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Asym./Biol. Unit (Jmol Viewer)

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Title :   N-ACETYLNEURAMINATE LYASE IN COMPLEX WITH HYDROXYPYRUVATE

Authors :   M. C. Lawrence, J. A. R. G. Barbosa, B. J. Smith, N. E. Hall, P. A. Pilling, S. M. Marcuccio

Date :   08 Jul 96 (Deposition) - 22 Oct 97 (Release) - 21 Jun 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.45

Chains :   Asym./Biol. Unit : A,B,C,D

Keywords :   Lyase, Aldolase, Oxo-Acid Lyase, Alpha-Keto-Acid Lyase, Carbon-Carbon Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. C. Lawrence, J. A. R. G. Barbosa, B. J. Smith, N. E. Hall, P. A. Pilling H. C. Ooi, S. M. Marcuccio
Structure And Mechanism Of A Sub-Family Of Enzymes Related To N-Acetylneuraminate Lyase.
J. Mol. Biol. V. 266 381 1997
PubMed-ID: 9047371 | Reference-DOI: 10.1006/JMBI.1996.0769
(for further references see the PDB file header)

Molecule 1 - N-ACETYLNEURAMINATE LYASE
	Chains	:	A, B, C, D
	EC Number	:	4.1.3.3
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	NPL
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Other Details	:	COVALENT COMPLEX
	Other Details - Source	:	DESCRIBED IN LILLEY, G.G. ET AL. (1992) SEE REFERENCE 2 BELOW
	Strain	:	TG1
	Synonym	:	N-ACETYLNEURAMINIC ACID ALDOLASE

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 4)

No.	Name	Count	Type	Full Name
1	3PY	4	Ligand/Ion	3-HYDROXYPYRUVIC ACID

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ALA A:11 , TYR A:43 , GLY A:46 , SER A:47 , THR A:48 , TYR A:137 , LYS A:165	BINDING SITE FOR RESIDUE 3PY A 802
2	AC2	SOFTWARE	ALA B:11 , TYR B:43 , GLY B:46 , SER B:47 , THR B:48 , TYR B:137 , LYS B:165	BINDING SITE FOR RESIDUE 3PY B 804
3	AC3	SOFTWARE	TYR C:43 , GLY C:46 , SER C:47 , THR C:48 , TYR C:137 , LYS C:165	BINDING SITE FOR RESIDUE 3PY C 806
4	AC4	SOFTWARE	ALA D:11 , TYR D:43 , GLY D:46 , SER D:47 , THR D:48 , TYR D:137 , LYS D:165 , THR D:167	BINDING SITE FOR RESIDUE 3PY D 808

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

Asymmetric/Biological Unit

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

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

Asymmetric/Biological Unit (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DHDPS_1	PS00665	Dihydrodipicolinate synthase signature 1.	NANA_ECOLI	41-58	4	A:41-58 B:41-58 C:41-58 D:41-58
2	DHDPS_2	PS00666	Dihydrodipicolinate synthase signature 2.	NANA_ECOLI	137-167	4	A:137-167 B:137-167 C:137-167 D:137-167

(no "Exon" information available for 1FDY)

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
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Chain A from PDB  Type:PROTEIN  Length:292
 aligned with NANA_ECOLI | P0A6L4 from UniProtKB/Swiss-Prot  Length:297

