1W5Q - JenaLib

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Title :   STEPWISE INTRODUCTION OF ZINC BINDING SITE INTO PORPHOBILINOGEN SYNTHASE OF PSEUDOMONAS AERUGINOSA (MUTATIONS A129C, D131C, D139C, P132E, K229R)

Authors :   F. Frere, H. Reents, W. -D. Schubert, D. W. Heinz, D. Jahn

Date :   09 Aug 04 (Deposition) - 19 Jan 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.40

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

Keywords :   Synthase, Evolution, Metalloenzyme, Porphobilinogen Synthase, Pseudomonas Aeruginosa, Protein Engineering, (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   F. Frere, H. Reents, W. -D. Schubert, D. W. Heinz, D. Jahn
Tracking The Evolution Of Porphobilinogen Synthase Metal Dependence In Vitro
J. Mol. Biol. V. 345 1059 2005
PubMed-ID: 15644204 | Reference-DOI: 10.1016/J.JMB.2004.10.053

Molecule 1 - DELTA-AMINOLEVULINIC ACID DEHYDRATASE
	Chains	:	A, B
	EC Number	:	4.2.1.24
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector	:	PGEX-6P-1
	Mutation	:	YES
	Organism Scientific	:	PSEUDOMONAS AERUGINOSA
	Organism Taxid	:	208964
	Strain	:	PAO1
	Synonym	:	PORPHOBILINOGEN SYNTHASE, ALAD, ALADHPORPHOBILINOGEN SYNTHASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 11)

No.	Name	Count	Type	Full Name
1	FMT	2	Ligand/Ion	FORMIC ACID
2	MG	5	Ligand/Ion	MAGNESIUM ION
3	NA	2	Ligand/Ion	SODIUM ION
4	ZN	2	Ligand/Ion	ZINC ION

Biological Unit 1 (1, 8)

No.	Name	Count	Type	Full Name
1	FMT	8	Ligand/Ion	FORMIC ACID
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	NA	-1	Ligand/Ion	SODIUM ION
4	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (11, 11)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLU A:245 , HOH A:2215 , HOH A:2216 , HOH A:2259 , HOH A:2260 , HOH A:2261	BINDING SITE FOR RESIDUE MG A1338
02	AC2	SOFTWARE	CYS A:129 , CYS A:131 , CYS A:139 , HOH A:2304	BINDING SITE FOR RESIDUE ZN A1339
03	AC3	SOFTWARE	HOH A:2294 , HOH A:2298 , HOH A:2299 , HOH B:2053	BINDING SITE FOR RESIDUE MG A1340
04	AC4	SOFTWARE	HOH A:2053 , HOH B:2305 , HOH B:2306 , HOH B:2307	BINDING SITE FOR RESIDUE MG A1341
05	AC5	SOFTWARE	LEU A:27 , HOH A:2044 , HOH A:2046 , HOH A:2047 , HOH A:2049 , ASP B:37 , ASP B:319 , HOH B:2073	BINDING SITE FOR RESIDUE NA A1342
06	AC6	SOFTWARE	GLU B:245 , HOH B:2228 , HOH B:2230 , HOH B:2268 , HOH B:2269 , HOH B:2270	BINDING SITE FOR RESIDUE MG B1338
07	AC7	SOFTWARE	HOH A:2186 , ASN B:49 , HOH B:2081 , HOH B:2082 , HOH B:2115 , HOH B:2117	BINDING SITE FOR RESIDUE MG B1339
08	AC8	SOFTWARE	CYS B:129 , CYS B:131 , CYS B:139 , HOH B:2315	BINDING SITE FOR RESIDUE ZN B1340
09	AC9	SOFTWARE	ASP A:37 , ASP A:319 , HOH A:2071 , HOH A:2075 , LEU B:27 , HOH B:2048 , HOH B:2049 , HOH B:2051	BINDING SITE FOR RESIDUE NA B1342
10	BC1	SOFTWARE	PHE A:214 , TYR A:283 , VAL A:285 , SER A:286 , TYR A:324	BINDING SITE FOR RESIDUE FMT A1337
11	BC2	SOFTWARE	PHE B:214 , TYR B:283 , VAL B:285 , SER B:286 , TYR B:324	BINDING SITE FOR RESIDUE FMT B1337

