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Title :   HIGH RESOLUTION CRYSTAL STRUCTURE OF A MG2-DEPENDENT 5-AMINOLEVULINIC ACID DEHYDRATASE

Authors :   N. Frankenberg, D. Jahn, D. W. Heinz

Date :   22 Dec 98 (Deposition) - 13 Jul 99 (Release) - 18 Jan 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.67

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

Keywords :   Lyase, Heme Biosynthesis, Magnesium, Levulinic Acid (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. Frankenberg, P. T. Erskine, J. B. Cooper, P. M. Shoolingin-Jordan, D. Jahn, D. W. Heinz
High Resolution Crystal Structure Of A Mg2+-Dependent Porphobilinogen Synthase.
J. Mol. Biol. V. 289 591 1999
PubMed-ID: 10356331 | Reference-DOI: 10.1006/JMBI.1999.2808

Molecule 1 - PROTEIN (5-AMINOLEVULINIC ACID DEHYDRATASE)
	Atcc	:	ATCC 15692
	Cellular Location	:	CYTOPLASM
	Chains	:	A, B
	Collection	:	ATCC 15692
	EC Number	:	4.2.1.24
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Cellular Location	:	CYTOPLASM
	Expression System Gene	:	HEMB
	Expression System Plasmid	:	PGEX-6P-1
	Expression System Strain	:	BL21-DE3
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	HEMB
	Organism Scientific	:	PSEUDOMONAS AERUGINOSA
	Organism Taxid	:	208964
	Other Details	:	SCHIFF BASE LINK BETWEEN ATOM NZ OF LYS260 AND ATOM C4 OF LEVULINIC ACID
	Strain	:	PAO1
	Synonym	:	PORPHOBILINOGEN SYNTHASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 5)

No.	Name	Count	Type	Full Name
1	MG	1	Ligand/Ion	MAGNESIUM ION
2	SHF	2	Ligand/Ion	LAEVULINIC ACID
3	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 16)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION
2	SHF	8	Ligand/Ion	LAEVULINIC ACID
3	SO4	8	Ligand/Ion	SULFATE ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	AUTHOR	ASP A:139 , LYS A:205 , LYS A:260	ACTIVE SITE IN MOLECULE A
2	AC2	AUTHOR	ASP B:139 , LYS B:205 , LYS B:260	ACTIVE SITE IN MOLECULE A
3	AC3	SOFTWARE	LYS A:205 , TYR A:211 , ARG A:215 , LYS A:229 , GLN A:233 , SHF A:403 , HOH A:582 , HOH A:621	BINDING SITE FOR RESIDUE SO4 A 401
4	AC4	SOFTWARE	LYS B:205 , ARG B:215 , GLN B:233 , SHF B:402	BINDING SITE FOR RESIDUE SO4 B 401
5	AC5	SOFTWARE	GLU A:245 , HOH A:501 , HOH A:502 , HOH A:503 , HOH A:504 , HOH A:505	BINDING SITE FOR RESIDUE MG A 402
6	AC6	SOFTWARE	LYS A:205 , TYR A:211 , PHE A:214 , LYS A:260 , TYR A:283 , VAL A:285 , SER A:286 , TYR A:324 , SO4 A:401	BINDING SITE FOR RESIDUE SHF A 403
7	AC7	SOFTWARE	TYR B:211 , PHE B:214 , LYS B:260 , TYR B:283 , VAL B:285 , SER B:286 , TYR B:324 , SO4 B:401 , HOH B:690	BINDING SITE FOR RESIDUE SHF B 402
8	MG1	AUTHOR	MG A:402 , ASP A:179 , ARG A:181 , GLU A:245 , ASP A:249 , ARG B:19	MG2+-BINDING SITE IN MOLECULE A

(no "SS Bond" information available for 1B4K)

Asymmetric Unit

No.	Residues
1	Tyr A:10	-	Pro A:11
2	Lys A:260	-	Pro A:261
3	Tyr B:10	-	Pro B:11
4	Lys B:260	-	Pro B:261

(no "SAP(SNP)/Variant" information available for 1B4K)

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_PSEAE	253-265	2	A:253-265 B:253-265

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_PSEAE	253-265	8	A:253-265 B:253-265

(no "Exon" information available for 1B4K)

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
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Chain A from PDB  Type:PROTEIN  Length:326
 aligned with HEM2_PSEAE | Q59643 from UniProtKB/Swiss-Prot  Length:337