    Alignment length:292
                                    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 NLRGVMAALLTPFDQQQALDKASLRRLVQFNIQQGIDGLYVGGSTGEAFVQSLSEREQVLEIVAEEAKGKIKLIAHVGCVSTAESQQLAASAKRYGFDAVSAVTPFYYPFSFEEHCDHYRAIIDSADGLPMVVYNIPALSGVKLTLDQINTLVTLPGVGALKQTSGDLYQMEQIRREHPDLVLYNGYDEIFASGLLAGADGGIGSTYNIMGWRYQGIVKALKEGDIQTAQKLQTECNKVIDLLIKTGVFRGLKTVLHYMDVVSVPLCRKPFGPVDEKYLPELKALAQQLMQE 295
               SCOP domains d1fdya_ A: N-acetylneuraminate lyase                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains 1fdyA00 A:4-295 Aldolase class I                                                                                                                                                                                                                                                                     CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee............hhhhhhhhhhhhh....eeee......hhh..hhhhhhhhhhhhhh.....eeeee.....hhhhhhhhhhhhh....eeeee........hhhhhhhhhhhhhhh...eeeeee.hhhh.....hhhhhhhhh...eeeeee....hhhhhhhhhh....eeee..hhhhhhhhhh....eeehhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh.................hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------DHDPS_1           ------------------------------------------------------------------------------DHDPS_2  PDB: A:137-167        -------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1fdy A   4 NLRGVMAALLTPFDQQQALDKASLRRLVQFNIQQGIDGLYVGGSTGEAFVQSLSEREQVLEIVAEEGKGKIKLIAHVGCVTTAESQQLAASAKRYGFDAVSAVTPFYYPFSFEEHCDHYRAIIDSADGLPMVVYNIPALSGVKLTLDQINTLVTLPGVGALKQTSGDLYQMEQIRREHPDLVLYNGYDEIFASGLLAGADGGIGSTYNIMGWRYQGIVKALKEGDIQTAQKLQTECNKVIDLLIKTGVFRGLKTVLHYMDVVSVPLCRKPFGPVDEKYLPELKALAQQLMQE 295
                                    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 B 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 d1fdyb_ B: N-acetylneuraminate lyase                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 1fdyB00 B:4-294 Aldolase class I                                                                                                                                                                                                                                                                    CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee............hhhhhhhhhhhhh....eeee......hhh..hhhhhhhhhhhhhhh....eeeee.....hhhhhhhhhhhhhh...eeeee........hhhhhhhhhhhhhh....eeeeee.hhhh.....hhhhhhhhh...eeeeee....hhhhhhhhhh....eeee..hhhhhhhhhh....eeehhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh.................hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------DHDPS_1           ------------------------------------------------------------------------------DHDPS_2  PDB: B:137-167        ------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1fdy B   4 NLRGVMAALLTPFDQQQALDKASLRRLVQFNIQQGIDGLYVGGSTGEAFVQSLSEREQVLEIVAEEGKGKIKLIAHVGCVTTAESQQLAASAKRYGFDAVSAVTPFYYPFSFEEHCDHYRAIIDSADGLPMVVYNIPALSGVKLTLDQINTLVTLPGVGALKQTSGDLYQMEQIRREHPDLVLYNGYDEIFASGLLAGADGGIGSTYNIMGWRYQGIVKALKEGDIQTAQKLQTECNKVIDLLIKTGVFRGLKTVLHYMDVVSVPLCRKPFGPVDEKYLPELKALAQQLMQ 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 C 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 d1fdyc_ C: N-acetylneuraminate lyase                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 1fdyC00 C:4-294 Aldolase class I                                                                                                                                                                                                                                                                    CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee............hhhhhhhhhhhhhh...eeee..hhh.hhh..hhhhhhhhhhhhhhh....eeeee.....hhhhhhhhhhhhhh...eeeee........hhhhhhhhhhhhhhh...eeeeee.hhhh.....hhhhhhhhh...eeeeee....hhhhhhhhhh....eeee..hhhhhhhhh.....eee.hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh.................hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------DHDPS_1           ------------------------------------------------------------------------------DHDPS_2  PDB: C:137-167        ------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1fdy C   4 NLRGVMAALLTPFDQQQALDKASLRRLVQFNIQQGIDGLYVGGSTGEAFVQSLSEREQVLEIVAEEGKGKIKLIAHVGCVTTAESQQLAASAKRYGFDAVSAVTPFYYPFSFEEHCDHYRAIIDSADGLPMVVYNIPALSGVKLTLDQINTLVTLPGVGALKQTSGDLYQMEQIRREHPDLVLYNGYDEIFASGLLAGADGGIGSTYNIMGWRYQGIVKALKEGDIQTAQKLQTECNKVIDLLIKTGVFRGLKTVLHYMDVVSVPLCRKPFGPVDEKYLPELKALAQQLMQ 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 D 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 d1fdyd_ D: N-acetylneuraminate lyase                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 1fdyD00 D:4-294 Aldolase class I                                                                                                                                                                                                                                                                    CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee............hhhhhhhhhhhhh....eeee......hhh..hhhhhhhhhhhhhhh....eeeee.....hhhhhhhhhhhhhh...eeeee........hhhhhhhhhhhhhhh...eeeeee.hhhh.....hhhhhhhhh...eeeeee.....hhhhhhhhh....eeee..hhhhhhhhhh....eee.hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh.................hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------DHDPS_1           ------------------------------------------------------------------------------DHDPS_2  PDB: D:137-167        ------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1fdy D   4 NLRGVMAALLTPFDQQQALDKASLRRLVQFNIQQGIDGLYVGGSTGEAFVQSLSEREQVLEIVAEEGKGKIKLIAHVGCVTTAESQQLAASAKRYGFDAVSAVTPFYYPFSFEEHCDHYRAIIDSADGLPMVVYNIPALSGVKLTLDQINTLVTLPGVGALKQTSGDLYQMEQIRREHPDLVLYNGYDEIFASGLLAGADGGIGSTYNIMGWRYQGIVKALKEGDIQTAQKLQTECNKVIDLLIKTGVFRGLKTVLHYMDVVSVPLCRKPFGPVDEKYLPELKALAQQLMQ 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)
		→ 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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: TIM beta/alpha-barrel (3956)

Superfamily: Aldolase (457)

Family: Class I aldolase (182)

Protein domain: N-acetylneuraminate lyase (10)

Escherichia coli [TaxId: 562] (4)

1a	d1fdya_	A:
1b	d1fdyc_	C:
1c	d1fdyd_	D:
1d	d1fdyb_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Barrel (2994)

Topology: TIM Barrel (2806)

Homologous Superfamily: Aldolase class I (887)

Escherichia coli. Organism_taxid: 562. Strain: tg1. (2)

1a	1fdyB00	B:4-294
1b	1fdyC00	C:4-294
1c	1fdyD00	D:4-294
1d	1fdyA00	A:4-295

(no "Pfam Domain" information available for 1FDY)

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.

Asymmetric/Biological Unit
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		Lys A:272 - Pro A:273	[ RasMol ]
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		Lys C:272 - Pro C:273	[ RasMol ]
		Lys D:272 - Pro D:273	[ RasMol ]

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Description

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