Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit - manually
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit - manually
Asym./Biol. Unit - manually  (Jmol Viewer)
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  STRUCTURAL BASIS FOR THE CATALYTIC ACTIVITY OF ASPARTATE AMINOTRANSFERASE K258H LACKING ITS PYRIDOXAL-5'-PHOSPHATE-BINDING LYSINE RESIDUE
 
Authors :  V. N. Malashkevich, J. N. Jansonius
Date :  28 Feb 94  (Deposition) - 31 Jul 94  (Release) - 25 Jul 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Transferase(Aminotransferase) (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. N. Malashkevich, J. Jager, M. Ziak, U. Sauder, H. Gehring, P. Christen, J. N. Jansonius
Structural Basis For The Catalytic Activity Of Aspartate Aminotransferase K258H Lacking The Pyridoxal 5'-Phosphate-Binding Lysine Residue.
Biochemistry V. 34 405 1995
PubMed-ID: 7819232  |  Reference-DOI: 10.1021/BI00002A004
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ASPARTATE AMINOTRANSFERASE
    Chains: A, B
    EC Number: 2.6.1.1
    Engineered: YES
    Expression System: UNIDENTIFIED
    Expression System Taxid: 32644
    Mutation: YES
    Organ: HEART
    Organism Common: CHICKEN
    Organism Scientific: GALLUS GALLUS
    Organism Taxid: 9031

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1PLP1Ligand/IonPYRIDOXAL-5'-PHOSPHATE
2PO41Ligand/IonPHOSPHATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:70 , SER B:107 , GLY B:108 , THR B:109 , SER B:255 , ARG B:266BINDING SITE FOR RESIDUE PO4 B 411
2AC2SOFTWARESER A:107 , GLY A:108 , THR A:109 , TRP A:140 , ASN A:194 , ASP A:222 , TYR A:225 , SER A:255 , HIS A:258 , ARG A:266 , HOH A:448 , TYR B:70BINDING SITE FOR RESIDUE PLP A 411
3ACTAUTHORASP A:15 , ILE A:17 , LEU A:18 , VAL A:37 , GLY A:38 , ALA A:39 , TYR A:70 , SER A:107 , GLY A:108 , THR A:109 , TRP A:140 , ASN A:194 , ASP A:222 , ALA A:224 , TYR A:225 , SER A:255 , HIS A:258 , ARG A:266 , ARG A:292 , SER A:296 , ASN A:297 , PHE A:360 , ARG A:386 , PLP A:411ACTIVE SITE RESIDUES
4BCTAUTHORASP B:15 , ILE B:17 , LEU B:18 , VAL B:37 , GLY B:38 , ALA B:39 , TYR B:70 , SER B:107 , GLY B:108 , THR B:109 , TRP B:140 , ASN B:194 , ASP B:222 , ALA B:224 , TYR B:225 , SER B:255 , HIS B:258 , ARG B:266 , ARG B:292 , SER B:296 , ASN B:297 , PHE B:360 , ARG B:386 , PO4 B:411ACTIVE SITE RESIDUES

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Lys A:137 -Pro A:138
2Asn A:194 -Pro A:195
3Lys B:137 -Pro B:138
4Asn B:194 -Pro B:195

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AA_TRANSFER_CLASS_1PS00105 Aminotransferases class-I pyridoxal-phosphate attachment site.AATM_CHICK269-282
 		  2A:255-268
B:255-268

(-) Exons   (0, 0)

(no "Exon" information available for 1AKA)

(-) 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:401
 aligned with AATM_CHICK | P00508 from UniProtKB/Swiss-Prot  Length:423

