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(-) Description

Title :  CRYSTAL STRUCTURE OF ARNB TRANSFERASE WITH PYRIDOXAL 5' PHOSPHATE
 
Authors :  B. W. Noland, J. M. Newman, J. Hendle, J. Badger, J. A. Christopher, J. Tr M. D. Buchanan, T. A. Wright, M. E. Rutter, W. E. Sanderson, H. -J. Mulle Dieckmann, K. S. Gajiwala, S. G. Buchanan
Date :  07 Aug 02  (Deposition) - 11 Dec 02  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.96
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Type 1 Aminotransferase Fold, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. W. Noland, J. M. Newman, J. Hendle, J. Badger, J. A. Christopher, J. Tresser, M. D. Buchanan, T. Wright, M. E. Rutter, W. E. Sanderson, H. -J. Muller-Dieckmann, K. Gajiwala, S. G. Buchanan
Structural Studies Of Salmonella Typhimurium Arnb (Pmrh) Aminotransferase: A 4-Amino-4-Deoxy-L-Arabinose Lipopolysaccharide Modifying Enzyme
Structure V. 10 1569 2002
PubMed-ID: 12429098  |  Reference-DOI: 10.1016/S0969-2126(02)00879-1
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ARNB AMINOTRANSFERASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: SALMONELLA TYPHIMURIUM
    Organism Taxid: 602
    Synonym: PUTATIVE DEGT/DNRJ/ERYC1/STRS FAMILY

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (1x): A
Biological Unit 2 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric Unit (3, 4)
No.NameCountTypeFull Name
1AKG1Ligand/Ion2-OXOGLUTARIC ACID
2GOL2Ligand/IonGLYCEROL
3PLP1Ligand/IonPYRIDOXAL-5'-PHOSPHATE
Biological Unit 1 (3, 4)
No.NameCountTypeFull Name
1AKG1Ligand/Ion2-OXOGLUTARIC ACID
2GOL2Ligand/IonGLYCEROL
3PLP1Ligand/IonPYRIDOXAL-5'-PHOSPHATE
Biological Unit 2 (3, 8)
No.NameCountTypeFull Name
1AKG2Ligand/Ion2-OXOGLUTARIC ACID
2GOL4Ligand/IonGLYCEROL
3PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:62 , ALA A:63 , THR A:64 , ASP A:160 , ALA A:162 , HIS A:163 , SER A:183 , HIS A:185 , LYS A:188 , GLY A:195 , LYS A:241 , PHE A:330 , HOH A:404 , HOH A:406BINDING SITE FOR RESIDUE PLP A 400
2AC2SOFTWARETHR A:36 , TRP A:89 , HIS A:185 , GLU A:194 , PHE A:214 , ARG A:229 , LYS A:241 , ASN A:243 , HOH A:404 , HOH A:820BINDING SITE FOR RESIDUE AKG A 401
3AC3SOFTWARESER A:61 , GLU A:194 , LEU A:244 , PRO A:245 , ASN A:248BINDING SITE FOR RESIDUE GOL A 402
4AC4SOFTWAREPHE A:13 , ARG A:229 , GLY A:327 , LEU A:328 , HOH A:733 , HOH A:820 , HOH A:839BINDING SITE FOR RESIDUE GOL A 403

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1His A:329 -Phe A:330

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1MDX)

(-) Exons   (0, 0)

(no "Exon" information available for 1MDX)

(-) Sequences/Alignments

Asymmetric 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:366
 aligned with ARNB_SALTY | Q8ZNF3 from UniProtKB/Swiss-Prot  Length:385

