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Title :   CRYSTAL STRUCTURE ANALYSIS OF N-ACETYLNEURAMINATE LYASE FROM HAEMOPHILUS INFLUENZAE: CRYSTAL FORM II

Authors :   J. A. R. G. Barbosa, B. J. Smith, R. Degori, M. C. Lawrence

Date :   21 Jun 00 (Deposition) - 20 Dec 00 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.60

Chains :   Asym. Unit : A,C
Biol. Unit 1: A,C  (2x)

Keywords :   Beta Barrel, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. A. R. G. Barbosa, B. J. Smith, R. Degori, H. C. Ooi, S. M. Marcuccio, E. M. Campi, W. R. Jackson, R. Brossmer, M. Sommer, M. C. Lawrence
Active Site Modulation In The N-Acetylneuraminate Lyase Sub-Family As Revealed By The Structure Of The Inhibitor-Complexed Haemophilus Influenzae Enzyme.
J. Mol. Biol. V. 303 405 2000
PubMed-ID: 11031117 | Reference-DOI: 10.1006/JMBI.2000.4138

Molecule 1 - N-ACETYLNEURAMINATE LYASE
	Chains	:	A, C
	EC Number	:	4.1.3.3
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PKKTAC (VTT BIOTECH, FINLAND)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	HAEMOPHILUS INFLUENZAE
	Organism Taxid	:	727

		1	2
Asymmetric Unit	:	A	C
Biological Unit 1 (2x)	:	A	C

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 9)

No.	Name	Count	Type	Full Name
1	GOL	4	Ligand/Ion	GLYCEROL
2	SO4	5	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 18)

No.	Name	Count	Type	Full Name
1	GOL	8	Ligand/Ion	GLYCEROL
2	SO4	10	Ligand/Ion	SULFATE ION

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ALA A:10 , TYR A:43 , GLY A:46 , SER A:47 , THR A:48 , TYR A:136 , LYS A:164 , HOH A:2072 , HOH A:2429	BINDING SITE FOR RESIDUE SO4 A 2001
2	AC2	SOFTWARE	ALA C:10 , TYR C:43 , GLY C:46 , SER C:47 , THR C:48 , TYR C:136 , LYS C:164	BINDING SITE FOR RESIDUE SO4 C 2002
3	AC3	SOFTWARE	LYS C:38 , TYR C:180 , PRO C:181 , ASN C:182 , HIS C:183 , ARG C:217 , HOH C:2142 , HOH C:2365	BINDING SITE FOR RESIDUE SO4 C 2003
4	AC4	SOFTWARE	VAL A:281 , LYS A:285 , HOH A:2036 , HOH A:2043 , HOH A:2073 , HOH A:2161 , HOH A:2255 , HOH A:2486	BINDING SITE FOR RESIDUE SO4 A 2004
5	AC5	SOFTWARE	TYR A:180 , PRO A:181 , ASN A:182 , HIS A:183 , HOH A:2467	BINDING SITE FOR RESIDUE SO4 A 2005
6	AC6	SOFTWARE	LYS A:259 , GLY A:266 , TYR A:267 , HOH A:2114 , HOH A:2115 , HOH A:2117 , HOH A:2177 , HOH A:2344 , HOH A:2375	BINDING SITE FOR RESIDUE GOL A 1001
7	AC7	SOFTWARE	ARG A:2 , LYS A:67 , ASP A:72 , ASP A:101 , ALA A:289 , HOH A:2033 , HOH A:2365	BINDING SITE FOR RESIDUE GOL A 1003
8	AC8	SOFTWARE	GLY A:226 , LYS A:227 , LEU A:228 , LYS A:229 , GLU A:230 , HOH A:2408 , HOH A:2491 , HOH C:2381	BINDING SITE FOR RESIDUE GOL A 1004
9	AC9	SOFTWARE	HOH A:2370 , GLY C:226 , LYS C:227 , LEU C:228 , LYS C:229 , GLU C:230 , HOH C:2161 , HOH C:2387	BINDING SITE FOR RESIDUE GOL C 1005

