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Title :   CRYSTAL STRUCTURE OF N-ACETYLNEURAMINIC ACID LYASE FROM STAPHYLOCOCCUS AUREUS WITH THE CHEMICAL MODIFICATION THIA-LYSINE AT POSITION 165

Authors :   N. Timms, A. Polyakova, C. L. Windle, C. H. Trinh, A. Nelson, A. R. Trinh,

Date :   06 Feb 12 (Deposition) - 23 Jan 13 (Release) - 13 Mar 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

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

Reference :   N. Timms, C. L. Windle, A. Polyakova, J. R. Ault, C. H. Trinh, A. R. Pearson, A. Nelson, A. Berry
Structural Insights Into The Recovery Of Aldolase Activity In N-Acetylneuraminic Acid Lyase By Replacement Of The Catalytically Active Lysine With Gamma-Thialysine By Using Chemical Mutagenesis Strategy.
Chembiochem V. 14 474 2013
PubMed-ID: 23418011 | Reference-DOI: 10.1002/CBIC.201200714

Molecule 1 - N-ACETYLNEURAMINATE LYASE
	Atcc	:	25923
	Chains	:	A, B, C, D
	EC Number	:	4.1.3.3
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PKK223-3
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	STAPHYLOCOCCUS AUREUS SUBSP. AUREUS NCTC 8325
	Organism Taxid	:	93061
	Other Details	:	CHEMICAL MODIFICATION THIA-LYSINE AT POSITION 165. MISSING LOOP 138-146 CHAIN A, B, C, D
	Synonym	:	N-ACETYLNEURAMINIC ACID LYASE, N-ACETYLNEURAMINATE PYRUVATE-LYASE, N-ACETYLNEURAMINIC ACID ALDOLASE, SIALATE LYASE, SIALIC ACID ALDOLASE, SIALIC ACID LYASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 8)

No.	Name	Count	Type	Full Name
1	CL	4	Ligand/Ion	CHLORIDE ION
2	SLZ	4	Mod. Amino Acid	L-THIALYSINE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ALA A:11 , SER A:48 , SER A:49 , SLZ A:165	BINDING SITE FOR RESIDUE CL A1294
2	AC2	SOFTWARE	ALA B:11 , SER B:48 , SER B:49 , SLZ B:165	BINDING SITE FOR RESIDUE CL B1294
3	AC3	SOFTWARE	ALA C:11 , SER C:48 , SER C:49 , SLZ C:165	BINDING SITE FOR RESIDUE CL C1294
4	AC4	SOFTWARE	ALA D:11 , SER D:48 , SER D:49 , SLZ D:165	BINDING SITE FOR RESIDUE CL D1294

(no "SS Bond" information available for 4AHO)

Asymmetric/Biological Unit

No.	Residues
1	Arg A:271	-	Pro A:272
2	Arg B:271	-	Pro B:272
3	Arg C:271	-	Pro C:272
4	Arg D:271	-	Pro D:272

(no "SAP(SNP)/Variant" information available for 4AHO)

Asymmetric/Biological Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DHDPS_2	PS00666	Dihydrodipicolinate synthase signature 2.	NANA_STAA8	137-167	4	A:137-167 B:137-167 C:137-167 D:137-167

(no "Exon" information available for 4AHO)

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:283
 aligned with NANA_STAA8 | Q2G160 from UniProtKB/Swiss-Prot  Length:293

    Alignment length:292
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291  
           NANA_STAA8     2 NKDLKGLYAALLVPFDENGQVNEQGLKQIAQNAIETEELDGLYVNGSSGENFLLNTEQKKQVFKVAKEAVGDKVKLIAQVGSLDLNEAIELGKYATELGYDALSAVTPFYYPFTFEEIRDYYFDIIEATQNNMIIYAIPDLTGVNISIEQFSELFNHEKIVGVKYTAPNFFLLERIRKAFPDKLILSGFDEMLVQATISGVDGAIGSTYNVNGRRARKIFDLARQGQIQEAYQLQHDSNDIIETVLSMGIYPTLKEILRHRGIDAGLPKRPFKPFNEAHRQTLDQLIAKYDL 293
               SCOP domains d4ahoa_ A: automated matches                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee...........hhhhhhhhhhhhhhh....eeee.hhhhhhhhhhhhhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhhh..eee.........hhhhhhhhhhhhhhhhh..eee.---------.hhhhhhhhhh...eeeeee...hhhhhhhhhhhh...eeee.hhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------DHDPS_2  PDB: A:137-167        ------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4aho A   2 NKDLKGLYAALLVPFDENGQVNEQGLKQIAQNAIETEELDGLYVNGSSGENFLLNTEQKKQVFKVAKEAVGDKVKLIAQVGSLDLNEAIELGKYATELGYDALSAVTPFYYPFTFEEIRDYYFDIIEATQNNMIIY---------ISIEQFSELFNHEKIVGVkYTAPNFFLLERIRKAFPDKLILSGFDEMLVQATISGVDGAIGSTYNVNGRRARKIFDLARQGQIQEAYQLQHDSNDIIETVLSMGIYPTLKEILRHRGIDAGLPKRPFKPFNEAHRQTLDQLIAKYDL 293
                                    11        21        31        41        51        61        71        81        91       101       111       121       131     |   -     | 151       161   |   171       181       191       201       211       221       231       241       251       261       271       281       291  
                                                                                                                                                                 137       147               165-SLZ

