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(-) Description

Title :  STRUCTURE OF BIOSYNTHETIC N-ACETYLORNITHINE AMINOTRANSFERASE FROM SALMONELLA TYPHIMURIUM: STUDIES ON SUBSTRATE SPECIFICITY AND INHIBITOR BINDING
 
Authors :  V. Rajaram, P. Ratna Prasuna, H. S. Savithri, M. R. N. Murthy
Date :  28 Mar 07  (Deposition) - 25 Dec 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.91
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Argd, Pyridoxal 5'-Phosphate, Arginine Metabolism, Lysine Biosynthesis, Gabaculine, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. Rajaram, P. Ratna Prasuna, H. S. Savithri, M. R. N. Murthy
Structure Of Biosynthetic N-Acetylornithine Aminotransferas From Salmonella Typhimurium: Studies On Substrate Specificity And Inhibitor Binding
Proteins V. 70 429 2007
PubMed-ID: 17680699  |  Reference-DOI: 10.1002/PROT.21567

(-) Compounds

Molecule 1 - ACETYLORNITHINE/SUCCINYLDIAMINOPIMELATE AMINOTRANSFERASE
    Chains: A, B
    EC Number: 2.6.1.11, 2.6.1.17
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PRSET 'C'
    Expression System Strain: BL21 (DE3) PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: ARGD
    Organism Scientific: SALMONELLA TYPHIMURIUM
    Organism Taxid: 99287
    Strain: LT2
    Synonym: ACOAT, SUCCINYLDIAMINOPIMELATE TRANSFERASE, DAPATASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric/Biological Unit (3, 8)
No.NameCountTypeFull Name
1EDO6Ligand/Ion1,2-ETHANEDIOL
2GOL1Ligand/IonGLYCEROL
3PLP1Ligand/IonPYRIDOXAL-5'-PHOSPHATE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:107 , GLY A:108 , THR A:109 , ASN A:112 , PHE A:141 , HIS A:142 , GLU A:193 , ASP A:226 , VAL A:228 , GLN A:229 , LYS A:255 , HOH B:2152BINDING SITE FOR RESIDUE PLP A 1555
2AC2SOFTWAREGLY A:57 , HIS A:58 , CYS A:59 , HIS A:60 , GLY A:259 , HOH A:1825 , TRP B:75BINDING SITE FOR RESIDUE EDO A 1001
3AC3SOFTWAREHIS A:76 , THR A:77 , SER A:78 , PHE A:81 , HOH A:1567 , HOH A:1577 , ASP B:46 , GLY B:50 , HIS B:58BINDING SITE FOR RESIDUE EDO A 1002
4AC4SOFTWARETHR A:205 , PRO A:206 , THR B:205 , PRO B:206 , HOH B:2133 , HOH B:2138 , HOH B:2179BINDING SITE FOR RESIDUE EDO A 1004
5AC5SOFTWAREGLY A:245 , HOH A:1653 , HOH A:1669 , ASP B:326 , ILE B:335BINDING SITE FOR RESIDUE EDO A 1005
6AC6SOFTWARETRP A:75 , GLY B:57 , HIS B:58 , CYS B:59 , HIS B:60 , GLY B:259 , HOH B:2021BINDING SITE FOR RESIDUE EDO B 1003
7AC7SOFTWAREVAL B:102 , SER B:283 , THR B:284 , TYR B:285BINDING SITE FOR RESIDUE EDO B 1006
8AC8SOFTWARELYS B:133 , ILE B:168 , ILE B:169 , HIS B:170 , HOH B:2073 , HOH B:2074 , HOH B:2129 , HOH B:2184BINDING SITE FOR RESIDUE GOL B 2001

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2PB2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2PB2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2PB2)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AA_TRANSFER_CLASS_3PS00600 Aminotransferases class-III pyridoxal-phosphate attachment site.ARGD_SALTY223-260
 		  2A:223-260
B:223-260

