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Title :   CRYSTAL STRUCTURE OF ADENYLOSUCCINATE LYASE (PURB) FROM BACILLUS ANTHRACIS

Authors :   V. M. Levdikov, E. V. Blagova, M. Baumgart, O. V. Moroz, A. J. Wilkinson, K. S. Wilson

Date :   05 Apr 07 (Deposition) - 17 Apr 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Adenylosuccinate Lyase, Purb, Purine Biosynthesis, Ba0290, Bacillus Anthracis, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   V. M. Levdikov, E. V. Blagova, A. J. Wilkinson, K. S. Wilson
Crystal Structure Of Adenylosuccinate Lyase (Purb) From Bacillus Anthracis
To Be Published
PubMed: search

Molecule 1 - ADENYLOSUCCINATE LYASE
	Chains	:	A, B
	EC Number	:	4.3.2.2
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Plasmid	:	PET-YSBLIC
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Gene	:	PURB
	Organism Scientific	:	BACILLUS ANTHRACIS
	Organism Taxid	:	1392

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 3)

No.	Name	Count	Type	Full Name
1	MLI	3	Ligand/Ion	MALONATE ION

Biological Unit 1 (1, 6)

No.	Name	Count	Type	Full Name
1	MLI	6	Ligand/Ion	MALONATE ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR A:142 , HIS A:143 , HIS B:68 , SER B:96 , GLN B:214 , GLY B:263 , SER B:264 , MET B:267 , LYS B:270 , ASN B:272 , HOH B:649	BINDING SITE FOR RESIDUE MLI A 901
2	AC2	SOFTWARE	HIS A:68 , SER A:96 , GLN A:214 , GLY A:263 , SER A:264 , MET A:267 , LYS A:270 , ASN A:272 , THR B:142 , HIS B:143	BINDING SITE FOR RESIDUE MLI A 902
3	AC3	SOFTWARE	GLN A:110 , HOH A:951 , HOH A:991 , HOH A:1090 , HOH B:616 , HOH B:634	BINDING SITE FOR RESIDUE MLI A 903

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

Asymmetric Unit

No.	Residues
1	Ile A:2	-	Ser A:3

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

(no "PROSITE Motif" information available for 2PFM)

(no "Exon" information available for 2PFM)

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:434
 aligned with Q81ZH6_BACAN | Q81ZH6 from UniProtKB/TrEMBL  Length:435

    Alignment length:434
                                    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       301       311       321       331       341       351       361       371       381       391       401       411       421       431    
         Q81ZH6_BACAN     2 ISRYTRPEMGAIWTEENKFKAWLEVEILACEAWAELGDIPKEDVKKIREHASFDIDRIYEIEKETRHDVVAFTRAVSETPALGEERKWVHYGLTSTDVVDTALSYILKQANEIILKDLENFVSILANKAKEHKYTIMMGRTHGVHAEPTTFGLKLGLWYEEMKRNVERFKQAANTVRVGKLSGAVGTYANIDPFVEKYVCENLGLEAAPISTQTLQRDRHAHYMSTLALIATSIEKMAVEIRGLQKSETREVEEAFAKGQKGSSAMPHKRNPIGSENMTGLARVIRGYMMTAYENVPLWHERDISHSSAERVILPDATIALNYMLNRFGNIVKNLTVYPENMKRNMTRTYGLIYSQRVMLTLIDKGMVREEAYDIVQPKAMEAWETQVQFKELVEADERITSKLTQEEINECFNYEHHMQHVDTIFERLGLNEA 435
               SCOP domains d2pfma_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains 2pfmA01 A:2-94 Fumarase/aspartase (N-terminal domain)                                        2pfmA02 A:95-350 Fumarase/aspartase (Central domain)                                                                                                                                                                                                            2pfmA03 A:351-435 Fumarase/aspartase (C-terminal domain)                              CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee..eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhh.ee............hhhhhhhhhhhh..ee.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh......ee..................hhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eehhhhhhhhhh...hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pfm A   2 ISRYTRPEMGAIWTEENKFKAWLEVEILACEAWAELGDIPKEDVKKIREHASFDIDRIYEIEKETRHDVVAFTRAVSETPALGEERKWVHYGLTSTDVVDTALSYILKQANEIILKDLENFVSILANKAKEHKYTIMMGRTHGVHAEPTTFGLKLGLWYEEMKRNVERFKQAANTVRVGKLSGAVGTYANIDPFVEKYVCENLGLEAAPISTQTLQRDRHAHYMSTLALIATSIEKMAVEIRGLQKSETREVEEAFAKGQKGSSAMPHKRNPIGSENMTGLARVIRGYMMTAYENVPLWHERDISHSSAERVILPDATIALNYMLNRFGNIVKNLTVYPENMKRNMTRTYGLIYSQRVMLTLIDKGMVREEAYDIVQPKAMEAWETQVQFKELVEADERITSKLTQEEINECFNYEHHMQHVDTIFERLGLNEA 435
                                    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       301       311       321       331       341       351       361       371       381       391       401       411       421       431

Chain B from PDB  Type:PROTEIN  Length:434
 aligned with Q81ZH6_BACAN | Q81ZH6 from UniProtKB/TrEMBL  Length:435