Chain B from PDB  Type:PROTEIN  Length:284
 aligned with NANA_STAA8 | Q2G160 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_STAA8     1 MNKDLKGLYAALLVPFDENGQVNEQGLKQIAQNAIETEELDGLYVNGSSGENFLLNTEQKKQVFKVAKEAVGDKVKLIAQVGSLDLNEAIELGKYATELGYDALSAVTPFYYPFTFEEIRDYYFDIIEATQNNMIIYAIPDLTGVNISIEQFSELFNHEKIVGVKYTAPNFFLLERIRKAFPDKLILSGFDEMLVQATISGVDGAIGSTYNVNGRRARKIFDLARQGQIQEAYQLQHDSNDIIETVLSMGIYPTLKEILRHRGIDAGLPKRPFKPFNEAHRQTLDQLIAKYDL 293
               SCOP domains d4ahob_ B: automated matches                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee...........hhhhhhhhhhhhhhh....eeee.hhhhhhhhhhhhhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhhh..eee.........hhhhhhhhhhhhhhhhh..eee.---------.hhhhhhhhhh...eeeeee...hhhhhhhhhhhh...eeee.hhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------DHDPS_2  PDB: B:137-167        ------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4aho B   1 MNKDLKGLYAALLVPFDENGQVNEQGLKQIAQNAIETEELDGLYVNGSSGENFLLNTEQKKQVFKVAKEAVGDKVKLIAQVGSLDLNEAIELGKYATELGYDALSAVTPFYYPFTFEEIRDYYFDIIEATQNNMIIY---------ISIEQFSELFNHEKIVGVkYTAPNFFLLERIRKAFPDKLILSGFDEMLVQATISGVDGAIGSTYNVNGRRARKIFDLARQGQIQEAYQLQHDSNDIIETVLSMGIYPTLKEILRHRGIDAGLPKRPFKPFNEAHRQTLDQLIAKYDL 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       147               165-SLZ

Chain C from PDB  Type:PROTEIN  Length:283
 aligned with NANA_STAA8 | Q2G160 from UniProtKB/Swiss-Prot  Length:293

    Alignment length:292
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291  
           NANA_STAA8     2 NKDLKGLYAALLVPFDENGQVNEQGLKQIAQNAIETEELDGLYVNGSSGENFLLNTEQKKQVFKVAKEAVGDKVKLIAQVGSLDLNEAIELGKYATELGYDALSAVTPFYYPFTFEEIRDYYFDIIEATQNNMIIYAIPDLTGVNISIEQFSELFNHEKIVGVKYTAPNFFLLERIRKAFPDKLILSGFDEMLVQATISGVDGAIGSTYNVNGRRARKIFDLARQGQIQEAYQLQHDSNDIIETVLSMGIYPTLKEILRHRGIDAGLPKRPFKPFNEAHRQTLDQLIAKYDL 293
               SCOP domains d4ahoc_ C: automated matches                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee...........hhhhhhhhhhhhhhh....eeee.hhhhhhhhhhhhhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhhh..eee.........hhhhhhhhhhhhhhhhh..eee.---------.hhhhhhhhhh...eeeeee...hhhhhhhhhhhh...eeee.hhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------DHDPS_2  PDB: C:137-167        ------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4aho C   2 NKDLKGLYAALLVPFDENGQVNEQGLKQIAQNAIETEELDGLYVNGSSGENFLLNTEQKKQVFKVAKEAVGDKVKLIAQVGSLDLNEAIELGKYATELGYDALSAVTPFYYPFTFEEIRDYYFDIIEATQNNMIIY---------ISIEQFSELFNHEKIVGVkYTAPNFFLLERIRKAFPDKLILSGFDEMLVQATISGVDGAIGSTYNVNGRRARKIFDLARQGQIQEAYQLQHDSNDIIETVLSMGIYPTLKEILRHRGIDAGLPKRPFKPFNEAHRQTLDQLIAKYDL 293
                                    11        21        31        41        51        61        71        81        91       101       111       121       131     |   -     | 151       161   |   171       181       191       201       211       221       231       241       251       261       271       281       291  
                                                                                                                                                                 137       147               165-SLZ

