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(-) Description

Title :  STRUCTURE OF THE E192N MUTANT OF E. COLI N-ACETYLNEURAMINIC ACID LYASE IN SPACE GROUP P21
 
Authors :  I. Campeotto, A. H. Bolt, T. A. Harman, C. H. Trinh, C. A. Dennis, S. E. V. P A. R. Pearson, A. Nelson, A. Berry
Date :  17 Jul 09  (Deposition) - 25 Aug 10  (Release) - 17 Nov 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Substrate Specificity, Carbohydrate Metabolism, Directed Evolution, Protein Engineering, Lyase, Aldolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  I. Campeotto, A. H. Bolt, T. A. Harman, C. A. Dennis, C. H. Trinh, S. E. V. Phillips, A. Nelson, A. R. Pearson, A. Berry
Structural Insights Into Substrate Specificity In Variants Of N-Acetylneuraminic Acid Lyase Produced By Directed Evolution.
J. Mol. Biol. V. 404 56 2010
PubMed-ID: 20826162  |  Reference-DOI: 10.1016/J.JMB.2010.08.008

(-) Compounds

Molecule 1 - N-ACETYLNEURAMINATE LYASE
    ChainsA, B, C, D
    EC Number4.1.3.3
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPKNANA
    Expression System StrainBL21 (DE3)
    Expression System Taxid469008
    FragmentRESIDUES 2-297
    MutationYES
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562
    SynonymN-ACETYLNEURAMINIC ACID LYASE, N-ACETYLNEURAMINATE PYRUVATE-LYASE, SIALIC ACID LYASE, SIALATE LYASE, SIALIC ACID ALDOLASE, NALASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit ABCD

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1CL4Ligand/IonCHLORIDE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:47 , THR A:48 , TYR A:137 , LYS A:165BINDING SITE FOR RESIDUE CL A1298
2AC2SOFTWARETYR B:43 , GLY B:46 , SER B:47 , THR B:48 , LYS B:165BINDING SITE FOR RESIDUE CL B1297
3AC3SOFTWARETYR C:43 , SER C:47 , THR C:48 , LYS C:165BINDING SITE FOR RESIDUE CL C1297
4AC4SOFTWARESER D:47 , THR D:48 , LYS D:165BINDING SITE FOR RESIDUE CL D1296

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2WNQ)

(-) Cis Peptide Bonds  (4, 4)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2WNQ)

(-) PROSITE Motifs  (2, 8)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2WNQ)

(-) 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:299
 aligned with NANA_ECOLI | P0A6L4 from UniProtKB/Swiss-Prot  Length:297

    Alignment length:299
                              1                                                                                                                                                                                                                                                                                                        
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288         
           NANA_ECOLI     - --MATNLRGVMAALLTPFDQQQALDKASLRRLVQFNIQQGIDGLYVGGSTGEAFVQSLSEREQVLEIVAEEAKGKIKLIAHVGCVSTAESQQLAASAKRYGFDAVSAVTPFYYPFSFEEHCDHYRAIIDSADGLPMVVYNIPALSGVKLTLDQINTLVTLPGVGALKQTSGDLYQMEQIRREHPDLVLYNGYDEIFASGLLAGADGGIGSTYNIMGWRYQGIVKALKEGDIQTAQKLQTECNKVIDLLIKTGVFRGLKTVLHYMDVVSVPLCRKPFGPVDEKYLPELKALAQQLMQERG 297
               SCOP domains d2wnqa_ A: automated matches                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 2wnqA00 A:-1-297 Aldolase class I                                                                                                                                                                                                                                                                           CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhh................hhhhhhhhhhhhhh......ee.....hhhhhhhhhhhhhhhhhhhhhh.....eee....hhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhhhh...eeeee.........hhhhhhhhhh......eee...hhhhhhhhhhhh....ee..hhhhh.............hhhhh.......hhhhhhh.hhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhh...............hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------DHDPS_1           ------------------------------------------------------------------------------DHDPS_2  PDB: A:137-167        ---------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wnq A  -1 HHHATNLRGVMAALLTPFDQQQALDKASLRRLVQFNIQQGIDGLYVGGSTGEAFVQSLSEREQVLEIVAEEAKGKIKLIAHVGCVSTAESQQLAASAKRYGFDAVSAVTPFYYPFSFEEHCDHYRAIIDSADGLPMVVYNIPALSGVKLTLDQINTLVTLPGVGALKQTSGDLYQMEQIRREHPDLVLYNGYDNIFASGLLAGADGGIGSTYNIMGWRYQGIVKALKEGDIQTAQKLQTECNKVIDLLIKTGVFRGLKTVLHYMDVVSVPLCRKPFGPVDEKYLPELKALAQQLMQERG 297
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288         

Chain B from PDB  Type:PROTEIN  Length:294
 aligned with NANA_ECOLI | P0A6L4 from UniProtKB/Swiss-Prot  Length:297