(no "SS Bond" information available for 1F6K)

(no "Cis Peptide Bond" information available for 1F6K)

(no "SAP(SNP)/Variant" information available for 1F6K)

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DHDPS_1	PS00665	Dihydrodipicolinate synthase signature 1.	NANA_HAEIN	41-58	2	A:41-58 C:41-58
2	DHDPS_2	PS00666	Dihydrodipicolinate synthase signature 2.	NANA_HAEIN	136-166	2	A:136-166 C:136-166

Biological Unit 1 (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DHDPS_1	PS00665	Dihydrodipicolinate synthase signature 1.	NANA_HAEIN	41-58	4	A:41-58 C:41-58
2	DHDPS_2	PS00666	Dihydrodipicolinate synthase signature 2.	NANA_HAEIN	136-166	4	A:136-166 C:136-166

(no "Exon" information available for 1F6K)

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:293
 aligned with NANA_HAEIN | P44539 from UniProtKB/Swiss-Prot  Length:293

    Alignment length:293
                                    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_HAEIN     1 MRDLKGIFSALLVSFNEDGTINEKGLRQIIRHNIDKMKVDGLYVGGSTGENFMLSTEEKKEIFRIAKDEAKDQIALIAQVGSVNLKEAVELGKYATELGYDCLSAVTPFYYKFSFPEIKHYYDTIIAETGNNMIVYSIPFLTGVNMGIEQFGELYKNPKVLGVKFTAGDFYLLERLKKAYPNHLIWAGFDEMMLPAASLGVDGAIGSTFNVNGVRARQIFELTKAGKLAEALEIQHVTNDLIEGILANGLYLTIKELLKLEGVDAGYCREPMTSKATEEQLAKAKDLKAKFLS 293
               SCOP domains d1f6ka_ A: N-acetylneuraminate lyase                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 1f6kA00 A:1-293 Aldolase class I                                                                                                                                                                                                                                                                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee...........hhhhhhhhhhhhhhh....eeee.hhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhh..eeeee.......hhhhhhhhhhhhhhhhh..eeeeehhhhhh...hhhhhhhhhh...eeeeee...hhhhhhhhhhhh...eeee.hhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------DHDPS_1           -----------------------------------------------------------------------------DHDPS_2  PDB: A:136-166        ------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1f6k A   1 MRDLKGIFSALLVSFNEDGTINEKGLRQIIRHNIDKMKVDGLYVGGSTGENFMLSTEEKKEIFRIAKDEAKDQIALIAQVGSVNLKEAVELGKYATELGYDCLSAVTPFYYKFSFPEIKHYYDTIIAETGSNMIVYSIPFLTGVNMGIEQFGELYKNPKVLGVKFTAGDFYLLERLKKAYPNHLIWAGFDEMMLPAASLGVDGAIGSTFNVNGVRARQIFELTKAGKLKEALEIQHVTNDLIEGILANGLYLTIKELLKLEGVDAGYCREPMTSKATAEQVAKAKDLKAKFLS 293
                                    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 C from PDB  Type:PROTEIN  Length:285
 aligned with NANA_HAEIN | P44539 from UniProtKB/Swiss-Prot  Length:293