(no "SS Bond" information available for 1W5Q)

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 1W5Q)

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 1W5Q)

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:321
 aligned with HEM2_PSEAE | Q59643 from UniProtKB/Swiss-Prot  Length:337

    Alignment length:331
                                    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 ANRAYPYTRLRRNRRDDFSRRLVRENVLTVDDLILPVFVLDGVNQRESIPSMPGVERLSIDQLLIEAEEWVALGIPALALFPVTPVEKKSLDAAEAYNPEGIAQRATRALRERFPELGIITDVALDPFTTHGQDGILDDDGYVLNDVSIDVLVRQALSHAEAGAQVVAPSDMMDGRIGAIREALESAGHTNVRIMAYSAKYASAYYGPFRDAVGSASNLGKGNKATYQMDPANSDEALHEVAADLAEGADMVMVKPGMPYLDIVRRVKDEFRAPTFVYQVSGEYAMHMGAIQNGWLAESVILESLTAFKRAGADGILTYFAKQAAEQLRRG 336
               SCOP domains d1w5qa_ A: automated matches                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 1w5qA00 A:6-336 Aldolase class I                                                                                                                                                                                                                                                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhhhhhhhh....hhh.eeeeeeee...................hhhhhhhhhhhhhh...eeeeee..hhhhh...hhhhhh..hhhhhhhhhhhhhh...eeeeee....................hhhhhhhhhhhhhhhhhhh...eeee.....hhhhhhhhhhhhh.....eeeeeeee..hhhhhhhhhh----------hhhhh......hhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhh.....hhhhhhhhhhhhhh..eeee.hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------D_ALA_DEHYDRA----------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1w5q A   6 ANRAYPYTRLRRNRRDDFSRRLVRENVLTVDDLILPVFVLDGVNQRESIPSMPGVERLSIDQLLIEAEEWVALGIPALALFPVTPVEKKSLDAAEAYNPEGIAQRATRALRERFPELGIITDVCLCEFTTHGQCGILDDDGYVLNDVSIDVLVRQALSHAEAGAQVVAPSDMMDGRIGAIREALESAGHTNVRVMAYSAKYASAYYGPFRDA----------NRATYQMDPANSDEALHEVAADLAEGADMVMVKPGMPYLDIVRRVKDEFRAPTFVYQVSGEYAMHMGAIQNGWLAESVILESLTAFKRAGADGILTYFAKQAAEQLRRG 336
                                    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 
                                                                                                                                                                                                                                             217        228

Chain B from PDB  Type:PROTEIN  Length:319
 aligned with HEM2_PSEAE | Q59643 from UniProtKB/Swiss-Prot  Length:337

