1I8J - JenaLib

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Title :   CRYSTAL STRUCTURE OF PORPHOBILINOGEN SYNTHASE COMPLEXED WITH THE INHIBITOR 4,7-DIOXOSEBACIC ACID

Authors :   J. Kervinen, E. K. Jaffe, F. Stauffer, R. Neier, A. Wlodawer, A. Zdanov

Date :   14 Mar 01 (Deposition) - 20 Jun 01 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (4x)

Keywords :   Lyase, Heme Biosynthesis, Magnesium, 4, 7-Dioxosebacic Acid (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Kervinen, E. K. Jaffe, F. Stauffer, R. Neier, A. Wlodawer, A. Zdanov
Mechanistic Basis For Suicide Inactivation Of Porphobilinogen Synthase By 4, 7-Dioxosebacic Acid, An Inhibitor That Shows Dramatic Species Selectivity.
Biochemistry V. 40 8227 2001
PubMed-ID: 11444968 | Reference-DOI: 10.1021/BI010656K

Molecule 1 - PORPHOBILINOGEN SYNTHASE
	Chains	:	A, B
	EC Number	:	4.2.1.24
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	DELTA-AMINOLEVULINIC ACID DEHYDRATASE, 5-AMINOLEVULINIC ACID DEHYDRATASE

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (4x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 6)

No.	Name	Count	Type	Full Name
1	DSB	2	Ligand/Ion	4,7-DIOXOSEBACIC ACID
2	MG	2	Ligand/Ion	MAGNESIUM ION
3	ZN	2	Ligand/Ion	ZINC ION

Biological Unit 1 (1, 8)

No.	Name	Count	Type	Full Name
1	DSB	8	Ligand/Ion	4,7-DIOXOSEBACIC ACID
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:119 , CYS A:121 , CYS A:129 , HOH A:685	BINDING SITE FOR RESIDUE ZN A 400
2	AC2	SOFTWARE	GLU A:231 , HOH A:403 , HOH A:422 , HOH A:433 , HOH A:439 , HOH A:483	BINDING SITE FOR RESIDUE MG A 401
3	AC3	SOFTWARE	CYS B:119 , CYS B:121 , CYS B:129 , HOH B:686	BINDING SITE FOR RESIDUE ZN B 400
4	AC4	SOFTWARE	GLU B:231 , HOH B:412 , HOH B:421 , HOH B:427 , HOH B:430 , HOH B:448	BINDING SITE FOR RESIDUE MG B 401
5	AC5	SOFTWARE	SER A:164 , TYR A:191 , LYS A:194 , TYR A:200 , PHE A:203 , ARG A:204 , ARG A:215 , GLN A:219 , LYS A:246 , TYR A:269 , VAL A:271 , SER A:272 , TYR A:311 , HOH A:463	BINDING SITE FOR RESIDUE DSB A 350
6	AC6	SOFTWARE	SER B:164 , TYR B:191 , LYS B:194 , PHE B:199 , TYR B:200 , PHE B:203 , ARG B:204 , ARG B:215 , GLN B:219 , LYS B:246 , TYR B:269 , VAL B:271 , SER B:272 , TYR B:311 , HOH B:511	BINDING SITE FOR RESIDUE DSB B 350

(no "SS Bond" information available for 1I8J)

Asymmetric Unit

No.	Residues
1	Lys A:246	-	Pro A:247
2	Lys B:246	-	Pro B:247

(no "SAP(SNP)/Variant" information available for 1I8J)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	D_ALA_DEHYDRATASE	PS00169	Delta-aminolevulinic acid dehydratase active site.	HEM2_ECOLI	240-252	2	A:239-251 B:239-251

Biological Unit 1 (1, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	D_ALA_DEHYDRATASE	PS00169	Delta-aminolevulinic acid dehydratase active site.	HEM2_ECOLI	240-252	8	A:239-251 B:239-251

(no "Exon" information available for 1I8J)

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:323
 aligned with HEM2_ECOLI | P0ACB2 from UniProtKB/Swiss-Prot  Length:324

    Alignment length:323
                                    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   
           HEM2_ECOLI     2 TDLIQRPRRLRKSPALRAMFEETTLSLNDLVLPIFVEEEIDDYKAVEAMPGVMRIPEKHLAREIERIANAGIRSVMTFGISHHTDETGSDAWREDGLVARMSRICKQTVPEMIVMSDTCFCEYTSHGHCGVLCEHGVDNDATLENLGKQAVVAAAAGADFIAPSAAMDGQVQAIRQALDAAGFKDTAIMSYSTKFASSFYGPFREAAGSALKGDRKSYQMNPMNRREAIRESLLDEAQGADCLMVKPAGAYLDIVRELRERTELPIGAYQVSGEYAMIKFAALAGAIDEEKVVLESLGSIKRAGADLIFSYFALDLAEKKILR 324
               SCOP domains d1i8ja_ A: 5-aminolaevulinate dehydratase, ALAD (porphobilinogen synthase)                                                                                                                                                                                                                                                          SCOP domains
               CATH domains 1i8jA00 A:1-323 Aldolase class I                                                                                                                                                                                                                                                                                                    CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhh.....hhh.eeeeeeee......ee.......eeee..hhhhhhhhhhhh...eeeeeee.......hhhhhh..hhhhhhhhhhhhhh...eeeeee...................hhhhhhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhh.....ee....ee.....hhhhhhhhh...............hhhhhhhhhhhhhhh....eeee....hhhhhhhhhh.....eeee.hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh...eee..hhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------D_ALA_DEHYDRA------------------------------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1i8j A   1 TDLIQRPRRLRKSPALRAMFEETTLSLNDLVLPIFVEEEIDDYKAVEAMPGVMRIPEKHLAREIERIANAGIRSVMTFGISHHTDETGSDAWREDGLVARMSRICKQTVPEMIVMSDTCFCEYTSHGHCGVLCEHGVDNDATLENLGKQAVVAAAAGADFIAPSAAMDGQVQAIRQALDAAGFKDTAIMSYSTKFASSFYGPFREAAGSALKGDRKSYQMNPMNRREAIRESLLDEAQGADCLMVKPAGAYLDIVRELRERTELPIGAYQVSGEYAMIKFAALAGAIDEEKVVLESLGSIKRAGADLIFSYFALDLAEKKILR 323
                                    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

