKGKIKLIAHVGCVTTAESQQLAASAKRYGFDAVSAVTPFYYPFSFEEHCDHYRAIIDSADGLPMVVYNIPALSGVKLTLDQINTLVTLPGVGALKQTSGDLYQMEQIRREHPDLVLYNGYDEIFASGLLAGADGGIGSTYNIMGWRYQGIVKALKEGDIQTAQKLQTECNKVIDLLIKTGVFRGLKTVLHYMDVVSVPLCRKPFGPVDEKYQPELKALAQQLMQ 294
                                    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 


Chain 2 from PDB  Type:PROTEIN  Length:291
 aligned with NANA_ECOLI | P0A6L4 from UniProtKB/Swiss-Prot  Length:297

    Alignment length:291
                                    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 
           NANA_ECOLI     4 NLRGVMAALLTPFDQQQALDKASLRRLVQFNIQQGIDGLYVGGSTGEAFVQSLSEREQVLEIVAEEAKGKIKLIAHVGCVSTAESQQLAASAKRYGFDAVSAVTPFYYPFSFEEHCDHYRAIIDSADGLPMVVYNIPALSGVKLTLDQINTLVTLPGVGALKQTSGDLYQMEQIRREHPDLVLYNGYDEIFASGLLAGADGGIGSTYNIMGWRYQGIVKALKEGDIQTAQKLQTECNKVIDLLIKTGVFRGLKTVLHYMDVVSVPLCRKPFGPVDEKYLPELKALAQQLMQ 294
               SCOP domains d1nal2_ 2: N-acetylneuraminate lyase                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 1nal200 2:4-294 Aldolase class I                                                                                                                                                                                                                                                                    CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee............hhhhhhhhhhhh.....eeee...........hhhhhhhhhhhhh......eeeee......hhhhhhhhhhhh....eeeee........hhhhhhhhhhhhhh.....eeeee..........hhhhhhh.....eeeeee....hhhhhhhhhh....eeee..hhhhhhhhhh...eeee..hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh....................hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------DHDPS_1           ------------------------------------------------------------------------------DHDPS_2  PDB: 2:137-167        ------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nal 2   4 NLRGVMAALLTPFDQQQALDKASLRRLVQFNIQQGIDGLYVGGSTGEAFVQSLSEREQVLEIVAEEGKGKIKLIAHVGCVTTAESQQLAASAKRYGFDAVSAVTPFYYPFSFEEHCDHYRAIIDSADGLPMVVYNIPALSGVKLTLDQINTLVTLPGVGALKQTSGDLYQMEQIRREHPDLVLYNGYDEIFASGLLAGADGGIGSTYNIMGWRYQGIVKALKEGDIQTAQKLQTECNKVIDLLIKTGVFRGLKTVLHYMDVVSVPLCRKPFGPVDEKYQPELKALAQQLMQ 294
                                    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 


Chain 3 from PDB  Type:PROTEIN  Length:291
 aligned with NANA_ECOLI | P0A6L4 from UniProtKB/Swiss-Prot  Length:297

    Alignment length:291
                                    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 
           NANA_ECOLI     4 NLRGVMAALLTPFDQQQALDKASLRRLVQFNIQQGIDGLYVGGSTGEAFVQSLSEREQVLEIVAEEAKGKIKLIAHVGCVSTAESQQLAASAKRYGFDAVSAVTPFYYPFSFEEHCDHYRAIIDSADGLPMVVYNIPALSGVKLTLDQINTLVTLPGVGALKQTSGDLYQMEQIRREHPDLVLYNGYDEIFASGLLAGADGGIGSTYNIMGWRYQGIVKALKEGDIQTAQKLQTECNKVIDLLIKTGVFRGLKTVLHYMDVVSVPLCRKPFGPVDEKYLPELKALAQQLMQ 294
               SCOP domains d1nal3_ 3: N-acetylneuraminate lyase                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 1nal300 3:4-294 Aldolase class I                                                                                                                                                                                                                                                                    CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee............hhhhhhhhhhhh.....eeee...........hhhhhhhhhhhhh......eeeee......hhhhhhhhhhhh....eeeee........hhhhhhhhhhhhhh.....eeeee..........hhhhhhh.....eeeeee....hhhhhhhhhh....eeee..hhhhhhhhhh...eeee..hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh....................hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------DHDPS_1           ------------------------------------------------------------------------------DHDPS_2  PDB: 3:137-167        ------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nal 3   4 NLRGVMAALLTPFDQQQALDKASLRRLVQFNIQQGIDGLYVGGSTGEAFVQSLSEREQVLEIVAEEGKGKIKLIAHVGCVTTAESQQLAASAKRYGFDAVSAVTPFYYPFSFEEHCDHYRAIIDSADGLPMVVYNIPALSGVKLTLDQINTLVTLPGVGALKQTSGDLYQMEQIRREHPDLVLYNGYDEIFASGLLAGADGGIGSTYNIMGWRYQGIVKALKEGDIQTAQKLQTECNKVIDLLIKTGVFRGLKTVLHYMDVVSVPLCRKPFGPVDEKYQPELKALAQQLMQ 294
                                    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 