    Alignment length:294
                                    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    
           NANA_ECOLI     3 TNLRGVMAALLTPFDQQQALDKASLRRLVQFNIQQGIDGLYVGGSTGEAFVQSLSEREQVLEIVAEEAKGKIKLIAHVGCVSTAESQQLAASAKRYGFDAVSAVTPFYYPFSFEEHCDHYRAIIDSADGLPMVVYNIPALSGVKLTLDQINTLVTLPGVGALKQTSGDLYQMEQIRREHPDLVLYNGYDEIFASGLLAGADGGIGSTYNIMGWRYQGIVKALKEGDIQTAQKLQTECNKVIDLLIKTGVFRGLKTVLHYMDVVSVPLCRKPFGPVDEKYLPELKALAQQLMQER 296
               SCOP domains d2wnqb_ B: automated matches                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 2wnqB00 B:3-296 Aldolase class I                                                                                                                                                                                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....................hhhhhhhhhhhhhhh.....ee.....hhhhhhhhhhhhhhhhhhhhhh.....eee....hhhhhhhhhhhhhhh...eee.........hhhhhhhhhhhhhhhhh...eeeee..........hhhhhhhhh......eee...hhhhhhhhhhhh....ee..hhhhh.............hhhhh.......hhhhhhh.hhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhh...............hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------DHDPS_1           ------------------------------------------------------------------------------DHDPS_2  PDB: B:137-167        --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2wnq B   3 TNLRGVMAALLTPFDQQQALDKASLRRLVQFNIQQGIDGLYVGGSTGEAFVQSLSEREQVLEIVAEEAKGKIKLIAHVGCVSTAESQQLAASAKRYGFDAVSAVTPFYYPFSFEEHCDHYRAIIDSADGLPMVVYNIPALSGVKLTLDQINTLVTLPGVGALKQTSGDLYQMEQIRREHPDLVLYNGYDNIFASGLLAGADGGIGSTYNIMGWRYQGIVKALKEGDIQTAQKLQTECNKVIDLLIKTGVFRGLKTVLHYMDVVSVPLCRKPFGPVDEKYLPELKALAQQLMQER 296
                                    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    

Chain C from PDB  Type:PROTEIN  Length:296
 aligned with NANA_ECOLI | P0A6L4 from UniProtKB/Swiss-Prot  Length:297

    Alignment length:296
                                    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      
           NANA_ECOLI     1 MATNLRGVMAALLTPFDQQQALDKASLRRLVQFNIQQGIDGLYVGGSTGEAFVQSLSEREQVLEIVAEEAKGKIKLIAHVGCVSTAESQQLAASAKRYGFDAVSAVTPFYYPFSFEEHCDHYRAIIDSADGLPMVVYNIPALSGVKLTLDQINTLVTLPGVGALKQTSGDLYQMEQIRREHPDLVLYNGYDEIFASGLLAGADGGIGSTYNIMGWRYQGIVKALKEGDIQTAQKLQTECNKVIDLLIKTGVFRGLKTVLHYMDVVSVPLCRKPFGPVDEKYLPELKALAQQLMQER 296
               SCOP domains d2wnqc_ C: automated matches                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 2wnqC00 C:1-296 Aldolase class I                                                                                                                                                                                                                                                                         CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh................hhhhhhhhhhhhhhh.....ee.....hhhhhhhhhhhhhhhhhhhhhh.....eee....hhhhhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhh...eeeee.........hhhhhhhhhhh.....eee...hhhhhhhhhhhh....ee..hhhhh.............hhhhh.......hhhhhhh.hhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhh...............hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------DHDPS_1           ------------------------------------------------------------------------------DHDPS_2  PDB: C:137-167        --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wnq C   1 HATNLRGVMAALLTPFDQQQALDKASLRRLVQFNIQQGIDGLYVGGSTGEAFVQSLSEREQVLEIVAEEAKGKIKLIAHVGCVSTAESQQLAASAKRYGFDAVSAVTPFYYPFSFEEHCDHYRAIIDSADGLPMVVYNIPALSGVKLTLDQINTLVTLPGVGALKQTSGDLYQMEQIRREHPDLVLYNGYDNIFASGLLAGADGGIGSTYNIMGWRYQGIVKALKEGDIQTAQKLQTECNKVIDLLIKTGVFRGLKTVLHYMDVVSVPLCRKPFGPVDEKYLPELKALAQQLMQER 296
                                    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 D from PDB  Type:PROTEIN  Length:297
 aligned with NANA_ECOLI | P0A6L4 from UniProtKB/Swiss-Prot  Length:297