Chain D from PDB  Type:PROTEIN  Length:281
 aligned with NANA_STAA8 | Q2G160 from UniProtKB/Swiss-Prot  Length:293

    Alignment length:291
                                    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_STAA8     3 KDLKGLYAALLVPFDENGQVNEQGLKQIAQNAIETEELDGLYVNGSSGENFLLNTEQKKQVFKVAKEAVGDKVKLIAQVGSLDLNEAIELGKYATELGYDALSAVTPFYYPFTFEEIRDYYFDIIEATQNNMIIYAIPDLTGVNISIEQFSELFNHEKIVGVKYTAPNFFLLERIRKAFPDKLILSGFDEMLVQATISGVDGAIGSTYNVNGRRARKIFDLARQGQIQEAYQLQHDSNDIIETVLSMGIYPTLKEILRHRGIDAGLPKRPFKPFNEAHRQTLDQLIAKYDL 293
               SCOP domains d4ahod_ D: automated matches                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee...........hhhhhhhhhhhhhhh....eeee.hhhhhhhhhhhhhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhhh..eeee........hhhhhhhhhhhhhhhhh..eee.----------hhhhhhhhhh...eeeeee...hhhhhhhhhhhh...eeee.hhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------DHDPS_2  PDB: D:137-167        ------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4aho D   3 KDLKGLYAALLVPFDENGQVNEQGLKQIAQNAIETEELDGLYVNGSSGENFLLNTEQKKQVFKVAKEAVGDKVKLIAQVGSLDLNEAIELGKYATELGYDALSAVTPFYYPFTFEEIRDYYFDIIEATQNNMIIY----------SIEQFSELFNHEKIVGVkYTAPNFFLLERIRKAFPDKLILSGFDEMLVQATISGVDGAIGSTYNVNGRRARKIFDLARQGQIQEAYQLQHDSNDIIETVLSMGIYPTLKEILRHRGIDAGLPKRPFKPFNEAHRQTLDQLIAKYDL 293
                                    12        22        32        42        52        62        72        82        92       102       112       122       132    |    -     | 152       162  |    172       182       192       202       212       222       232       242       252       262       272       282       292 
                                                                                                                                                                137        148              165-SLZ

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: automated matches (113)

Protein domain: automated matches (113)

Staphylococcus aureus [TaxId: 93061] (5)

1a	d4ahoa_	A:
1b	d4ahob_	B:
1c	d4ahoc_	C:
1d	d4ahod_	D:

(no "CATH Domain" information available for 4AHO)

(no "Pfam Domain" information available for 4AHO)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C,D (NANA_STAA8 | Q2G160)

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: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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Arg A:271 - Pro A:272	[ RasMol ]
		Arg B:271 - Pro B:272	[ RasMol ]
		Arg C:271 - Pro C:272	[ RasMol ]
		Arg D:271 - Pro D:272	[ RasMol ]

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	4aho
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	4.1.3.3
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	NANA_STAA8 \| Q2G160	:	4ah7 4ahp 4ahq 4ama 5a8g 5kzd 5kze 5lky

4ah7	STRUCTURE OF WILD TYPE STAPYLOCOCCUS AUREUS N- ACETYLNEURAMINIC ACID LYASE IN COMPLEX WITH PYRUVATE
4ahp	CRYSTAL STRUCTURE OF WILD TYPE N-ACETYLNEURAMINIC ACID LYASE FROM STAPHYLOCOCCUS AUREUS
4ahq	CRYSTAL STRUCTURE OF N-ACETYLNEURAMINIC ACID LYASE MUTANT K165C FROM STAPHYLOCOCCUS AUREUS

Description

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Ligands, Modified Residues, Ions (2, 8)

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SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

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