1W1Z - JenaLib

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Asymmetric Unit (Jmol Viewer)

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Biol. Unit 1 - sites (Jmol Viewer)

Title :   STRUCTURE OF THE PLANT LIKE 5-AMINO LAEVULINIC ACID DEHYDRATASE FROM CHLOROBIUM VIBRIOFORME

Authors :   L. Coates, G. Beaven, P. T. Erskine, S. I. Beale, Y. J. Avissar, R. Gill, F. Mohammed, S. P. Wood, P. Shoolingin-Jordan, J. B. Cooper

Date :   24 Jun 04 (Deposition) - 02 Sep 04 (Release) - 28 Dec 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

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

Keywords :   Synthase, Tetrapyrrole Biosynthesis, Alad, Porphyrin Biosynthesis, Heme Biosynthesis, Lyase, Magnesium (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. Coates, G. Beaven, P. T. Erskine, S. I. Beale, Y. J. Avissar, R. Gill, F. Mohammed, S. P. Wood, P. Shoolingin-Jordan, J. B. Cooper
The X-Ray Structure Of The Plant Like 5-Aminolaevulinic Acid Dehydratase From Chlorobium Vibrioforme Complexed With The Inhibitor Laevulinic Acid At 2. 6A Resolution
J. Mol. Biol. V. 342 563 2004
PubMed-ID: 15327955 | Reference-DOI: 10.1016/J.JMB.2004.07.007

Molecule 1 - DELTA-AMINOLEVULINIC ACID DEHYDRATASE
	Chains	:	A, B
	EC Number	:	4.2.1.24
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Cell Line	:	BL21
	Expression System Plasmid	:	PET 11A
	Expression System Taxid	:	562
	Organism Scientific	:	PROSTHECOCHLORIS VIBRIOFORMIS
	Organism Taxid	:	1098
	Synonym	:	5-AMINOLAEVULINIC ACID DEHYDRATASE PORPHOBILINOGEN SYNTHASE, ALAD, ALADH

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 4)

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

Biological Unit 1 (1, 8)

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

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:238 , HOH A:2086 , HOH A:2087 , HOH A:2089 , HOH A:2119 , HOH A:2120	BINDING SITE FOR RESIDUE MG A1329
2	AC2	SOFTWARE	GLU B:238 , HOH B:2111 , HOH B:2115 , HOH B:2141 , HOH B:2142	BINDING SITE FOR RESIDUE MG B1329
3	AC3	SOFTWARE	PHE A:209 , LYS A:253 , TYR A:276 , VAL A:278 , SER A:279 , TYR A:318	BINDING SITE FOR RESIDUE SHF A1253
4	AC4	SOFTWARE	TYR B:206 , PHE B:209 , LYS B:253 , TYR B:276 , VAL B:278 , SER B:279 , TYR B:318	BINDING SITE FOR RESIDUE SHF B1253

(no "SS Bond" information available for 1W1Z)

Asymmetric Unit

No.	Residues
1	Lys A:253	-	Pro A:254
2	Lys B:253	-	Pro B:254

(no "SAP(SNP)/Variant" information available for 1W1Z)

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_CHLP8	246-258	2	A:246-258 B:246-258

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_CHLP8	246-258	8	A:246-258 B:246-258

(no "Exon" information available for 1W1Z)

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:319
 aligned with HEM2_CHLP8 | Q59334 from UniProtKB/Swiss-Prot  Length:328

    Alignment length:319
                                    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         
           HEM2_CHLP8    10 VHRPRRLRRTAALRNLVQENTLTVNDLVFPLFVMPGTNAVEEVSSMPGSFRFTIDRAVEECKELYDLGIQGIDLFGIPEQKTEDGSEAYNDNGILQQAIRAIKKAVPELCIMTDVALDPFTPFGHDGLVKDGIILNDETVEVLQKMAVSHAEAGADFVSPSDMMDGRIGAIREALDETDHSDVGILSYAAKYASSFYGPFRDALHSAPQFGDKSTYQMNPANTEEAMKEVELDIVEGADIVMVKPGLAYLDIVWRTKERFDVPVAIYHVSGEYAMVKAAAAKGWIDEDRVMMESLLCMKRAGADIIFTYYAKEAAKKLR 328
               SCOP domains d1w1za_ A: 5-aminolaevulinate dehydratase, ALAD (porphobilinogen synthase)                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1w1zA00 A:10-328 Aldolase class I                                                                                                                                                                                                                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh.hhhhhhhhh....hhh.eeeeeeee...................hhhhhhhhhhhhhh...eeeeee........hhhhhh..hhhhhhhhhhhhhh...eeeeee............ee....eehhhhhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhh.....eeee...........hhhhhh..................hhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh..eeee.hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------D_ALA_DEHYDRA---------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1w1z A  10 VHRPRRLRRTAALRNLVQENTLTVNDLVFPLFVMPGTNAVEEVSSMPGSFRFTIDRAVEECKELYDLGIQGIDLFGIPEQKTEDGSEAYNDNGILQQAIRAIKKAVPELCIMTDVALDPFTPFGHDGLVKDGIILNDETVEVLQKMAVSHAEAGADFVSPSDMMDGRIGAIREALDETDHSDVGILSYAAKYASSFYGPFRDALHSAPQFGDKSTYQMNPANTEEAMKEVELDIVEGADIVMVKPGLAYLDIVWRTKERFDVPVAIYHVSGEYAMVKAAAAKGWIDEDRVMMESLLCMKRAGADIIFTYYAKEAAKKLR 328
                                    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