    Alignment length:331
                                    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 ANRAYPYTRLRRNRRDDFSRRLVRENVLTVDDLILPVFVLDGVNQRESIPSMPGVERLSIDQLLIEAEEWVALGIPALALFPVTPVEKKSLDAAEAYNPEGIAQRATRALRERFPELGIITDVALDPFTTHGQDGILDDDGYVLNDVSIDVLVRQALSHAEAGAQVVAPSDMMDGRIGAIREALESAGHTNVRIMAYSAKYASAYYGPFRDAVGSASNLGKGNKATYQMDPANSDEALHEVAADLAEGADMVMVKPGMPYLDIVRRVKDEFRAPTFVYQVSGEYAMHMGAIQNGWLAESVILESLTAFKRAGADGILTYFAKQAAEQLRRG 336
               SCOP domains d1w5qb_ B: automated matches                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 1w5qB00 B:6-336 Aldolase class I                                                                                                                                                                                                                                                                                                            CATH domains
           Pfam domains (1) ----ALAD-1w5qB01 B:10-333                                                                                                                                                                                                                                                                                                               --- Pfam domains (1)
           Pfam domains (2) ----ALAD-1w5qB02 B:10-333                                                                                                                                                                                                                                                                                                               --- Pfam domains (2)
         Sec.struct. author ...............hhhhhhhhh....hhh.eeeeeeee...................hhhhhhhhhhhhhhh..eeeeee..hhhhh...hhhhhh..hhhhhhhhhhhhhh...eeeeee....................hhhhhhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhh....eeeeeeee..hhhhhhhh------------hhhhh......hhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhh.....hhhhhhhhhhhhhh..eeee.hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------D_ALA_DEHYDRA----------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1w5q B   6 ANRAYPYTRLRRNRRDDFSRRLVRENVLTVDDLILPVFVLDGVNQRESIPSMPGVERLSIDQLLIEAEEWVALGIPALALFPVTPVEKKSLDAAEAYNPEGIAQRATRALRERFPELGIITDVCLCEFTTHGQCGILDDDGYVLNDVSIDVLVRQALSHAEAGAQVVAPSDMMDGRIGAIREALESAGHTNVRVMAYSAKYASAYYGPFR------------NRATYQMDPANSDEALHEVAADLAEGADMVMVKPGMPYLDIVRRVKDEFRAPTFVYQVSGEYAMHMGAIQNGWLAESVILESLTAFKRAGADGILTYFAKQAAEQLRRG 336
                                    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 
                                                                                                                                                                                                                                           215          228

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: automated matches (15)

Pseudomonas aeruginosa [TaxId: 208964] (6)

1a	d1w5qa_	A:
1b	d1w5qb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

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Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Barrel (2994)

Topology: TIM Barrel (2806)

Homologous Superfamily: Aldolase class I (887)

Pseudomonas aeruginosa. Organism_taxid: 208964. Strain: pao1. (6)

1a	1w5qB00	B:6-336
1b	1w5qA00	A:6-336

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: TIM_barrel (694)

Family: ALAD (17)

Pseudomonas aeruginosa (7)

1a	ALAD-1w5qB01	B:10-333
1b	ALAD-1w5qB02	B:10-333

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.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
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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 ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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	1w5q
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	4.2.1.24
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1b4k	HIGH RESOLUTION CRYSTAL STRUCTURE OF A MG2- DEPENDENT 5- AMINOLEVULINIC ACID DEHYDRATASE
1gzg	COMPLEX OF A MG2-DEPENDENT PORPHOBILINOGEN SYNTHASE (MUTANT D139N) WITH 5-FLUOROLEVULINIC ACID
1w54	STEPWISE INTRODUCTION OF A ZINC BINDING SITE INTO PORPHOBILINOGEN SYNTHASE FROM PSEUDOMONAS AERUGINOSA (MUTATION D139C)
1w56	STEPWISE INTRODUCTION OF ZINC BINDING SITE INTO PORPHOBILINOGEN SYNTHASE OF PSEUDOMONAS AERUGINOSA (MUTATIONS A129C AND D131C)
1w5m	STEPWISE INTRODUCTION OF ZINC BINDING SITE INTO PORPHOBILINOGEN SYNTHASE OF PSEUDOMONAS AERUGINOSA (MUTATIONS A129C AND D139C)
1w5n	STEPWISE INTRODUCTION OF ZINC BINDING SITE INTO PORPHOBILINOGEN SYNTHASE OF PSEUDOMONAS AERUGINOSA (MUTATIONS D131C AND D139C)
1w5o	STEPWISE INTRODUCTION OF ZINC BINDING SITE INTO PORPHOBILINOGEN SYNTHASE OF PSEUDOMONAS AERUGINOSA (MUTATIONS A129C, D131C AND D139C)
1w5p	STEPWISE INTRODUCTION OF ZINC BINDING SITE INTO PORPHOBILINOGEN SYNTHASE OF PSEUDOMONAS AERUGINOSA (MUTATIONS A129C, D131C, D139C, P132E)

Description

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Ligands, Modified Residues, Ions (4, 11)

Sites (11, 11)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

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SCOP Domains (1, 2)

CATH Domains (1, 2)

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Gene Ontology (10, 10)

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