Chain 4 from PDB  Type:PROTEIN  Length:291
 aligned with NANA_ECOLI | P0A6L4 from UniProtKB/Swiss-Prot  Length:297

    Alignment length:291
                                    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 
           NANA_ECOLI     4 NLRGVMAALLTPFDQQQALDKASLRRLVQFNIQQGIDGLYVGGSTGEAFVQSLSEREQVLEIVAEEAKGKIKLIAHVGCVSTAESQQLAASAKRYGFDAVSAVTPFYYPFSFEEHCDHYRAIIDSADGLPMVVYNIPALSGVKLTLDQINTLVTLPGVGALKQTSGDLYQMEQIRREHPDLVLYNGYDEIFASGLLAGADGGIGSTYNIMGWRYQGIVKALKEGDIQTAQKLQTECNKVIDLLIKTGVFRGLKTVLHYMDVVSVPLCRKPFGPVDEKYLPELKALAQQLMQ 294
               SCOP domains d1nal4_ 4: N-acetylneuraminate lyase                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 1nal400 4:4-294 Aldolase class I                                                                                                                                                                                                                                                                    CATH domains
           Pfam domains (1) DHDPS-1nal401 4:4-293                                                                                                                                                                                                                                                                             - Pfam domains (1)
           Pfam domains (2) DHDPS-1nal402 4:4-293                                                                                                                                                                                                                                                                             - Pfam domains (2)
           Pfam domains (3) DHDPS-1nal403 4:4-293                                                                                                                                                                                                                                                                             - Pfam domains (3)
           Pfam domains (4) DHDPS-1nal404 4:4-293                                                                                                                                                                                                                                                                             - Pfam domains (4)
         Sec.struct. author .....eee............hhhhhhhhhhhh.....eeee...........hhhhhhhhhhhhh......eeeee......hhhhhhhhhhhh....eeeee........hhhhhhhhhhhhhh.....eeeee..........hhhhhhh.....eeeeee....hhhhhhhhhh....eeee..hhhhhhhhhh...eeee..hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh....................hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------DHDPS_1           ------------------------------------------------------------------------------DHDPS_2  PDB: 4:137-167        ------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nal 4   4 NLRGVMAALLTPFDQQQALDKASLRRLVQFNIQQGIDGLYVGGSTGEAFVQSLSEREQVLEIVAEEGKGKIKLIAHVGCVTTAESQQLAASAKRYGFDAVSAVTPFYYPFSFEEHCDHYRAIIDSADGLPMVVYNIPALSGVKLTLDQINTLVTLPGVGALKQTSGDLYQMEQIRREHPDLVLYNGYDEIFASGLLAGADGGIGSTYNIMGWRYQGIVKALKEGDIQTAQKLQTECNKVIDLLIKTGVFRGLKTVLHYMDVVSVPLCRKPFGPVDEKYQPELKALAQQLMQ 294
                                    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
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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, 4)

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

(-) CATH Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Clan: TIM_barrel (694)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain 1,2,3,4   (NANA_ECOLI | P0A6L4)
molecular function
    GO:0008747    N-acetylneuraminate lyase activity    Catalysis of the reaction: N-acetylneuraminate = N-acetyl-D-mannosamine + pyruvate.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
biological process
    GO:0019262    N-acetylneuraminate catabolic process    The chemical reactions and pathways resulting in the breakdown of N-acetylneuraminate, the anion of 5-(acetylamino)-3,5-dideoxy-D-glycero-D-galacto-non-3-ulosonic acid.
    GO:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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 Related Entries

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

UniProtKB/Swiss-Prot
        NANA_ECOLI | P0A6L4: 1fdy 1fdz 1hl2 2wkj 2wnn 2wnq 2wnz 2wo5 2wpb 2xfw 2ygy 3lbc 3lbm 3lcf 3lcg 3lch 3lci 3lcl 3lcw 3lcx 4bwl 4uui

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1NAL)