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(-) Description

Title :  CRYSTAL STRUCTURE OF THE D147N 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 :  2.10
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)

(-) Compounds

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

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1LLP2Mod. Amino Acid2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)
2NA2Ligand/IonSODIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:96 , THR A:99 , PRO A:100 , LEU A:103 , HOH A:1563BINDING SITE FOR RESIDUE NA A 1501
2AC2SOFTWAREVAL B:96 , THR B:99 , PRO B:100 , LEU B:103 , HOH B:1559BINDING SITE FOR RESIDUE NA B 1502

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1S08)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1S08)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1S08)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AA_TRANSFER_CLASS_3PS00600 Aminotransferases class-III pyridoxal-phosphate attachment site.BIOA_ECOLI242-279
 		  2A:242-279
B:242-279

(-) Exons   (0, 0)

(no "Exon" information available for 1S08)

(-) Sequences/Alignments

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:411
 aligned with BIOA_ECOLI | P12995 from UniProtKB/Swiss-Prot  Length:429

    Alignment length:429
                                    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 MTTDDLAFDQRHIWHPYTSMTSPLPVYPVVSAEGCELILSDGRRLVDGMSSWWAAIHGYNHPQLNAAMKSQIDAMSHVMFGGITHAPAIELCRKLVAMTPQPLECVFLADSGSVAVEVAMKMALQYWQAKGEARQRFLTFRNGYHGDTFGAMSVCDPDNSMHSLWKGYLPENLFAPAPQSRMDGEWDERDMVGFARLMAAHRHEIAAVIIEPIVQGAGGMRMYHPEWLKRIRKICDREGILLIADEIATGFGRTGKLFACEHAEIAPDILCLGKALTGGTMTLSATLTTREVAETISNGEAGCFMHGPTFMGNPLACAAANASLAILESGDWQQQVADIEVQLREQLAPARDAEMVADVRVLGAIGVVETTHPVNMAALQKFFVEQGVWIRPFGKLIYLMPPYIILPQQLQRLTAAVNRAVQDETFFCQ 429
               SCOP domains d1s08a_ A: Adenosylmethionine-8-amino-7-oxononanoate aminotransferase, BioA                                                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 1s08A01 A:1-60,A:331-425                                    1s08A02 A:61-330 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                                                          1s08A01 A:1-60,A:331-425 Aspartate Aminotransferase, domain 1                                  ---- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh.............eeeeeee..eeee....eeee.............hhhhhhhhhhhhhhh.......eehhhhhhhhhhhhhhh.....eeeee.hhhhhhhhhhhhhhhhhhhh.....eeeee.......hhhhhh....-------------..eee.......-...hhhhhhhhhhhhhhhh..eeeeee...ee.....ee..hhhhhhhhhhhhhhh.eeeee............hhhhhhh....eeeehhhhhh.....eeeeehhhhhhhhhh.----.........hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh..eeeeeee..eeeeee....hhhhhhhhhhhh.ee......eeee......hhhhhhhhhhhhhhhh.hhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AA_TRANSFER_CLASS_3  PDB: A:242-279   ------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1s08 A   1 MTTDDLAFDQRHILHPYTSMTSPLPVYPVVSAEGCELILSDGRRLVDGMSSWWAAIHGYNHPQLNAAMKSQIDAMSHVMFGGITHAPAIELCRKLVAMTPQPLECVFLADSGSVAVEVAMKMALQYWQAKGEARQRFLTFRNGYHGNTFGAMSVCDP-------------ENLFAPAPQSRM-GEWDERDMVGFARLMAAHRHEIAAVIIEPIVQGAGGMRMYHPEWLKRIRKICDREGILLIADEIATGFGRTGKLFACEHAEIAPDILCLGkALTGGTMTLSATLTTREVAETISNG----FMHGPTFMGNPLACAAANASLAILESGDWQQQVADIEVQLREQLAPARDAEMVADVRVLGAIGVVETTHPVNMAALQKFFVEQGVWIRPFGKLIYLMPPYIILPQQLQRLTAAVNRAVQDETFFCQ 429
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150      |  -         -|      180 | |   190       200       210       220       230       240       250       260       270   |   280       290        |-   |   310       320       330       340       350       360       370       380       390       400       410       420         
                                                                                                                                                                                      157           171        182 |                                                                                       274-LLP                  299  304                                                                                                                             
                                                                                                                                                                                                                 184                                                                                                                                                                                                                                                     