(-) Exons   (0, 0)

(no "Exon" information available for 2PB2)

(-) 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:378
 aligned with ARGD_SALTY | P40732 from UniProtKB/Swiss-Prot  Length:405

    Alignment length:382
                                    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  
           ARGD_SALTY    24 ADFIPVKGKGSRVWDQQGKEYIDFAGGIAVTALGHCHPALVEALKSQGETLWHTSNVFTNEPALRLGRKLIDATFAERVLFMNSGTEANETAFKLARHYACVRHSPFKTKIIAFHNAFHGRSLFTVSVGGQPKYSDGFGPKPADIIHVPFNDLHAVKAVMDDHTCAVVVEPIQGEGGVQAATPEFLKGLRDLCDEHQALLVFDEVQCGMGRTGDLFAYMHYGVTPDILTSAKALGGGFPVSAMLTTQEIASAFHVGSHGSTYGGNPLACAVAGAAFDIINTPEVLQGIHTKRQQFVQHLQAIDEQFDIFSDIRGMGLLIGAELKPKYKGRARDFLYAGAEAGVMVLNAGADVMRFAPSLVVEEADIHEGMQRFAQAVGKVVA 405
               SCOP domains d2pb2a_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------2pb2A02 A:60-305 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                                  ---------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee..eeee....eeee.hhhhhh......hhhhhhhhhhhhh..........hhhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhhhhhhhhhhh.....eeeee.......hhhhhhhh.hhhhhh........eeee...hhhhhhhhh...eeeeee..ee.....ee.hhhhhhhhhhhhhhh..eeeee............hhhhhhh....eeeehhhhhh....eeeeehhhhhh...----..ee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee..eeeeee.hhhh.hhhhhhhhhhhh.ee.ee....eeee......hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AA_TRANSFER_CLASS_3  PDB: A:223-260   ------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pb2 A  24 ADFIPVKGKGSRVWDQQGKEYIDFAGGIAVTALGHCHPALVEALKSQGETLWHTSNVFTNEPALRLGRKLIDATFAERVLFMNSGTEANETAFKLARHYACVRHSPFKTKIIAFHNAFHGRSLFTVSVGGQPKYSDGFGPKPADIIHVPFNDLHAVKAVMDDHTCAVVVEPIQGEGGVQAATPEFLKGLRDLCDEHQALLVFDEVQCGMGRTGDLFAYMHYGVTPDILTSAKALGGGFPVSAMLTTQEIASAFH----GSTYGGNPLACAVAGAAFDIINTPEVLQGIHTKRQQFVQHLQAIDEQFDIFSDIRGMGLLIGAELKPKYKGRARDFLYAGAEAGVMVLNAGADVMRFAPSLVVEEADIHEGMQRFAQAVGKVVA 405
                                    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  
                                                                                                                                                                                                                                                                                       277  282                                                                                                                           


Chain B from PDB  Type:PROTEIN  Length:382
 aligned with ARGD_SALTY | P40732 from UniProtKB/Swiss-Prot  Length:405

