1S09 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE Y144F MUTANT OF 7,8-DIAMINOPELARGONIC ACID SYNTHASE

Authors :   J. Sandmark, A. C. Eliot, K. Famm, G. Schneider, J. F. Kirsch

Date :   30 Dec 03 (Deposition) - 23 Mar 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.83

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

Keywords :   Aminotransferase, Fold Type I, Subclass Ii, Homodimer (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Sandmark, A. C. Eliot, K. Famm, G. Schneider, J. F. Kirsch
Conserved And Nonconserved Residues In The Substrate Binding Site Of 7, 8-Diaminopelargonic Acid Synthase From Escherichia Coli Are Essential For Catalysis.
Biochemistry V. 43 1213 2004
PubMed-ID: 14756557 | Reference-DOI: 10.1021/BI0358059
(for further references see the PDB file header)

Molecule 1 - ADENOSYLMETHIONINE-8-AMINO-7-OXONONANOATE AMINOTRANSFERASE
	Chains	:	A, B
	EC Number	:	2.6.1.62
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PT7BIOA
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PET24
	Gene	:	BIOA, B0774
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	7,8-DIAMINO-PELARGONIC ACID AMINOTRANSFERASE, DAPA AMINOTRANSFERASE

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 4)

No.	Name	Count	Type	Full Name
1	LLP	2	Mod. Amino Acid	2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)
2	NA	2	Ligand/Ion	SODIUM ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	VAL A:96 , THR A:99 , PRO A:100 , LEU A:103 , HOH A:1586	BINDING SITE FOR RESIDUE NA A 1501
2	AC2	SOFTWARE	VAL B:96 , THR B:99 , PRO B:100 , LEU B:103 , HOH B:1590	BINDING SITE FOR RESIDUE NA B 1502

(no "SS Bond" information available for 1S09)

(no "Cis Peptide Bond" information available for 1S09)

(no "SAP(SNP)/Variant" information available for 1S09)

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.	BIOA_ECOLI	242-279	2	A:242-279 B:242-279

(no "Exon" information available for 1S09)

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 BIOA_ECOLI | P12995 from UniProtKB/Swiss-Prot  Length:429

    Alignment length:428
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420        
           BIOA_ECOLI     1 MTTDDLAFDQRHIWHPYTSMTSPLPVYPVVSAEGCELILSDGRRLVDGMSSWWAAIHGYNHPQLNAAMKSQIDAMSHVMFGGITHAPAIELCRKLVAMTPQPLECVFLADSGSVAVEVAMKMALQYWQAKGEARQRFLTFRNGYHGDTFGAMSVCDPDNSMHSLWKGYLPENLFAPAPQSRMDGEWDERDMVGFARLMAAHRHEIAAVIIEPIVQGAGGMRMYHPEWLKRIRKICDREGILLIADEIATGFGRTGKLFACEHAEIAPDILCLGKALTGGTMTLSATLTTREVAETISNGEAGCFMHGPTFMGNPLACAAANASLAILESGDWQQQVADIEVQLREQLAPARDAEMVADVRVLGAIGVVETTHPVNMAALQKFFVEQGVWIRPFGKLIYLMPPYIILPQQLQRLTAAVNRAVQDETFFC 428
               SCOP domains d1s09a_ A: Adenosylmethionine-8-amino-7-oxononanoate aminotransferase, BioA                                                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 1s09A01 A:1-60,A:331-427                                    1s09A02 A:61-330 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                                                          1s09A01 A:1-60,A:331-427 Aspartate Aminotransferase, domain 1                                    - CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh.............eeeeeee..eeee....eeee.............hhhhhhhhhhhhhhh.......eehhhhhhhhhhhhhhh.....eeeee.hhhhhhhhhhhhhhhhhhhh.....eeeee.......hhhhhh.......hhhhhh......eee.......-...hhhhhhhhhhhhhhhh..eeeeee...ee.....ee..hhhhhhhhhhhhhhh.eeeee............hhhhhhh....eeeehhhhhh.....eeeeehhhhhhhhhh..............hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee..eeeeee....hhhhhhhhhhhh.ee......eeee......hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AA_TRANSFER_CLASS_3  PDB: A:242-279   ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1s09 A   1 MTTDDLAFDQRHILHPYTSMTSPLPVYPVVSAEGCELILSDGRRLVDGMSSWWAAIHGYNHPQLNAAMKSQIDAMSHVMFGGITHAPAIELCRKLVAMTPQPLECVFLADSGSVAVEVAMKMALQYWQAKGEARQRFLTFRNGFHGDTFGAMSVCDPDNSMHSLWKGYLPENLFAPAPQSRM-GEWDERDMVGFARLMAAHRHEIAAVIIEPIVQGAGGMRMYHPEWLKRIRKICDREGILLIADEIATGFGRTGKLFACEHAEIAPDILCLGkALTGGTMTLSATLTTREVAETISNGEAGCFMHGPTFMGNPLACAAANASLAILESGDWQQQVADIEVQLREQLAPARDAEMVADVRVLGAIGVVETTHPVNMAALQKFFVEQGVWIRPFGKLIYLMPPYIILPQQLQRLTAAVNRAVQDETFFC 428
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180 | |   190       200       210       220       230       240       250       260       270   |   280       290       300       310       320       330       340       350       360       370       380       390       400       410       420        
                                                                                                                                                                                                               182 |                                                                                       274-LLP                                                                                                                                                      
                                                                                                                                                                                                                 184