    Alignment length:376
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378      
           ARNB_SALTY     9 DFLPFSRPAMGAEELAAVKTVLDSGWITTGPKNQELEAAFCRLTGNQYAVAVSSATAGMHIALMALGIGEGDEVITPSMTWVSTLNMIVLLGANPVMVDVDRDTLMVTPEHIEAAITPQTKAIIPVHYAGAPADLDAIYALGERYGIPVIEDAAHATGTSYKGRHIGARGTAIFSFHAIKNITCAEGGIVVTDNPQFADKLRSLKFHGLGVDAWDRQSGGRAPQAEVLAPGYKYNLPDLNAAIALAQLQKLDALNARRAAIAAQYHQAMADLPFQPLSLPSWEHIHAWHLFIIRVDEARCGITRDALMASLKTKGIGTGLHFRAAHTQKYYRERFPTLTLPDTEWNSERICSLPLFPDMTESDFDRVITALHQIAG 384
               SCOP domains d1mdxa_ A: Aminotransferase ArnB                                                                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 1mdxA01 A:9-258 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                                       1mdxA02 A:259-384 Aspartate Aminotransferase, domain 1                                                                         CATH domains
               Pfam domains -DegT_DnrJ_EryC1-1mdxA01 A:10-374                                                                                                                                                                                                                                                                                                                                             ---------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhh......eeeee...hhhhhhhhhhh..eeeee.........hhhhhhhhh...eeee...hhhhh..hhhhhhhhhhhhh...eee.......ee..ee.....eeeee............eeeee.hhhhhhhhhhhh.....----------................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...ee.......ee.....eeee.hhhhhh.hhhhhhhhhhhh.........hhhhhhhhhhhh....hhhhhhhhhheeee......hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1mdx A   9 DFLPFSRPAMGAEELAAVKTVLDSGWITTGPKNQELEAAFCRLTGNQYAVAVSSATAGMHIALMALGIGEGDEVITPSMTWVSTLNMIVLLGANPVMVDVDRDTLMVTPEHIEAAITPQTKAIIPVHYAGAPADLDAIYALGERYGIPVIEDAAHATGTSYKGRHIGARGTAIFSFHAIKNITCAEGGIVVTDNPQFADKLRSLKFHGLG----------RAPQAEVLAPGYKYNLPDLNAAIALAQLQKLDALNARRAAIAAQYHQAMADLPFQPLSLPSWEHIHAWHLFIIRVDEARCGITRDALMASLKTKGIGTGLHFRAAHTQKYYRERFPTLTLPDTEWNSERICSLPLFPDMTESDFDRVITALHQIAG 384
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218         -|      238       248       258       268       278       288       298       308       318       328       338       348       358       368       378      
                                                                                                                                                                                                                                           218        229
   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, 1)

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

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: PLP_aminotran (240)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A   (ARNB_SALTY | Q8ZNF3)
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: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.
    GO:0099621    undecaprenyl-phosphate 4-deoxy-4-formamido-L-arabinose transferase activity    Catalysis of the reaction: UDP-4-deoxy-4-formamido-beta-L-arabinopyranose + ditrans,octacis-undecaprenyl phosphate = UDP + 4-deoxy-4-formamido-alpha-L-arabinopyranosyl ditrans,octacis-undecaprenyl phosphate.
biological process
    GO:0009245    lipid A biosynthetic process    The chemical reactions and pathways resulting in the formation of lipid A, the glycolipid group of bacterial lipopolysaccharides, consisting of four to six fatty acyl chains linked to two glucosamine residues. Further modifications of the backbone are common.
    GO:0046493    lipid A metabolic process    The chemical reactions and pathways involving lipid A, the glycolipid group of bacterial lipopolysaccharides, consisting of four to six fatty acyl chains linked to two glucosamine residues. Further modifications of the backbone are common.
    GO:0006629    lipid metabolic process    The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
    GO:0009103    lipopolysaccharide biosynthetic process    The chemical reactions and pathways resulting in the formation of lipopolysaccharides, any of a group of related, structurally complex components of the outer membrane of Gram-negative bacteria.
    GO:0046677    response to antibiotic    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms.

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 Related Entries

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

UniProtKB/Swiss-Prot
        ARNB_SALTY | Q8ZNF3: 1mdo 1mdz 4oca

(-) Related Entries Specified in the PDB File

1mdo CRYSTAL STRUCTURE OF ARNB TRANSFERASE WITH PYRIDOXAL 5' PHOSPHATE
1mdz CRYSTAL STRUCTURE OF ARNB AMINOTRANSFERASE WITH CYLOSERINE PYRIDOXAL 5' PHOSPHATE