    Alignment length:434
                                    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       301       311       321       331       341       351       361       371       381       391       401       411       421       431    
         Q81ZH6_BACAN     2 ISRYTRPEMGAIWTEENKFKAWLEVEILACEAWAELGDIPKEDVKKIREHASFDIDRIYEIEKETRHDVVAFTRAVSETPALGEERKWVHYGLTSTDVVDTALSYILKQANEIILKDLENFVSILANKAKEHKYTIMMGRTHGVHAEPTTFGLKLGLWYEEMKRNVERFKQAANTVRVGKLSGAVGTYANIDPFVEKYVCENLGLEAAPISTQTLQRDRHAHYMSTLALIATSIEKMAVEIRGLQKSETREVEEAFAKGQKGSSAMPHKRNPIGSENMTGLARVIRGYMMTAYENVPLWHERDISHSSAERVILPDATIALNYMLNRFGNIVKNLTVYPENMKRNMTRTYGLIYSQRVMLTLIDKGMVREEAYDIVQPKAMEAWETQVQFKELVEADERITSKLTQEEINECFNYEHHMQHVDTIFERLGLNEA 435
               SCOP domains d2pfmb_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains 2pfmB01 B:2-94 Fumarase/aspartase (N-terminal domain)                                        2pfmB02 B:95-350 Fumarase/aspartase (Central domain)                                                                                                                                                                                                            2pfmB03 B:351-435 Fumarase/aspartase (C-terminal domain)                              CATH domains
           Pfam domains (1) -Lyase_1-2pfmB03 B:3-288                                                                                                                                                                                                                                                                       --------------------------------------------------------------ADSL_C-2pfmB01 B:351-431                                                         ---- Pfam domains (1)
           Pfam domains (2) -Lyase_1-2pfmB04 B:3-288                                                                                                                                                                                                                                                                       --------------------------------------------------------------ADSL_C-2pfmB02 B:351-431                                                         ---- Pfam domains (2)
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee..eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhh.ee............hhhhhhhhhhhh..ee.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh......ee..................hhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eehhhhhhhhhh...hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pfm B   2 ISRYTRPEMGAIWTEENKFKAWLEVEILACEAWAELGDIPKEDVKKIREHASFDIDRIYEIEKETRHDVVAFTRAVSETPALGEERKWVHYGLTSTDVVDTALSYILKQANEIILKDLENFVSILANKAKEHKYTIMMGRTHGVHAEPTTFGLKLGLWYEEMKRNVERFKQAANTVRVGKLSGAVGTYANIDPFVEKYVCENLGLEAAPISTQTLQRDRHAHYMSTLALIATSIEKMAVEIRGLQKSETREVEEAFAKGQKGSSAMPHKRNPIGSENMTGLARVIRGYMMTAYENVPLWHERDISHSSAERVILPDATIALNYMLNRFGNIVKNLTVYPENMKRNMTRTYGLIYSQRVMLTLIDKGMVREEAYDIVQPKAMEAWETQVQFKELVEADERITSKLTQEEINECFNYEHHMQHVDTIFERLGLNEA 435
                                    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       301       311       321       331       341       351       361       371       381       391       401       411       421       431

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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: L-aspartase-like (67)

Superfamily: L-aspartase-like (67)

Family: L-aspartase/fumarase (39)

Protein domain: automated matches (7)

Anthrax bacillus (Bacillus anthracis) [TaxId: 1392] (1)

1a	d2pfma_	A:
1b	d2pfmb_	B:

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: ADSL_C] (6)

Family: ADSL_C (6)

Bacillus anthracis (1)

1a	ADSL_C-2pfmB01	B:351-431
1b	ADSL_C-2pfmB02	B:351-431

Clan: no clan defined [family: Lyase_1] (27)

Family: Lyase_1 (27)

Bacillus anthracis (1)

2a	Lyase_1-2pfmB03	B:3-288
2b	Lyase_1-2pfmB04	B:3-288

Asymmetric Unit(hide GO term definitions)

Chain A,B (Q81ZH6_BACAN | Q81ZH6)

molecular function
	GO:0070626	(S)-2-(5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamido)succinate AMP-lyase (fumarate-forming) activity	Catalysis of the reaction: (S)-2-(5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamido)succinate = fumarate + 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide.
	GO:0004018	N6-(1,2-dicarboxyethyl)AMP AMP-lyase (fumarate-forming) activity	Catalysis of the reaction: N6-(1,2-dicarboxyethyl)AMP = fumarate + AMP.
	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:0044208	'de novo' AMP biosynthetic process	The chemical reactions and pathways resulting in the formation of adenosine monophosphate (AMP) from inosine 5'-monophosphate (IMP).
	GO:0006189	'de novo' IMP biosynthetic process	The chemical reactions and pathways resulting in the formation of IMP, inosine monophosphate, by the stepwise assembly of a purine ring on ribose 5-phosphate.
	GO:0006164	purine nucleotide biosynthetic process	The chemical reactions and pathways resulting in the formation of a purine nucleotide, a compound consisting of nucleoside (a purine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
	GO:0009152	purine ribonucleotide biosynthetic process	The chemical reactions and pathways resulting in the formation of a purine ribonucleotide, a compound consisting of ribonucleoside (a purine base linked to a ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.

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