2PTR - JenaLib

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Title :   CRYSTAL STRUCTURE OF ESCHERICHIA COLI ADENYLOSUCCINATE LYASE MUTANT H171A WITH BOUND ADENYLOSUCCINATE SUBSTRATE

Authors :   M. Tsai, P. L. Howell

Date :   08 May 07 (Deposition) - 03 Jul 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.85

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

Keywords :   Adenylosuccinate Lyase, Mutant-Substrate Complex, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Tsai, J. Koo, P. Yip, R. F. Colman, M. L. Segall, P. L. Howell
Substrate And Product Complexes Of Escherichia Coli Adenylosuccinate Lyase Provide New Insights Into The Enzymatic Mechanism.
J. Mol. Biol. V. 370 541 2007
PubMed-ID: 17531264 | Reference-DOI: 10.1016/J.JMB.2007.04.052

Molecule 1 - ADENYLOSUCCINATE LYASE
	Chains	:	A, B
	EC Number	:	4.3.2.2
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-28A
	Expression System Strain	:	BL21C+
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	PURB
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	ADENYLOSUCCINATE, ASL

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	2SA	2	Ligand/Ion	2-[9-(3,4-DIHYDROXY-5-PHOSPHONOOXYMETHYL-TETRAHYDRO-FURAN-2-YL)-9H-PURIN-6-YLAMINO]-SUCCINIC ACID

Biological Unit 1 (1, 4)

No.	Name	Count	Type	Full Name
1	2SA	4	Ligand/Ion	2-[9-(3,4-DIHYDROXY-5-PHOSPHONOOXYMETHYL-TETRAHYDRO-FURAN-2-YL)-9H-PURIN-6-YLAMINO]-SUCCINIC ACID

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:15 , TYR A:16 , GLY A:294 , SER A:295 , SER A:296 , THR A:297 , MET A:298 , LYS A:301 , ASN A:303 , ASN A:309 , GLU B:86 , ASN B:90 , HIS B:91 , ASP B:92 , THR B:122 , SER B:123 , GLU B:124 , THR B:170 , GLN B:247 , ARG B:335 , LEU B:337 , SER B:340 , THR B:341 , ARG B:344 , HOH B:1226 , HOH B:1229 , HOH B:1231 , HOH B:1313 , HOH B:1315 , HOH B:1317	BINDING SITE FOR RESIDUE 2SA B 1100
2	AC2	SOFTWARE	ASN A:90 , HIS A:91 , ASP A:92 , THR A:122 , SER A:123 , GLU A:124 , THR A:170 , GLN A:247 , ARG A:335 , SER A:340 , THR A:341 , ARG A:344 , HOH A:469 , HOH A:479 , HOH A:514 , HOH A:706 , ARG B:15 , TYR B:16 , MET B:298 , LYS B:301 , ASN B:303 , ASN B:309 , HOH B:1306 , HOH B:1342	BINDING SITE FOR RESIDUE 2SA B 1200

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

(no "Cis Peptide Bond" information available for 2PTR)

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

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FUMARATE_LYASES	PS00163	Fumarate lyases signature.	PUR8_ECOLI	294-303	2	A:294-303 B:294-303

Biological Unit 1 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FUMARATE_LYASES	PS00163	Fumarate lyases signature.	PUR8_ECOLI	294-303	4	A:294-303 B:294-303

(no "Exon" information available for 2PTR)

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:454
 aligned with PUR8_ECOLI | P0AB89 from UniProtKB/Swiss-Prot  Length:456

