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Title :   CRYSTAL STRUCTURE OF GLUTAMATE-1-SEMIALDEHYDE AMINOMUTASE IN COMPLEX WITH GABACULINE

Authors :   M. Hennig, J. N. Jansonius

Date :   26 Jun 98 (Deposition) - 17 Aug 99 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.00

Chains :   Asym./Biol. Unit : A,B

Keywords :   Chlorophyll Biosynthesis, Pyridoxal-5'-Phosphate, Pyridoxamine-5'-Phosphate, Asymmetric Dimer, Gabaculine, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Hennig, B. Grimm, R. Contestabile, R. A. John, J. N. Jansonius
Crystal Structure Of Glutamate-1-Semialdehyde Aminomutase: An Alpha2-Dimeric Vitamin B6-Dependent Enzyme With Asymmetry In Structure And Active Site Reactivity.
Proc. Natl. Acad. Sci. Usa V. 94 4866 1997
PubMed-ID: 9144156 | Reference-DOI: 10.1073/PNAS.94.10.4866
(for further references see the PDB file header)

Molecule 1 - PROTEIN (GLUTAMATE SEMIALDEHYDE AMINOTRANSFERASE)
	Chains	:	A, B
	EC Number	:	5.4.3.8
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	SG13009
	Expression System Taxid	:	562
	Organism Scientific	:	SYNECHOCOCCUS SP.
	Organism Taxid	:	1131
	Strain	:	GR6
	Synonym	:	GLUTAMATE SEMIALDEHYDE AMINOMUTASE

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 3)

No.	Name	Count	Type	Full Name
1	GAB	1	Ligand/Ion	3-AMINOBENZOIC ACID
2	PMP	2	Ligand/Ion	4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:122 , GLY A:123 , THR A:124 , TYR A:150 , ASN A:217 , ASP A:245 , VAL A:247 , MET A:248 , LYS A:273 , GAB A:500 , HOH A:2015 , HOH A:2110 , HOH A:2208 , THR B:305	BINDING SITE FOR RESIDUE PMP A 600
2	AC2	SOFTWARE	SER A:29 , VAL A:31 , ARG A:32 , TRP A:67 , SER A:163 , PMP A:600 , GLY B:94 , GLY B:304 , THR B:305 , HOH B:2336	BINDING SITE FOR RESIDUE GAB A 500
3	AC3	SOFTWARE	THR A:305 , SER B:122 , GLY B:123 , THR B:124 , TYR B:150 , GLY B:152 , ASN B:217 , ASP B:245 , MET B:248 , LYS B:273 , HOH B:2024 , HOH B:2101 , HOH B:2168	BINDING SITE FOR RESIDUE PMP B 601

(no "SS Bond" information available for 3GSB)

Asymmetric/Biological Unit

No.	Residues
1	Ala A:295	-	Pro A:296
2	Gly A:370	-	Pro A:371
3	Ala B:295	-	Pro B:296
4	Gly B:370	-	Pro B:371

(no "SAP(SNP)/Variant" information available for 3GSB)

Asymmetric/Biological Unit (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_SYNP6	242-278	2	A:242-278 B:242-278

(no "Exon" information available for 3GSB)

Asymmetric/Biological 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:427
 aligned with GSA_SYNP6 | P24630 from UniProtKB/Swiss-Prot  Length:433

    Alignment length:427
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       
            GSA_SYNP6     7 FKTIKSDEIFAAAQKLMPGGVSSPVRAFKSVGGQPIVFDRVKDAYAWDVDGNRYIDYVGTWGPAICGHAHPEVIEALKVAMEKGTSFGAPCALENVLAEMVIDAVPSIEMVRFVNSGTEACMAVLRLMRAYTGRDKIIKFEGCYHGHADMFLVKAGSGVATLGLPDSPGVPKSTTANTLTAPYNDLEAVKALFAENPGEIAGVILEPIVGNSGFIVPDAGFLEGLREITLEHDALLVFDEVMTGFRIAYGGVQEKFGVTPDLTTLGKIIGGGLPVGAYGGKREIMQLVAPAGPMYQAGTLSGNPLAMTAGIKTLELLRQPATYEYLDQITKRLSDGLLAIAQETGHAACGGQVSGMFGFFFTEGPVHNYEDAKKSDLQKFSRFHRGMLEQGIYLAPSQFEAGFTSLAHTEEDIDATLAAARTVMSAL 433
               SCOP domains d3gsba_ A: Glutamate-1-semialdehyde aminomutase (aminotransferase)                                                                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains 3gsbA01 A:7-76,A:326-433 Aspartate Aminotransferase, domain 1         3gsbA02 A:77-325 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                                     3gsbA01 A:7-76,A:326-433 Aspartate Aminotransferase, domain 1                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhh.hhhhh..........eeeee..eeee....eeee.hhhhh.......hhhhhhhhhhhhh........hhhhhhhhhhhhhhh....eeeee.hhhhhhhhhhhhhhhhhh..eeeee.......hhhhh...hhhhhhhh.......hhhhhh.eeee...hhhhhhhhhhh....eeeeee..............hhhhhhhhhhhhh..eeeee...........hhhhhh.....eeeehhhhh.....eeeeehhhhhh................hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh....eeeee..eeeee.......hhhhhh..hhhhhhhhhhhhhh..ee........ee.....hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AA_TRANSFER_CLASS_3  PDB: A:242-278  ----------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gsb A   7 FKTIKSDEIFAAAQKLMPGGVSSPVRAFKSVGGQPIVFDRVKDAYAWDVDGNRYIDYVGTWGPAICGHAHPEVIEALKVAMEKGTSFGAPCALENVLAEMVNDAVPSIEMVRFVNSGTEACMAVLRLMRAYTGRDKIIKFEGCYHGHADMFLVKAGSGVATLGLPSSPGVPKKTTANTLTTPYNDLEAVKALFAENPGEIAGVILEPIVGNSGFIVPDAGFLEGLREITLEHDALLVFDEVMTGFRIAYGGVQEKFGVTPDLTTLGKIIGGGLPVGAYGGKREIMQLVAPAGPMYQAGTLSGNPLAMTAGIKTLELLRQPGTYEYLDQITKRLSDGLLAIAQETGHAACGGQVSGMFGFFFTEGPVHNYEDAKKSDLQKFSRFHRGMLEQGIYLAPSQFEAGFTSLAHTEEDIDATLAAARTVMSAL 433
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426