Chain B from PDB  Type:PROTEIN  Length:323
 aligned with HEM2_ECOLI | P0ACB2 from UniProtKB/Swiss-Prot  Length:324

    Alignment length:323
                                    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   
           HEM2_ECOLI     2 TDLIQRPRRLRKSPALRAMFEETTLSLNDLVLPIFVEEEIDDYKAVEAMPGVMRIPEKHLAREIERIANAGIRSVMTFGISHHTDETGSDAWREDGLVARMSRICKQTVPEMIVMSDTCFCEYTSHGHCGVLCEHGVDNDATLENLGKQAVVAAAAGADFIAPSAAMDGQVQAIRQALDAAGFKDTAIMSYSTKFASSFYGPFREAAGSALKGDRKSYQMNPMNRREAIRESLLDEAQGADCLMVKPAGAYLDIVRELRERTELPIGAYQVSGEYAMIKFAALAGAIDEEKVVLESLGSIKRAGADLIFSYFALDLAEKKILR 324
               SCOP domains d1i8jb_ B: 5-aminolaevulinate dehydratase, ALAD (porphobilinogen synthase)                                                                                                                                                                                                                                                          SCOP domains
               CATH domains 1i8jB00 B:1-323 Aldolase class I                                                                                                                                                                                                                                                                                                    CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhh.....hhh.eeeeeeee......ee.......eeee..hhhhhhhhhhhh...eeeeeee.......hhhhhh..hhhhhhhhhhhhhh...eeeeee...................hhhhhhhhhhhhhhhhhhh...eeee.....hhhhhhhhhhhhh.....ee....ee.....hhhhhhhhh...............hhhhhhhhhhhhhhh....eeee....hhhhhhhhhh.....eeee.hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh...eee..hhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------D_ALA_DEHYDRA------------------------------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1i8j B   1 TDLIQRPRRLRKSPALRAMFEETTLSLNDLVLPIFVEEEIDDYKAVEAMPGVMRIPEKHLAREIERIANAGIRSVMTFGISHHTDETGSDAWREDGLVARMSRICKQTVPEMIVMSDTCFCEYTSHGHCGVLCEHGVDNDATLENLGKQAVVAAAAGADFIAPSAAMDGQVQAIRQALDAAGFKDTAIMSYSTKFASSFYGPFREAAGSALKGDRKSYQMNPMNRREAIRESLLDEAQGADCLMVKPAGAYLDIVRELRERTELPIGAYQVSGEYAMIKFAALAGAIDEEKVVLESLGSIKRAGADLIFSYFALDLAEKKILR 323
                                    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

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( (-)

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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: 5-aminolaevulinate dehydratase, ALAD (porphobilinogen synthase) (36)

Protein domain: 5-aminolaevulinate dehydratase, ALAD (porphobilinogen synthase) (21)

Escherichia coli [TaxId: 562] (4)

1a	d1i8ja_	A:
1b	d1i8jb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

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Class: Alpha Beta (26913)

Architecture: Alpha-Beta Barrel (2994)

Topology: TIM Barrel (2806)

Homologous Superfamily: Aldolase class I (887)

Escherichia coli. Organism_taxid: 562. (44)

1a	1i8jA00	A:1-323
1b	1i8jB00	B:1-323

(no "Pfam Domain" information available for 1I8J)

Asymmetric Unit(hide GO term definitions)

Chain A,B (HEM2_ECOLI | P0ACB2)

molecular function
	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.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0004655	porphobilinogen synthase activity	Catalysis of the reaction: 2 5-aminolevulinate = 2 H(2)O + H(+) + porphobilinogen.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0006783	heme biosynthetic process	The chemical reactions and pathways resulting in the formation of heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring, from less complex precursors.
	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.
	GO:0006779	porphyrin-containing compound biosynthetic process	The chemical reactions and pathways resulting in the formation of any member of a large group of derivatives or analogs of porphyrin. Porphyrin consists of a ring of four pyrrole nuclei linked each to the next at their alpha positions through a methine group.
	GO:0006782	protoporphyrinogen IX biosynthetic process	The chemical reactions and pathways resulting in the formation of protoporphyrinogen IX.
	GO:0033014	tetrapyrrole biosynthetic process	The chemical reactions and pathways leading to the formation of tetrapyrroles, natural pigments containing four pyrrole rings joined by one-carbon units linking position 2 of one pyrrole ring to position 5 of the next.
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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	Cis Peptide Bonds
		Lys A:246 - Pro A:247	[ RasMol ]
		Lys B:246 - Pro B:247	[ RasMol ]

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	1i8j
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	HEM2_ECOLI \| P0ACB2	:	1b4e 1l6s 1l6y 5mhb

(no "Related Entries Specified in the PDB File" available for 1I8J)

Description

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Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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