Chain B from PDB  Type:PROTEIN  Length:428
 aligned with BIOA_ECOLI | P12995 from UniProtKB/Swiss-Prot  Length:429

    Alignment length:428
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420        
           BIOA_ECOLI     1 MTTDDLAFDQRHIWHPYTSMTSPLPVYPVVSAEGCELILSDGRRLVDGMSSWWAAIHGYNHPQLNAAMKSQIDAMSHVMFGGITHAPAIELCRKLVAMTPQPLECVFLADSGSVAVEVAMKMALQYWQAKGEARQRFLTFRNGYHGDTFGAMSVCDPDNSMHSLWKGYLPENLFAPAPQSRMDGEWDERDMVGFARLMAAHRHEIAAVIIEPIVQGAGGMRMYHPEWLKRIRKICDREGILLIADEIATGFGRTGKLFACEHAEIAPDILCLGKALTGGTMTLSATLTTREVAETISNGEAGCFMHGPTFMGNPLACAAANASLAILESGDWQQQVADIEVQLREQLAPARDAEMVADVRVLGAIGVVETTHPVNMAALQKFFVEQGVWIRPFGKLIYLMPPYIILPQQLQRLTAAVNRAVQDETFFC 428
               SCOP domains d1s09b_ B: Adenosylmethionine-8-amino-7-oxononanoate aminotransferase, BioA                                                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 1s09B01 B:1-60,B:331-428                                    1s09B02 B:61-330 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                                                          1s09B01 B:1-60,B:331-428 Aspartate Aminotransferase, domain 1                                      CATH domains
           Pfam domains (1) ---------------------------Aminotran_3-1s09B01 B:28-372                                                                                                                                                                                                                                                                                                                             -------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ---------------------------Aminotran_3-1s09B02 B:28-372                                                                                                                                                                                                                                                                                                                             -------------------------------------------------------- Pfam domains (2)
         Sec.struct. author .hhhhhhhhhhhh.............eeeeeee..eeee....eeee.............hhhhhhhhhhhhhhh.......eehhhhhhhhhhhhhhh...eeeeeee.hhhhhhhhhhhhhhhhhhhhh....eeeee.......hhhhhh.......hhhhhh......eee...........hhhhhhhhhhhhhhhh..eeeeee...ee.....ee..hhhhhhhhhhhhhhh.eeeee............hhhhhh.....eeeehhhhhh.....eeeeeehhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee..eeeeee....hhhhhhhhhhhh.ee......eeee......hhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AA_TRANSFER_CLASS_3  PDB: B:242-279   ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1s09 B   1 MTTDDLAFDQRHILHPYTSMTSPLPVYPVVSAEGCELILSDGRRLVDGMSSWWAAIHGYNHPQLNAAMKSQIDAMSHVMFGGITHAPAIELCRKLVAMTPQPLECVFLADSGSVAVEVAMKMALQYWQAKGEARQRFLTFRNGFHGDTFGAMSVCDPDNSMHSLWKGYLPENLFAPAPQSRMDGEWDERDMVGFARLMAAHRHEIAAVIIEPIVQGAGGMRMYHPEWLKRIRKICDREGILLIADEIATGFGRTGKLFACEHAEIAPDILCLGkALTGGTMTLSATLTTREVAETISNGEAGCFMHGPTFMGNPLACAAANASLAILESGDWQQQVADIEVQLREQLAPARDAEMVADVRVLGAIGVVETTHPVNMAALQKFFVEQGVWIRPFGKLIYLMPPYIILPQQLQRLTAAVNRAVQDETFFC 428
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270   |   280       290       300       310       320       330       340       350       360       370       380       390       400       410       420        
                                                                                                                                                                                                                                                                                                           274-LLP