Chain B from PDB  Type:PROTEIN  Length:427
 aligned with GSA_SYNP6 | P24630 from UniProtKB/Swiss-Prot  Length:433

    Alignment length:427
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       
            GSA_SYNP6     7 FKTIKSDEIFAAAQKLMPGGVSSPVRAFKSVGGQPIVFDRVKDAYAWDVDGNRYIDYVGTWGPAICGHAHPEVIEALKVAMEKGTSFGAPCALENVLAEMVIDAVPSIEMVRFVNSGTEACMAVLRLMRAYTGRDKIIKFEGCYHGHADMFLVKAGSGVATLGLPDSPGVPKSTTANTLTAPYNDLEAVKALFAENPGEIAGVILEPIVGNSGFIVPDAGFLEGLREITLEHDALLVFDEVMTGFRIAYGGVQEKFGVTPDLTTLGKIIGGGLPVGAYGGKREIMQLVAPAGPMYQAGTLSGNPLAMTAGIKTLELLRQPATYEYLDQITKRLSDGLLAIAQETGHAACGGQVSGMFGFFFTEGPVHNYEDAKKSDLQKFSRFHRGMLEQGIYLAPSQFEAGFTSLAHTEEDIDATLAAARTVMSAL 433
               SCOP domains d3gsbb_ B: Glutamate-1-semialdehyde aminomutase (aminotransferase)                                                                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains 3gsbB01 B:7-76,B:326-433 Aspartate Aminotransferase, domain 1         3gsbB02 B:77-325 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                                     3gsbB01 B:7-76,B:326-433 Aspartate Aminotransferase, domain 1                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhh.hhhhhhhhhh.....eeeee..eeee....eeee.hhhhh.......hhhhhhhhhhhhhhh......hhhhhhhhhhhhhhh....eeeee.hhhhhhhhhhhhhhhhhh..eeeee.....................................eeee...hhhhhhhhhhh....eeeeee..............hhhhhhhhhhhhhh.eeeee..........hhhhhhh.....eeeee.hhhh....eeeeehhhhhh................hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh....eeeee..eeeee.......hhhhhh..hhhhhhhhhhhhhhh.ee........ee.....hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AA_TRANSFER_CLASS_3  PDB: B:242-278  ----------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gsb B   7 FKTIKSDEIFAAAQKLMPGGVSSPVRAFKSVGGQPIVFDRVKDAYAWDVDGNRYIDYVGTWGPAICGHAHPEVIEALKVAMEKGTSFGAPCALENVLAEMVNDAVPSIEMVRFVNSGTEACMAVLRLMRAYTGRDKIIKFEGCYHGHADMFLVKAGSGVATLGLPSSPGVPKKTTANTLTTPYNDLEAVKALFAENPGEIAGVILEPIVGNSGFIVPDAGFLEGLREITLEHDALLVFDEVMTGFRIAYGGVQEKFGVTPDLTTLGKIIGGGLPVGAYGGKREIMQLVAPAGPMYQAGTLSGNPLAMTAGIKTLELLRQPGTYEYLDQITKRLSDGLLAIAQETGHAACGGQVSGMFGFFFTEGPVHNYEDAKKSDLQKFSRFHRGMLEQGIYLAPSQFEAGFTSLAHTEEDIDATLAAARTVMSAL 433
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426

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/Biological 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: GABA-aminotransferase-like (167)

Protein domain: Glutamate-1-semialdehyde aminomutase (aminotransferase) (4)

Synechococcus sp., strain GR6 [TaxId: 1131] (3)

1a	d3gsba_	A:
1b	d3gsbb_	B:

(no "Pfam Domain" information available for 3GSB)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (GSA_SYNP6 | P24630)

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:0015995	chlorophyll biosynthetic process	The chemical reactions and pathways resulting in the formation of chlorophyll, any compound of magnesium complexed in a porphyrin (tetrapyrrole) ring and which functions as a photosynthetic pigment, 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:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Ala A:295 - Pro A:296	[ RasMol ]
		Ala B:295 - Pro B:296	[ RasMol ]
		Gly A:370 - Pro A:371	[ RasMol ]
		Gly B:370 - Pro B:371	[ RasMol ]

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