    Alignment length:459
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 456   
                                    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       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450     |   
           PUR8_ECOLI     1 MELSSLTAVSPVDGRYGDKVSALRGIFSEYGLLKFRVQVEVRWLQKLAAHAAIKEVPAFAADAIGYLDAIVASFSEEDAARIKTIERTTNHDVKAVEYFLKEKVAEIPELHAVSEFIHFACTSEDINNLSHALMLKTARDEVILPYWRQLIDGIKDLAVQYRDIPLLSRTHGQPATPSTIGKEMANVAYRMERQYRQLNQVEILGKINGAVGNYNAHIAAYPEVDWHQFSEEFVTSLGIQWNPYTTQIEPHDYIAELFDCVARFNTILIDFDRDVWGYIALNHFKQKTIAGEIGSSTMPHKVNPIDFENSEGNLGLSNAVLQHLASKLPVSRWQRDLTDSTVLRNLGVGIGYALIAYQSTLKGVSKLEVNRDHLLDELDHNWEVLAEPIQTVMRRYGIEKPYEKLKELTRGKRVDAEGMKQFIDGLALPEEEKARLKAMTPANYIGRAITMVDELK---   -
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2ptrA01 A:1-117 Fumarase/aspartase (N-terminal domain)                                                               2ptrA02 A:118-381,A:446-459 Fumarase/aspartase (Central domain)                                                                                                                                                                                                         2ptrA03 A:382-445 Fumarase/     aspartase (C-terminal domain)   2ptrA02        CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee..eeeeeeehhhhhhhhhhhhhhhhhhhhhh..ee........hhhhhhhh...hhhhhhhhhhhhh..ee.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee.................hhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhh.hhhhhhhhhhhhhhhhhhhhhheeehhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhh-----.hhhhhhhhhhh...hhhhhhhhhh.hhhhh..hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------FUMARATE_L------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ptr A   1 MELSSLTAVSPVDGRYGDKVSALRGIFSEYGLLKFRVQVEVRWLQKLAAHAAIKEVPAFAADAIGYLDAIVASFSEEDAARIKTIERTTNHDVKAVEYFLKEKVAEIPELHAVSEFIHFACTSEDINNLSHALMLKTARDEVILPYWRQLIDGLKDLAVQYRDIPLLSRTAGQPATPSTIGKEMANVAYRMERQYRQLNQVEILGKINGAVGNYNAHIAAYPEVDWHQFSEEFVTSLGIQWNPYTTQIEPHDYIAELFDCVARFNTILIDFDRDVWGYIALNHFKQKTIAGEIGSSTMPHKVNPIDFENSEGNLGLSNAVLQHLASKLPVSRWQRDLTDSTVLRNLGVGIGYALIAYQSTLKGVSKLEVNRDHLLDELDHNWEVLAEPIQTVMRRYGIEKPYEKLKEL-----VDAEGMKQFIDGLALPEEEKARLKAMTPANYIGRAITMVDELKHHH 459
                                    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       300       310       320       330       340       350       360       370       380       390       400       | -   |   420       430       440       450         
                                                                                                                                                                                                                                                                                                                                                                                                                                                 408   414

Chain B from PDB  Type:PROTEIN  Length:456
 aligned with PUR8_ECOLI | P0AB89 from UniProtKB/Swiss-Prot  Length:456