Chain B from PDB  Type:PROTEIN  Length:410
 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 d1s08b_ B: Adenosylmethionine-8-amino-7-oxononanoate aminotransferase, BioA                                                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 1s08B01 B:1-60,B:331-425                                    1s08B02 B:61-330 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                                                          1s08B01 B:1-60,B:331-425 Aspartate Aminotransferase, domain 1                                  --- CATH domains
           Pfam domains (1) ---------------------------Aminotran_3-1s08B01 B:28-372                                                                                                                                                                                                                                                                                                                             -------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ---------------------------Aminotran_3-1s08B02 B:28-372                                                                                                                                                                                                                                                                                                                             -------------------------------------------------------- Pfam domains (2)
         Sec.struct. author .hhhhhhhhhhhh.............eeeeeee..eeee....eeee.............hhhhhhhhhhhhhhh.......eehhhhhhhhhhhhhhh.....eeeee.hhhhhhhhhhhhhhhhhhh......eeeee.......hhhhhhh...--------------.eee...........hhhhhhhhhhhhhhhh..eeeeee...ee.....ee..hhhhhhhhhhhhhhh.eeeee............hhhhhh.....eeeehhhhhh.....eeeeehhhhhhhhhh----..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee..eeeeee....hhhhhhhhhhhh.ee......eeee......hhhhhhhhhhhhhhhh.hhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AA_TRANSFER_CLASS_3  PDB: B:242-279   ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1s08 B   1 MTTDDLAFDQRHILHPYTSMTSPLPVYPVVSAEGCELILSDGRRLVDGMSSWWAAIHGYNHPQLNAAMKSQIDAMSHVMFGGITHAPAIELCRKLVAMTPQPLECVFLADSGSVAVEVAMKMALQYWQAKGEARQRFLTFRNGYHGNTFGAMSVCDP--------------NLFAPAPQSRMDGEWDERDMVGFARLMAAHRHEIAAVIIEPIVQGAGGMRMYHPEWLKRIRKICDREGILLIADEIATGFGRTGKLFACEHAEIAPDILCLGkALTGGTMTLSATLTTREVAETISN----CFMHGPTFMGNPLACAAANASLAILESGDWQQQVADIEVQLREQLAPARDAEMVADVRVLGAIGVVETTHPVNMAALQKFFVEQGVWIRPFGKLIYLMPPYIILPQQLQRLTAAVNRAVQDETFFC 428
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150      |  -         - |     180       190       200       210       220       230       240       250       260       270   |   280       290       | -  |    310       320       330       340       350       360       370       380       390       400       410       420        
                                                                                                                                                                                      157            172                                                                                                   274-LLP                 298  303
   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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: PLP_aminotran (240)

(-) Gene Ontology  (8, 8)

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.

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  1s08
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  2.6.1.62
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        BIOA_ECOLI | P12995: 1dty 1mgv 1mly 1mlz 1qj3 1qj5 1s06 1s07 1s09 1s0a

(-) Related Entries Specified in the PDB File

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 THE 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
1s09 CRYSTAL STRUCTURE OF THE Y144F MUTANT OF 7,8- DIAMINOPELARGONIC ACID SYNTHASE
1s0a CRYSTAL STRUCTURE OF THE Y17F MUTANT OF 7,8- DIAMINOPELARGONIC ACID SYNTHASE