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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 :  1.96
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  (2, 6)

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
1EDO4Ligand/Ion1,2-ETHANEDIOL
2PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
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 A:1154 , HOH A:1225 , HOH A:1226 , THR B:284 , HOH B:1108BINDING SITE FOR RESIDUE PLP A 555
2AC2SOFTWARESER B:107 , GLY B:108 , THR B:109 , ASN B:112 , PHE B:141 , HIS B:142 , GLU B:193 , ASP B:226 , VAL B:228 , GLN B:229 , LYS B:255 , HOH B:1142BINDING SITE FOR RESIDUE PLP B 555
3AC3SOFTWARETRP A:75 , GLY B:57 , HIS B:58 , CYS B:59 , HIS B:60 , GLY B:259 , HOH B:1031BINDING SITE FOR RESIDUE EDO B 1001
4AC4SOFTWAREGLY A:57 , HIS A:58 , CYS A:59 , HIS A:60 , GLY A:259 , HOH A:1037 , TRP B:75BINDING SITE FOR RESIDUE EDO A 1002
5AC5SOFTWARETHR A:109 , ARG A:144 , SER A:145 , MET B:105 , GLU B:110 , GLU B:113 , THR B:114 , HIS B:281 , HOH B:1147BINDING SITE FOR RESIDUE EDO B 1003
6AC6SOFTWAREPRO A:206 , HOH A:1260 , HOH A:1261 , HOH A:1266 , PRO B:206BINDING SITE FOR RESIDUE EDO A 1004

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2PB0)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1His B:281 -Gly B:282

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2PB0)

(-) 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 2PB0)

(-) 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:389
 aligned with ARGD_SALTY | P40732 from UniProtKB/Swiss-Prot  Length:405

    Alignment length:394
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401    
           ARGD_SALTY    12 TFDEVILPVYAPADFIPVKGKGSRVWDQQGKEYIDFAGGIAVTALGHCHPALVEALKSQGETLWHTSNVFTNEPALRLGRKLIDATFAERVLFMNSGTEANETAFKLARHYACVRHSPFKTKIIAFHNAFHGRSLFTVSVGGQPKYSDGFGPKPADIIHVPFNDLHAVKAVMDDHTCAVVVEPIQGEGGVQAATPEFLKGLRDLCDEHQALLVFDEVQCGMGRTGDLFAYMHYGVTPDILTSAKALGGGFPVSAMLTTQEIASAFHVGSHGSTYGGNPLACAVAGAAFDIINTPEVLQGIHTKRQQFVQHLQAIDEQFDIFSDIRGMGLLIGAELKPKYKGRARDFLYAGAEAGVMVLNAGADVMRFAPSLVVEEADIHEGMQRFAQAVGKVVA 405
               SCOP domains d2pb0a_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ------------------------------------------------2pb0A02 A:60-305 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                                  ---------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh..........eeeee..eeee....eeee.hhhhhh......hhhhhhhhhhhhh..........hhhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhhhhhhhhhhh.....eeeee.......hhhhhhhh.hhhhhh........eeee...hhhhhhhhh...eeeeee..ee.....ee.hhhhhhhhhhhhhhhh.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
                 2pb0 A  12 TFDEVILPVYAPADFIPVKGKGSRVWDQQGKEYIDFAGGIAVTALGHCHPALVEALKSQGETLWHTSNVFTNEPALRLGRKLIDATFAERVLFMNSGTEANETAFKLARHYACVRHSPFKTKIIAFHNAFHGRSLFTVSVGGQPKYSDGFGPKPADIIHVPFNDLHAVKAVMDDHTCAVVVEPIQGEGGVQAATPEFLKGLRDLCDEHQALLVFDEVQCGMGRTGDLFAYMHYGVTPDILTSAKALGGGFPVSAMLTTQEIASAF-----GSTYGGNPLACAVAGAAFDIINTPEVLQGIHTKRQQFVQHLQAIDEQFDIFSDIRGMGLLIGAELKPKYKGRARDFLYAGAEAGVMVLNAGADVMRFAPSLVVEEADIHEGMQRFAQAVGKVVA 405
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271    |    -|      291       301       311       321       331       341       351       361       371       381       391       401    
                                                                                                                                                                                                                                                                                                  276   282                                                                                                                           


Chain B from PDB  Type:PROTEIN  Length:387
 aligned with ARGD_SALTY | P40732 from UniProtKB/Swiss-Prot  Length:405

    Alignment length:387
                                    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 LPVYAPADFIPVKGKGSRVWDQQGKEYIDFAGGIAVTALGHCHPALVEALKSQGETLWHTSNVFTNEPALRLGRKLIDATFAERVLFMNSGTEANETAFKLARHYACVRHSPFKTKIIAFHNAFHGRSLFTVSVGGQPKYSDGFGPKPADIIHVPFNDLHAVKAVMDDHTCAVVVEPIQGEGGVQAATPEFLKGLRDLCDEHQALLVFDEVQCGMGRTGDLFAYMHYGVTPDILTSAKALGGGFPVSAMLTTQEIASAFHVGSHGSTYGGNPLACAVAGAAFDIINTPEVLQGIHTKRQQFVQHLQAIDEQFDIFSDIRGMGLLIGAELKPKYKGRARDFLYAGAEAGVMVLNAGADVMRFAPSLVVEEADIHEGMQRFAQAVGKVV 404
               SCOP domains d2pb0b_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------2pb0B02 B:60-305 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                                  --------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---------Aminotran_3-2pb0B01 B:27-348                                                                                                                                                                                                                                                                                                      -------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ---------Aminotran_3-2pb0B02 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....eeeehhhhhh....eeeeehhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee..eeeeee.hhhh.hhhhhhhhhhhh.ee.ee....eeee......hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AA_TRANSFER_CLASS_3  PDB: B:223-260   ------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pb0 B  18 LPVYAPADFIPVKGKGSRVWDQQGKEYIDFAGGIAVTALGHCHPALVEALKSQGETLWHTSNVFTNEPALRLGRKLIDATFAERVLFMNSGTEANETAFKLARHYACVRHSPFKTKIIAFHNAFHGRSLFTVSVGGQPKYSDGFGPKPADIIHVPFNDLHAVKAVMDDHTCAVVVEPIQGEGGVQAATPEFLKGLRDLCDEHQALLVFDEVQCGMGRTGDLFAYMHYGVTPDILTSAKALGGGFPVSAMLTTQEIASAFHVGSHGSTYGGNPLACAVAGAAFDIINTPEVLQGIHTKRQQFVQHLQAIDEQFDIFSDIRGMGLLIGAELKPKYKGRARDFLYAGAEAGVMVLNAGADVMRFAPSLVVEEADIHEGMQRFAQAVGKVV 404
                                    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
   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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  2pb0
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  ARGD_SALTY | P40732
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 Related Entries

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

UniProtKB/Swiss-Prot
        ARGD_SALTY | P40732: 2pb2 4jev 4jew 4jex 4jey 4jez 4jf0 4jf1

(-) Related Entries Specified in the PDB File

2pb2