    Alignment length:293
                                    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_HAEIN     1 MRDLKGIFSALLVSFNEDGTINEKGLRQIIRHNIDKMKVDGLYVGGSTGENFMLSTEEKKEIFRIAKDEAKDQIALIAQVGSVNLKEAVELGKYATELGYDCLSAVTPFYYKFSFPEIKHYYDTIIAETGNNMIVYSIPFLTGVNMGIEQFGELYKNPKVLGVKFTAGDFYLLERLKKAYPNHLIWAGFDEMMLPAASLGVDGAIGSTFNVNGVRARQIFELTKAGKLAEALEIQHVTNDLIEGILANGLYLTIKELLKLEGVDAGYCREPMTSKATEEQLAKAKDLKAKFLS 293
               SCOP domains d1f6kc_ C: N-acetylneuraminate lyase                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 1f6kC00 C:1-293 Aldolase class I                                                                                                                                                                                                                                                                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee...........hhhhhhhhhhhhhhh....eeee.hhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhh..eee.........hhhhhhhhhhhhhhhhh..eeeee--------.hhhhhhhhhh...eeeeee...hhhhhhhhhhhh...eeee.hhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------DHDPS_1           -----------------------------------------------------------------------------DHDPS_2  PDB: C:136-166        ------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1f6k C   1 MRDLKGIFSALLVSFNEDGTINEKGLRQIIRHNIDKMKVDGLYVGGSTGENFMLSTEEKKEIFRIAKDEAKDQIALIAQVGSVNLKEAVELGKYATELGYDCLSAVTPFYYKFSFPEIKHYYDTIIAETGSNMIVYS--------MGIEQFGELYKNPKVLGVKFTAGDFYLLERLKKAYPNHLIWAGFDEMMLPAASLGVDGAIGSTFNVNGVRARQIFELTKAGKLKEALEIQHVTNDLIEGILANGLYLTIKELLKLEGVDAGYCREPMTSKATAEQVAKAKDLKAKFLS 293
                                    10        20        30        40        50        60        70        80        90       100       110       120       130      |  -     | 150       160       170       180       190       200       210       220       230       240       250       260       270       280       290   
                                                                                                                                                                  137      146

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 Unit

Classes(

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Folds(

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Superfamilies( (-)

)

Families(

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Protein Domains( (-)

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Organisms( (-)

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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)

Haemophilus influenzae [TaxId: 727] (6)

1a	d1f6ka_	A:
1b	d1f6kc_	C:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

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Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Barrel (2994)

Topology: TIM Barrel (2806)

Homologous Superfamily: Aldolase class I (887)

Haemophilus influenzae. Organism_taxid: 727. (5)

1a	1f6kC00	C:1-293
1b	1f6kA00	A:1-293

(no "Pfam Domain" information available for 1F6K)

Asymmetric Unit(hide GO term definitions)

Chain A,C (NANA_HAEIN | P44539)

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: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: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.

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	4.1.3.3
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	NANA_HAEIN \| P44539	:	1f5z 1f6p 1f73 1f74 1f7b

1f5z	CRYSTAL STRUCTURE ANALYSIS OF N-ACETYLNEURAMINATE LYASE FROM HAEMOPHILUS INFLUENZAE: CRYSTAL FORM I
1f6p
1f73
1f74
1f7b
1fdy	STRUCTURE AND MECHANSISM OF A SUB-FAMILY OF ENZYMES RELATED TO N-ACETYLNEURAMINATE LYASE M.C. LAWRENCE, J.A.R.G. BARBOSA, B.J. SMITH, N.E. HALL, P.A. PILLING, H,C, OOI, S.M. MARCUCCIO J. MOL. BIOL. (1997) 266, 381-399
1fdz	STRUCTURE AND MECHANSISM OF A SUB-FAMILY OF ENZYMES RELATED TO N-ACETYLNEURAMINATE LYASE M.C. LAWRENCE, J.A.R.G. BARBOSA, B.J. SMITH, N.E. HALL, P.A. PILLING, H,C, OOI, S.M. MARCUCCIO J. MOL. BIOL. (1997) 266, 381-399
1nal	N-ACETYLNEURAMINATE LYASE FROM ESCHERICHIA COLI IZARD, T., LAWRENCE, M.C., MALBY, R.L., LILLEY, G.G., COLMAN, P.M.: THE THREE-DIMENSIONAL STRUTURE OF N-ACETYLNEURAMINATE LYASE ESCHERICHIA COLI. STRUCTURE (1994) 2, 361.

Description

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Ligands, Modified Residues, Ions (2, 9)

Sites (9, 9)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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SCOP Domains (1, 2)

CATH Domains (1, 2)

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Gene Ontology (6, 6)

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