    Alignment length:459
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 456   
                                    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       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450     |   
           PUR8_ECOLI     1 MELSSLTAVSPVDGRYGDKVSALRGIFSEYGLLKFRVQVEVRWLQKLAAHAAIKEVPAFAADAIGYLDAIVASFSEEDAARIKTIERTTNHDVKAVEYFLKEKVAEIPELHAVSEFIHFACTSEDINNLSHALMLKTARDEVILPYWRQLIDGIKDLAVQYRDIPLLSRTHGQPATPSTIGKEMANVAYRMERQYRQLNQVEILGKINGAVGNYNAHIAAYPEVDWHQFSEEFVTSLGIQWNPYTTQIEPHDYIAELFDCVARFNTILIDFDRDVWGYIALNHFKQKTIAGEIGSSTMPHKVNPIDFENSEGNLGLSNAVLQHLASKLPVSRWQRDLTDSTVLRNLGVGIGYALIAYQSTLKGVSKLEVNRDHLLDELDHNWEVLAEPIQTVMRRYGIEKPYEKLKELTRGKRVDAEGMKQFIDGLALPEEEKARLKAMTPANYIGRAITMVDELK---   -
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2ptrB01 B:1-117 Fumarase/aspartase (N-terminal domain)                                                               2ptrB02 B:118-381,B:446-459 Fumarase/aspartase (Central domain)                                                                                                                                                                                                         2ptrB03 B:382-445 Fumarase/aspartase (C-terminal domain)        2ptrB02        CATH domains
           Pfam domains (1) -------------Lyase_1-2ptrB03 B:14-320                                                                                                                                                                                                                                                                                           ----------ASL_C-2ptrB01 B:331-445                                                                                            -------------- Pfam domains (1)
           Pfam domains (2) -------------Lyase_1-2ptrB04 B:14-320                                                                                                                                                                                                                                                                                           ----------ASL_C-2ptrB02 B:331-445                                                                                            -------------- Pfam domains (2)
         Sec.struct. author ...............hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee..eeeeeeehhhhhhhhhhhhhhhhhhhhhh..ee........hhhhhhhh...hhhhhhhhhhhhh..ee.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee........---......hhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhh.hhhhhhhhhhhhhhhhhhhhhheeehhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhh....hhhhhhhhhhh...hhhhhhhhhhh.......hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------FUMARATE_L------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ptr B   1 MELSSLTAVSPVDGRYGDKVSALRGIFSEYGLLKFRVQVEVRWLQKLAAHAAIKEVPAFAADAIGYLDAIVASFSEEDAARIKTIERTTNHDVKAVEYFLKEKVAEIPELHAVSEFIHFACTSEDINNLSHALMLKTARDEVILPYWRQLIDGLKDLAVQYRDIPLLSRTAGQPATPSTIGKEMANVAYRMERQYRQLNQVEILGKINGAVGNYNAHIAAYPEVDWHQFSEEFVTSLGIQWNPYTTQIEPHDYIAELFDCVARFNTILIDFDRDVWGYIALNHFKQKTIAGEIG---MPHKVNPIDFENSEGNLGLSNAVLQHLASKLPVSRWQRDLTDSTVLRNLGVGIGYALIAYQSTLKGVSKLEVNRDHLLDELDHNWEVLAEPIQTVMRRYGIEKPYEKLKELTRGKRVDAEGMKQFIDGLALPEEEKARLKAMTPANYIGRAITMVDELKHHH 459
                                    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   |   300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450         
                                                                                                                                                                                                                                                                                                                               294 298

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 '\|'

(no "SCOP Domain" information available for 2PTR)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: ASL_C] (4)

Family: ASL_C (4)

Escherichia coli (strain K12) (3)

1a	ASL_C-2ptrB01	B:331-445
1b	ASL_C-2ptrB02	B:331-445

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

Family: Lyase_1 (27)

Escherichia coli (strain K12) (7)

2a	Lyase_1-2ptrB03	B:14-320
2b	Lyase_1-2ptrB04	B:14-320

Asymmetric Unit(hide GO term definitions)

Chain A,B (PUR8_ECOLI | P0AB89)

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:0006188	IMP biosynthetic process	The chemical reactions and pathways resulting in the formation of IMP, inosine monophosphate.
	GO:0006974	cellular response to DNA damage stimulus	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
	GO:0051262	protein tetramerization	The formation of a protein tetramer, a macromolecular structure consisting of four noncovalently associated identical or nonidentical subunits.
	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:0006163	purine nucleotide metabolic process	The chemical reactions and pathways involving 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.
cellular component
	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 Unit
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Biological Unit
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	2ptr
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	PUR8_ECOLI \| P0AB89	:	2ptq 2pts

2ptq	ANOTHER MUTANT (H171N) OF THE SAME PROTEIN COMPLEXED WITH PRODUCTS AMP AND FUMARATE.
2pts	SELENOMETHIONINE SUBSTITUTED WILD TYPE PROTEIN

Description

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Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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