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(-) Description

Title :  CRYSTAL STRUCTURE OF THE Y138F MUTANT OF C.GLUTAMICUM N-ACETYLNEURAMINIC ACID LYASE IN COMPLEX WITH PYRUVATE
 
Authors :  Y. Shen, J. Zhou, J. Xie
Date :  19 Jun 15  (Deposition) - 22 Jun 16  (Release) - 22 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Complex, Aldolase Type Tim Barrel, Schiff Base Intermediate, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Shen, J. Zhou, J. Xie
Crystal Structure Of The Y138F Mutant Of C. Glutamicum N-Acetylneuraminic Acid Lyase In Complex With Pyruvate
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - DIHYDRODIPICOLINATE SYNTHASE/N-ACETYLNEURAMINATE LYASE
    Chains: A, B
    EC Number: 4.1.3.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: CGL2646
    Mutation: YES
    Organism Scientific: CORYNEBACTERIUM GLUTAMICUM ATCC 13032
    Organism Taxid: 196627
    Strain: ATCC 13032

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 17)

Asymmetric Unit (4, 17)
No.NameCountTypeFull Name
1ACT3Ligand/IonACETATE ION
2EDO11Ligand/Ion1,2-ETHANEDIOL
3GOL1Ligand/IonGLYCEROL
4PYR2Ligand/IonPYRUVIC ACID
Biological Unit 1 (4, 34)
No.NameCountTypeFull Name
1ACT6Ligand/IonACETATE ION
2EDO22Ligand/Ion1,2-ETHANEDIOL
3GOL2Ligand/IonGLYCEROL
4PYR4Ligand/IonPYRUVIC ACID

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPRO A:12 , GLY A:47 , SER A:48 , SER A:49 , LYS A:166 , SER A:168 , VAL A:213 , HOH A:559 , HOH A:638binding site for residue PYR A 401
02AC2SOFTWAREEDO A:403 , EDO A:405binding site for residue EDO A 402
03AC3SOFTWAREPRO A:150 , EDO A:402binding site for residue EDO A 403
04AC4SOFTWAREASP A:41binding site for residue EDO A 404
05AC5SOFTWAREEDO A:402binding site for residue EDO A 405
06AC6SOFTWARELYS A:30 , ILE A:280 , ILE A:281 , GLU A:282binding site for residue EDO A 406
07AC7SOFTWARELYS A:125binding site for residue EDO A 407
08AC8SOFTWARETHR A:199 , HOH A:609binding site for residue ACT A 408
09AC9SOFTWARELYS A:158 , HIS A:277binding site for residue ACT A 409
10AD1SOFTWAREARG A:113 , HOH A:501 , VAL B:253 , GLY B:263 , GOL B:403binding site for residue EDO A 410
11AD2SOFTWAREVAL A:253 , ARG B:113binding site for residue EDO B 401
12AD3SOFTWAREARG A:113 , EDO A:410 , SER B:49 , GLU B:198 , PYR B:402binding site for residue GOL B 403
13AD4SOFTWAREGLY B:8 , TYR B:205 , ASP B:210 , LEU B:232 , HOH B:525binding site for residue EDO B 405
14AD5SOFTWARELYS B:158binding site for residue EDO B 406
15AD6SOFTWARETYR B:205 , HOH B:646binding site for residue ACT B 407
16AD7SOFTWAREPRO B:12 , PHE B:44 , SER B:48 , SER B:49 , VAL B:105 , PHE B:136 , ALA B:137 , PHE B:138 , ASN B:139 , THR B:165 , ASP B:167 , SER B:168 , LEU B:194 , VAL B:213 , GOL B:403 , HOH B:591binding site for Di-peptide PYR B 402 and LYS B 166

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5C55)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Val A:288 -Pro A:289
2Val B:288 -Pro B:289

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5C55)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5C55)

(-) Exons   (0, 0)

(no "Exon" information available for 5C55)

(-) 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:307
                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee..............hhhhhhhhhhhhhhh....eee.hhhhh....hhhhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhhh...eee........hhhhhhhhhhhhhhhh....eeeeehhhhhh...hhhhhhhhhhh....eeee...hhhhhhhhhhhhhhh......eeee....hhhhhhhh...ee.hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5c55 A   5 TFTGVIPPVMTPLHADGSVDVESLRKLVDHLINGGVDGLFALGSSGEAAFLTRAQRKLALTTIIEHTAGRVPVTAGVIETTTARVIELVEDALEAGAEGLVATAPFYTRTHDVEIEEHFRKIHAAAPELPLFAFNIPVSVHSNLNPVMLLTLAKDGVLAGTKDSSGNDGAIRSLIEARDDAGLTEQFKILTGSETTVDFAYLAGADGVVPGLGNVDPAAYAALAKLCLDGKWAEAAALQKRINHLFHIVFVGDTSHMSGSSAGLGGFKTALAHLGIIESNAMAVPHQSLSDEETARIHAIVDEFLYT 311
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       


Chain B from PDB  Type:PROTEIN  Length:306
                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...ee..............hhhhhhhhhhhhhhh....eee.hhhhhhhhhhhhhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhhh..eeee........hhhhhhhhhhhhhhhh....eeeeehhhhhh...hhhhhhhhhhh....eeee...hhhhhhhhhhhhhhh......eeee....hhhhhhhh...ee.hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5c55 B   5 TFTGVIPPVMTPLHADGSVDVESLRKLVDHLINGGVDGLFALGSSGEAAFLTRAQRKLALTTIIEHTAGRVPVTAGVIETTTARVIELVEDALEAGAEGLVATAPFYTRTHDVEIEEHFRKIHAAAPELPLFAFNIPVSVHSNLNPVMLLTLAKDGVLAGTKDSSGNDGAIRSLIEARDDAGLTEQFKILTGSETTVDFAYLAGADGVVPGLGNVDPAAYAALAKLCLDGKWAEAAALQKRINHLFHIVFVGDTSHMSGSSAGLGGFKTALAHLGIIESNAMAVPHQSLSDEETARIHAIVDEFLY 310
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304
   Legend:   → Mismatch (orange background)
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  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 5C55)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5C55)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5C55)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)

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        Q8NMD2_CORGL | Q8NMD2: 5c54

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5c54