    Alignment length:388
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397        
           ARGD_SALTY    18 LPVYAPADFIPVKGKGSRVWDQQGKEYIDFAGGIAVTALGHCHPALVEALKSQGETLWHTSNVFTNEPALRLGRKLIDATFAERVLFMNSGTEANETAFKLARHYACVRHSPFKTKIIAFHNAFHGRSLFTVSVGGQPKYSDGFGPKPADIIHVPFNDLHAVKAVMDDHTCAVVVEPIQGEGGVQAATPEFLKGLRDLCDEHQALLVFDEVQCGMGRTGDLFAYMHYGVTPDILTSAKALGGGFPVSAMLTTQEIASAFHVGSHGSTYGGNPLACAVAGAAFDIINTPEVLQGIHTKRQQFVQHLQAIDEQFDIFSDIRGMGLLIGAELKPKYKGRARDFLYAGAEAGVMVLNAGADVMRFAPSLVVEEADIHEGMQRFAQAVGKVVA 405
               SCOP domains d2pb2b_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains ------------------------------------------2pb2B02 B:60-305 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                                  ---------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---------Aminotran_3-2pb2B01 B:27-348                                                                                                                                                                                                                                                                                                      --------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ---------Aminotran_3-2pb2B02 B:27-348                                                                                                                                                                                                                                                                                                      --------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ..........eeeee..eeee....eeee.hhhhhh......hhhhhhhhhhhhh..........hhhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhhhhhhhhhhh.....eeeee.......hhhhhhhh.hhhhhh........eeee...hhhhhhhhh...eeeeee..ee.....ee.hhhhhhhhhhhhhhhh.eeeee............hhhhhhh....eeeehhhhh.....eeeeehhhhhh..------.ee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee..eeeeee.hhhh.hhhhhhhhhhhh.ee.ee....eeee......hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AA_TRANSFER_CLASS_3  PDB: B:223-260   ------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pb2 B  18 LPVYAPADFIPVKGKGSRVWDQQGKEYIDFAGGIAVTALGHCHPALVEALKSQGETLWHTSNVFTNEPALRLGRKLIDATFAERVLFMNSGTEANETAFKLARHYACVRHSPFKTKIIAFHNAFHGRSLFTVSVGGQPKYSDGFGPKPADIIHVPFNDLHAVKAVMDDHTCAVVVEPIQGEGGVQAATPEFLKGLRDLCDEHQALLVFDEVQCGMGRTGDLFAYMHYGVTPDILTSAKALGGGFPVSAMLTTQEIASAF------STYGGNPLACAVAGAAFDIINTPEVLQGIHTKRQQFVQHLQAIDEQFDIFSDIRGMGLLIGAELKPKYKGRARDFLYAGAEAGVMVLNAGADVMRFAPSLVVEEADIHEGMQRFAQAVGKVVA 405
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267        |-     | 287       297       307       317       327       337       347       357       367       377       387       397        
                                                                                                                                                                                                                                                                                            276    283
   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  (1, 2)

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

(-) Pfam Domains  (1, 2)

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

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (ARGD_SALTY | P40732)
molecular function
    GO:0003992    N2-acetyl-L-ornithine:2-oxoglutarate 5-aminotransferase activity    Catalysis of the reaction: 2-oxoglutarate + N(2)-acetyl-L-ornithine = N-acetyl-L-glutamate 5-semialdehyde + L-glutamate.
    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:0009016    succinyldiaminopimelate transaminase activity    Catalysis of the reaction: 2-oxoglutarate + N-succinyl-LL-2,6-diaminopimelate = L-2-succinylamino-6-oxopimelate + L-glutamate.
    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:0006526    arginine biosynthetic process    The chemical reactions and pathways resulting in the formation of arginine, 2-amino-5-(carbamimidamido)pentanoic acid.
    GO:0006525    arginine metabolic process    The chemical reactions and pathways involving arginine, 2-amino-5-(carbamimidamido)pentanoic acid.
    GO:0008652    cellular amino acid biosynthetic process    The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
    GO:0006520    cellular amino acid metabolic process    The chemical reactions and pathways involving amino acids, carboxylic acids containing one or more amino groups, as carried out by individual cells.
    GO:0009085    lysine biosynthetic process    The chemical reactions and pathways resulting in the formation of lysine, 2,6-diaminohexanoic acid.
    GO:0009089    lysine biosynthetic process via diaminopimelate    The chemical reactions and pathways resulting in the formation of lysine, via the intermediate diaminopimelate.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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  2pb2
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  ARGD_SALTY | P40732
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  2.6.1.11
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 Related Entries

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

UniProtKB/Swiss-Prot
        ARGD_SALTY | P40732: 2pb0 4jev 4jew 4jex 4jey 4jez 4jf0 4jf1

(-) Related Entries Specified in the PDB File

2pb0