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: Adenosylmethionine-8-amino-7-oxononanoate aminotransferase, BioA (13)

Escherichia coli [TaxId: 562] (11)

1a	d1s09a_	A:
1b	d1s09b_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Aspartate Aminotransferase; domain 2 (384)

Homologous Superfamily: Type I PLP-dependent aspartate aminotransferase-like (Major domain) (384)

Escherichia coli. Organism_taxid: 562. (37)

1a	1s09A02	A:61-330
1b	1s09B02	B:61-330

Architecture: Alpha-Beta Complex (3881)

Topology: Aspartate Aminotransferase, domain 1 (355)

Homologous Superfamily: Aspartate Aminotransferase, domain 1 (354)

Escherichia coli. Organism_taxid: 562. (32)

2a	1s09A01	A:1-60,A:331-427
2b	1s09B01	B:1-60,B:331-428

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: PLP_aminotran (240)

Family: Aminotran_3 (44)

Escherichia coli (strain K12) (13)

1a	Aminotran_3-1s09B01	B:28-372
1b	Aminotran_3-1s09B02	B:28-372

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (BIOA_ECOLI | P12995)

molecular function
	GO:0004015	adenosylmethionine-8-amino-7-oxononanoate transaminase activity	Catalysis of the reaction: 8-amino-7-oxononanoate + S-adenosyl-L-methionine(1+) = 7,8-diaminononanoate + S-adenosyl-4-methylthio-2-oxobutanoate.
	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:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	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.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
	GO:0009102	biotin biosynthetic process	The chemical reactions and pathways resulting in the formation of biotin, cis-tetrahydro-2-oxothieno(3,4-d)imidazoline-4-valeric acid.
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
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	1s09
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	2.6.1.62
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UniProtKB/Swiss-Prot
	BIOA_ECOLI \| P12995	:	1dty 1mgv 1mly 1mlz 1qj3 1qj5 1s06 1s07 1s08 1s0a

1dty	WT STRUCTURE OF 7,8-DIAMINOPELARGONIC ACID SYNTHASE
1mgv	R391A MUTANT OF 7,8-DIAMINOPELARGONIC ACID SYNTHASE
1mly	7,8-DIAMINOPELARGONIC ACID SYNTHASE IN COMPLEX WITH CIS- AMICLENOMYCIN
1mlz	7,8-DIAMINOPELARGONIC ACID SYNTHASE IN COMPLEX WITH TRANS- AMICLENOMYCIN
1qj3	7,8-DIAMINOPELARGONIC ACID SYNTHASE IN COMPLEX WITH THE KAPA SUBSTRATE
1qj5	WT STRUCTURE OF 7,8-DIAMINOPELARGONIC ACID SYNTHASE
1s06	CRYSTAL STRUCTURE OF THE R253K MUTANT OF 7,8- DIAMINOPELARGONIC ACID SYNTHASE
1s07	CRYSTAL STRUCTURE OF THE R253A MUTANT OF 7,8- DIAMINOPELARGONIC ACID SYNTHASE
1s08	CRYSTAL STRUCTURE OF THE D147N MUTANT OF 7,8- DIAMINOPELARGONIC ACID SYNTHASE
1s0a	CRYSTAL STRUCTURE OF THE Y17F MUTANT OF 7,8- DIAMINOPELARGONIC ACID SYNTHASE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (2, 4)

Pfam Domains (1, 2)

Gene Ontology (8, 8)

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