Chain B from PDB  Type:PROTEIN  Length:319
 aligned with HEM2_CHLP8 | Q59334 from UniProtKB/Swiss-Prot  Length:328

    Alignment length:319
                                    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         
           HEM2_CHLP8    10 VHRPRRLRRTAALRNLVQENTLTVNDLVFPLFVMPGTNAVEEVSSMPGSFRFTIDRAVEECKELYDLGIQGIDLFGIPEQKTEDGSEAYNDNGILQQAIRAIKKAVPELCIMTDVALDPFTPFGHDGLVKDGIILNDETVEVLQKMAVSHAEAGADFVSPSDMMDGRIGAIREALDETDHSDVGILSYAAKYASSFYGPFRDALHSAPQFGDKSTYQMNPANTEEAMKEVELDIVEGADIVMVKPGLAYLDIVWRTKERFDVPVAIYHVSGEYAMVKAAAAKGWIDEDRVMMESLLCMKRAGADIIFTYYAKEAAKKLR 328
               SCOP domains d1w1zb_ B: 5-aminolaevulinate dehydratase, ALAD (porphobilinogen synthase)                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1w1zB00 B:10-328 Aldolase class I                                                                                                                                                                                                                                                                                               CATH domains
           Pfam domains (1) ALAD-1w1zB01 B:10-327                                                                                                                                                                                                                                                                                                         - Pfam domains (1)
           Pfam domains (2) ALAD-1w1zB02 B:10-327                                                                                                                                                                                                                                                                                                         - Pfam domains (2)
         Sec.struct. author ..hhhhhh.hhhhhhhhh....hhh.eeeeeeee...................hhhhhhhhhhhhhh...eeeeee........hhhhhh..hhhhhhhhhhhhhh...eeeeee.hhhhh......ee....eehhhhhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhh.....eeee.........hhhhhhhh..................hhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh..eeee.hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------D_ALA_DEHYDRA---------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1w1z B  10 VHRPRRLRRTAALRNLVQENTLTVNDLVFPLFVMPGTNAVEEVSSMPGSFRFTIDRAVEECKELYDLGIQGIDLFGIPEQKTEDGSEAYNDNGILQQAIRAIKKAVPELCIMTDVALDPFTPFGHDGLVKDGIILNDETVEVLQKMAVSHAEAGADFVSPSDMMDGRIGAIREALDETDHSDVGILSYAAKYASSFYGPFRDALHSAPQFGDKSTYQMNPANTEEAMKEVELDIVEGADIVMVKPGLAYLDIVWRTKERFDVPVAIYHVSGEYAMVKAAAAKGWIDEDRVMMESLLCMKRAGADIIFTYYAKEAAKKLR 328
                                    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

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(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Barrel (2994)

Topology: TIM Barrel (2806)

Homologous Superfamily: Aldolase class I (887)

Prosthecochloris vibrioformis. Organism_taxid: 1098. (1)

1a	1w1zA00	A:10-328
1b	1w1zB00	B:10-328

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: TIM_barrel (694)

Family: ALAD (17)

Chlorobaculum parvum (strain NCIB 8327) (Chlorobium vibrioforme subsp. thiosulfatophilum (strain DSM (1)

1a	ALAD-1w1zB01	B:10-327
1b	ALAD-1w1zB02	B:10-327

Asymmetric Unit(hide GO term definitions)

Chain A,B (HEM2_CHLP8 | Q59334)

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.
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.

Asymmetric Unit
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	1w1z
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Description

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Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (0, 0)

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