2ZSL - JenaLib

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Title :   CRYSTAL STRUCTURE OF GLUTAMATE-1-SEMIALDEHYDE 2,1-AMINOMUTASE FROM AEROPYRUM PERNIX

Authors :   H. Mizutani, N. Kunishima

Date :   17 Sep 08 (Deposition) - 21 Oct 08 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

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

Keywords :   Plp Dependent Enzyme, Gsa, Cytoplasm, Isomerase, Porphyrin Biosynthesis, Pyridoxal Phosphate (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Mizutani, N. Kunishima
Crystal Structure Of Glutamate-1-Semialdehyde 2, 1-Aminomutase From Aeropyrum Pernix
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - GLUTAMATE-1-SEMIALDEHYDE 2,1-AMINOMUTASE
	Chains	:	A
	EC Number	:	5.4.3.8
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-HISTEV
	Expression System Strain	:	ROSETTA(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	AEROPYRUM PERNIX
	Organism Taxid	:	56636
	Strain	:	K1
	Synonym	:	GSA, GLUTAMATE-1-SEMIALDEHYDE AMINOTRANSFERASE, GSA-AT

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 1)

No.	Name	Count	Type	Full Name
1	PMP	1	Ligand/Ion	4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	PMP	2	Ligand/Ion	4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:120 , GLY A:121 , THR A:122 , TYR A:148 , HIS A:149 , GLU A:210 , ASN A:215 , ASP A:243 , VAL A:245 , VAL A:246 , LYS A:271 , GLY A:302 , THR A:303 , PHE A:304 , HOH A:520 , HOH A:551 , HOH A:602 , HOH A:714 , HOH A:749	BINDING SITE FOR RESIDUE PMP A 501

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

Asymmetric Unit

No.	Residues
1	Lys A:36	-	Pro A:37
2	Thr A:293	-	Pro A:294

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

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	AA_TRANSFER_CLASS_3	PS00600	Aminotransferases class-III pyridoxal-phosphate attachment site.	GSA_AERPE	235-271	1	A:240-276

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	AA_TRANSFER_CLASS_3	PS00600	Aminotransferases class-III pyridoxal-phosphate attachment site.	GSA_AERPE	235-271	2	A:240-276

(no "Exon" information available for 2ZSL)

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:420
 aligned with GSA_AERPE | Q9Y9I9 from UniProtKB/Swiss-Prot  Length:429

    Alignment length:426
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423      
            GSA_AERPE     4 GEKSRMLFERTKELFPGGVNSPVRAAVKPYPFYVKRGEGAYLYTVDGARIVDLVLAYGPLILGHKHPRVLEAVEEALARGWLYGAPGEAEVLLAEKILGYVKRGGMIRFVNSGTEATMTAIRLARGYTGRDLILKFDGCYHGSHDAVLVAAGSAAAHYGVPTSAGVPEAVARLTLVTPYNDVEALERVFAEYGDRIAGVIVEPVIANAGVIPPRREFLAALQRLSRESGALLILDEVVTGFRLGLEGAQGYFNIEGDIIVLGKIIGGGFPVGAVAGSREVMSLLTPQGKVFNAGTFNAHPITMAAGLATLKALEEEPVYSVSREAAKALEEAASEVLDRTGLPYTINRVESMMQLFIGVEEVSNAAQARKADKKFYVKLHEEMLRRGVFIAPSNLEAVFTGLPHQGEALEIAVEGLRSSLKTVLGS 429
               SCOP domains d2zsla_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhh.hhhhhhh......eeeee..eeee....eeee.hhhhh.......hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhhhhhhhh..eeeeee......hhhh.ee..------.ee.....hhhhhh.eeeee..hhhhhhhhhhhhh..eeeeee............hhhhhhhhhhhhhhhh.eeeeee.........hhhhhhhh....eeeee.hhhh....eeeeehhhhhh................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee..eeeeee......hhhhhh..hhhhhhhhhhhhhhh.ee........ee.....hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AA_TRANSFER_CLASS_3  PDB: A:240-276  -------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2zsl A   9 GEKSRMLFERTKELFPGGVNSPVRAAVKPYPFYVKRGEGAYLYTVDGARIVDLVLAYGPLILGHKHPRVLEAVEEALARGWLYGAPGEAEVLLAEKILGYVKRGGMIRFVNSGTEATMTAIRLARGYTGRDLILKFDGCYHGSHDAVLVAAG------GVPTSAGVPEAVARLTLVTPYNDVEALERVFAEYGDRIAGVIVEPVIANAGVIPPRREFLAALQRLSRESGALLILDEVVTGFRLGLEGAQGYFNIEGDIIVLGKIIGGGFPVGAVAGSREVMSLLTPQGKVFNAGTFNAHPITMAAGLATLKALEEEPVYSVSREAAKALEEAASEVLDRTGLPYTINRVESMMQLFIGVEEVSNAAQARKADKKFYVKLHEEMLRRGVFIAPSNLEAVFTGLPHQGEALEIAVEGLRSSLKTVLGS 434
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158 |     168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428      
                                                                                                                                                                                 160    167

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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: PLP-dependent transferase-like (627)

Superfamily: PLP-dependent transferases (625)

Family: automated matches (163)

Protein domain: automated matches (163)

Aeropyrum pernix [TaxId: 56636] (2)

d2zsla_

(no "CATH Domain" information available for 2ZSL)

(no "Pfam Domain" information available for 2ZSL)

Asymmetric Unit(hide GO term definitions)

Chain A (GSA_AERPE | Q9Y9I9)

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:0042286	glutamate-1-semialdehyde 2,1-aminomutase activity	Catalysis of the reaction: (S)-4-amino-5-oxopentanoate = 5-aminolevulinate.
	GO:0016853	isomerase activity	Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
	GO:0030170	pyridoxal phosphate binding	Interacting selectively and non-covalently with pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6.
	GO:0008483	transaminase activity	Catalysis of the transfer of an amino group to an acceptor, usually a 2-oxo acid.
biological process
	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:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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		PMP	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Lys A:36 - Pro A:37	[ RasMol ]
		Thr A:293 - Pro A:294	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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	2zsl
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	GSA_AERPE \| Q9Y9I9	:	2epj 2zsm

2zsm	THE SAME PROTEIN(ANOTHER CRYSTAL FORM, HEXAGONAL FORM)

Description

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Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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