    Alignment length:297
                              1                                                                                                                                                                                                                                                                                                      
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       
           NANA_ECOLI     - --MATNLRGVMAALLTPFDQQQALDKASLRRLVQFNIQQGIDGLYVGGSTGEAFVQSLSEREQVLEIVAEEAKGKIKLIAHVGCVSTAESQQLAASAKRYGFDAVSAVTPFYYPFSFEEHCDHYRAIIDSADGLPMVVYNIPALSGVKLTLDQINTLVTLPGVGALKQTSGDLYQMEQIRREHPDLVLYNGYDEIFASGLLAGADGGIGSTYNIMGWRYQGIVKALKEGDIQTAQKLQTECNKVIDLLIKTGVFRGLKTVLHYMDVVSVPLCRKPFGPVDEKYLPELKALAQQLMQE 295
               SCOP domains d2wnqd_ D: automated matches                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 2wnqD00 D:-1-295 Aldolase class I                                                                                                                                                                                                                                                                         CATH domains
           Pfam domains (1) -----DHDPS-2wnqD01 D:4-293                                                                                                                                                                                                                                                                             -- Pfam domains (1)
           Pfam domains (2) -----DHDPS-2wnqD02 D:4-293                                                                                                                                                                                                                                                                             -- Pfam domains (2)
           Pfam domains (3) -----DHDPS-2wnqD03 D:4-293                                                                                                                                                                                                                                                                             -- Pfam domains (3)
           Pfam domains (4) -----DHDPS-2wnqD04 D:4-293                                                                                                                                                                                                                                                                             -- Pfam domains (4)
         Sec.struct. author hhhhhhhh................hhhhhhhhhhhhhhh.....ee.....hhhhhhhhhhhhhhhhhhhhhh.....eee....hhhhhhhhhhhhhhh...eee.........hhhhhhhhhhhhhhhh....ee............hhhhhhhhhhh.....ee....hhhhhhhhhhhh....ee..hhhhh.............hhhhh.......hhhhhhh.hhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhh...............hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------DHDPS_1           ------------------------------------------------------------------------------DHDPS_2  PDB: D:137-167        -------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wnq D  -1 HHHATNLRGVMAALLTPFDQQQALDKASLRRLVQFNIQQGIDGLYVGGSTGEAFVQSLSEREQVLEIVAEEAKGKIKLIAHVGCVSTAESQQLAASAKRYGFDAVSAVTPFYYPFSFEEHCDHYRAIIDSADGLPMVVYNIPALSGVKLTLDQINTLVTLPGVGALKQTSGDLYQMEQIRREHPDLVLYNGYDNIFASGLLAGADGGIGSTYNIMGWRYQGIVKALKEGDIQTAQKLQTECNKVIDLLIKTGVFRGLKTVLHYMDVVSVPLCRKPFGPVDEKYLPELKALAQQLMQE 295
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       

   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

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (1, 4)

Asymmetric/Biological Unit

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (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 | P0A6L41fdy 1fdz 1hl2 1nal 2wkj 2wnn 2wnz 2wo5 2wpb 2xfw 2ygy 3lbc 3lbm 3lcf 3lcg 3lch 3lci 3lcl 3lcw 3lcx 4bwl 4uui

(-) Related Entries Specified in the PDB File

1fdy N-ACETYLNEURAMINATE LYASE IN COMPLEX WITH HYDROXYPYRUVATE
1fdz N-ACETYLNEURAMINATE LYASE IN COMPLEX WITH PYRUVATE VIA BOROHYDRIDE REDUCTION
1hl2 CRYSTAL STRUCTURE OF N-ACETYLNEURAMINATE LYASE FROM E. COLI MUTANT L142R IN COMPLEX WITH B-HYDROXYPYRUVATE
1nal THE THREE-DIMENSIONAL STRUCTURE OF N- ACETYLNEURAMINATE LYASE FROM ESCHERICHIA COLI
2wkj CRYSTAL STRUCTURE OF THE E192N MUTANT OF E .COLI N-ACETYLNEURAMINIC ACID LYASE IN COMPLEX WITH PYRUVATE AT 1.45A RESOLUTION IN SPACE GROUP P212121
2wnn STRUCTURE OF WILD TYPE E. COLI N- ACETYLNEURAMINIC ACID LYASE IN COMPLEX WITH PYRUVATE IN SPACE GROUP P21
2wnz STRUCTURE OF THE E192N MUTANT OF E. COLI N-ACETYLNEURAMINIC ACID LYASE IN COMPLEX WITH PYRUVATE IN SPACE GROUP P21 CRYSTAL FORM I
2wo5 STRUCTURE OF WILD TYPE E. COLI N- ACETYLNEURAMINIC ACID LYASE IN SPACE GROUP P21 CRYSTAL FORM I
2wpb CRYSTAL STRUCTURE OF THE E192N MUTANT OF E . COLI N-ACETYLNEURAMINIC ACID LYASE IN COMPLEX WITH PYRUVATE AND THE INHIBITOR (2R ,3R)-2,3,4-TRIHYDROXY-N,N- DIPROPYLBUTANAMIDE IN SPACE GROUP P21 CRYSTAL FORM I
2wsg STRUCTURE OF THE Y137A MUTANT OF E. COLI N-ACETYLNEURAMINIC ACID LYASE IN COMPLEX WITH PYRUVATE, N-ACETYL-D-MANNOSAMINE AND N-ACETYLNEURAMINIC ACID