    Alignment length:326
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329      
           HEM2_PSEAE    10 YPYTRLRRNRRDDFSRRLVRENVLTVDDLILPVFVLDGVNQRESIPSMPGVERLSIDQLLIEAEEWVALGIPALALFPVTPVEKKSLDAAEAYNPEGIAQRATRALRERFPELGIITDVALDPFTTHGQDGILDDDGYVLNDVSIDVLVRQALSHAEAGAQVVAPSDMMDGRIGAIREALESAGHTNVRIMAYSAKYASAYYGPFRDAVGSASNLGKGNKATYQMDPANSDEALHEVAADLAEGADMVMVKPGMPYLDIVRRVKDEFRAPTFVYQVSGEYAMHMGAIQNGWLAESVILESLTAFKRAGADGILTYFAKQAAEQLRR 335
               SCOP domains d1b4ka_ A: 5-aminolaevulinate dehydratase, ALAD (porphobilinogen synthase)                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 1b4kA00 A:10-335 Aldolase class I                                                                                                                                                                                                                                                                                                      CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhh..hhhhhhh......hhh.eeeeeee.....eee.......eeeehhhhhhhhhhhhhh...eeeeee...hhh.....hhhh....hhhhhhhhhhhh....eeeeee......................hhhhhhhhhhhhhhhhh...eeee......hhhhhhhhhhh........eeeeee...hhhhhhhhhh..hhhh...............hhhhhhhhhhhh....eeeee..hhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhhh....hhhhhhhhhhhhhh...eeee..hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------D_ALA_DEHYDRA---------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1b4k A  10 YPYTRLRRNRRDDFSRRLVRENVLTVDDLILPVFVLDGVNQRESIPSMPGVERLSIDQLLIEAEEWVALGIPALALFPVTPVEKKSLDAAEAYNPEGIAQRATRALRERFPELGIITDVALDPFTTHGQDGILDDDGYVLNDVSIDVLVRQALSHAEAGAQVVAPSDMMDGRIGAIREALESAGHTNVRIMAYSAKYASAYYGPFRDAVGSASNLGKGNKATYQMDPANSDEALHEVAADLAEGADMVMVKPGMPYLDIVRRVKDEFRAPTFVYQVSGEYAMHMGAIQNGWLAESVILESLTAFKRAGADGILTYFAKQAAEQLRR 335
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329

Chain B from PDB  Type:PROTEIN  Length:320
 aligned with HEM2_PSEAE | Q59643 from UniProtKB/Swiss-Prot  Length:337

    Alignment length:330
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335
           HEM2_PSEAE     6 ANRAYPYTRLRRNRRDDFSRRLVRENVLTVDDLILPVFVLDGVNQRESIPSMPGVERLSIDQLLIEAEEWVALGIPALALFPVTPVEKKSLDAAEAYNPEGIAQRATRALRERFPELGIITDVALDPFTTHGQDGILDDDGYVLNDVSIDVLVRQALSHAEAGAQVVAPSDMMDGRIGAIREALESAGHTNVRIMAYSAKYASAYYGPFRDAVGSASNLGKGNKATYQMDPANSDEALHEVAADLAEGADMVMVKPGMPYLDIVRRVKDEFRAPTFVYQVSGEYAMHMGAIQNGWLAESVILESLTAFKRAGADGILTYFAKQAAEQLRR 335
               SCOP domains d1b4kb_ B: 5-aminolaevulinate dehydratase, ALAD (porphobilinogen synthase)                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains 1b4kB00 B:6-335 Aldolase class I                                                                                                                                                                                                                                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ................hhhhhhh......hhh.eeeeee......eee.......eee.hhhhhhhhhhhhh....eeeeee...hhh.....hhhh....hhhhhhhhhhhh....eeeeee..hhh................hhhhhhhhhhhhhhhhhh...eeee......hhhhhhhhhhh........eeeeee...hhhhhhhhhh..----------.........hhhhhhhhhhhh....eeeee..hhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhh.....hhhhhhhhhhhhhh...eeee..hhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------D_ALA_DEHYDRA---------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1b4k B   6 ANRAYPYTRLRRNRRDDFSRRLVRENVLTVDDLILPVFVLDGVNQRESIPSMPGVERLSIDQLLIEAEEWVALGIPALALFPVTPVEKKSLDAAEAYNPEGIAQRATRALRERFPELGIITDVALDPFTTHGQDGILDDDGYVLNDVSIDVLVRQALSHAEAGAQVVAPSDMMDGRIGAIREALESAGHTNVRIMAYSAKYASAYYGPFRDAVGS----------TYQMDPANSDEALHEVAADLAEGADMVMVKPGMPYLDIVRRVKDEFRAPTFVYQVSGEYAMHMGAIQNGWLAESVILESLTAFKRAGADGILTYFAKQAAEQLRR 335
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215    |    -     | 235       245       255       265       275       285       295       305       315       325       335
                                                                                                                                                                                                                                                220        231

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)

Pseudomonas aeruginosa [TaxId: 287] (2)

1a	d1b4ka_	A:
1b	d1b4kb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

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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)

Pseudomonas aeruginosa pao1. Organism_taxid: 208964. Strain: pao1. (1)

1a	1b4kB00	B:6-335
1b	1b4kA00	A:10-335

(no "Pfam Domain" information available for 1B4K)

Asymmetric Unit(hide GO term definitions)

Chain A,B (HEM2_PSEAE | Q59643)

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: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.

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	Cis Peptide Bonds
		Lys A:260 - Pro A:261	[ RasMol ]
		Lys B:260 - Pro B:261	[ RasMol ]
		Tyr A:10 - Pro A:11	[ RasMol ]
		Tyr B:10 - Pro B:11	[ RasMol ]

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 5)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

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