    Alignment length:401
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422 
           AATM_CHICK    23 SSWWSHVEMGPPDPILGVTEAFKRDTNSKKMNLGVGAYRDDNGKSYVLNCVRKAEAMIAAKKMDKEYLPIAGLADFTRASAELALGENSEAFKSGRYVTVQGISGTGSLRVGANFLQRFFKFSRDVYLPKPSWGNHTPIFRDAGLQLQAYRYYDPKTCSLDFTGAMEDISKIPEKSIILLHACAHNPTGVDPRQEQWKELASVVKKRNLLAYFDMAYQGFASGDINRDAWALRHFIEQGIDVVLSQSYAKNMGLYGERAGAFTVICRDAEEAKRVESQLKILIRPMYSNPPMNGARIASLILNTPELRKEWLVEVKGMADRIISMRTQLVSNLKKEGSSHNWQHITDQIGMFCFTGLKPEQVERLTKEFSIYMTKDGRISVAGVASSNVGYLAHAIHQVTK 423
               SCOP domains d1akaa_ A: Aspartate aminotransferase, AAT                                                                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains ------------1akaA01 A:15-48,A:328-409         1akaA02 A:49-327 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                                                             1akaA01 A:15-48,A:328-409 Aspartate Aminotransferase, domain 1                   - CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhhhhhhh......eee...............hhhhhhhhhhhhh............hhhhhhhhhhhh....hhhhh.eeeeeee..hhhhhhhhhhhhhhh....eeeeeee...hhhhhhhhhh..eeeee...........hhhhhhhhhh....eeeeee............hhhhhhhhhhhhhh..eeeeee.........hhhhhhhhhhhhhh...eeeeee............eeeeeee..hhhhhhhhhhhhhhhhh......hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhh...eeeee...hhhhhhhhhhheee....eeeee....hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AA_TRANSFER_CL--------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1aka A   3 SSWWSHVEMGPPDPILGVTEAFKRDTNSKKMNLGVGAYRDDNGKPYVLNCVRKAEAMIAAKKMDKEYLPIAGLADFTRASAELALGENSEAFKSGRYVTVQGISGTGSLRVGANFLQRFFKFSRDVYLPKPSWGNHTPIFRDAGLQLQAYRYYDPKTCSLDFTGAMEDISKIPEKSIILLHACAHNPTGVDPRQEQWKELASVVKKRNLLAYFDMAYQGFASGDINRDAWALRHFIEQGIDVVLSQSYAHNMGLYGERAGAFTVICRDAEEAKRVESQLKILIRPMYSNPPMNGARIASLILNTPELRKEWLVEVKGMADRIISMRTQLVSNLKKEGSSHNWQHITDQIGMFCFTGLKPEQVERLTKEFSIYMTKDGRISVAGVASSNVGYLAHAIHQVTK 410
                                    12        22        32        42        52        62 ||     73        83        93       103       113       123  |||| 137       147    || 158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       409 
                                                                                        64|                                                         126|||                152|                                                                                                                                                                                                                                                         406|  
                                                                                         66                                                          129||                 154                                                                                                                                                                                                                                                          408  
                                                                                                                                                      130|                                                                                                                                                                                                                                                                                   
                                                                                                                                                       133                                                                                                                                                                                                                                                                                   


Chain B from PDB  Type:PROTEIN  Length:401
 aligned with AATM_CHICK | P00508 from UniProtKB/Swiss-Prot  Length:423

    Alignment length:401
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422 
           AATM_CHICK    23 SSWWSHVEMGPPDPILGVTEAFKRDTNSKKMNLGVGAYRDDNGKSYVLNCVRKAEAMIAAKKMDKEYLPIAGLADFTRASAELALGENSEAFKSGRYVTVQGISGTGSLRVGANFLQRFFKFSRDVYLPKPSWGNHTPIFRDAGLQLQAYRYYDPKTCSLDFTGAMEDISKIPEKSIILLHACAHNPTGVDPRQEQWKELASVVKKRNLLAYFDMAYQGFASGDINRDAWALRHFIEQGIDVVLSQSYAKNMGLYGERAGAFTVICRDAEEAKRVESQLKILIRPMYSNPPMNGARIASLILNTPELRKEWLVEVKGMADRIISMRTQLVSNLKKEGSSHNWQHITDQIGMFCFTGLKPEQVERLTKEFSIYMTKDGRISVAGVASSNVGYLAHAIHQVTK 423
               SCOP domains d1akab_ B: Aspartate aminotransferase, AAT                                                                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains ------------1akaB01 B:15-48,B:328-409         1akaB02 B:49-327 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                                                             1akaB01 B:15-48,B:328-409 Aspartate Aminotransferase, domain 1                   - CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhhhhhhh......eee...............hhhhhhhhhhhhh............hhhhhhhhhhhh....hhhhh.eeeeeee..hhhhhhhhhhhhhhh....eeeeeee...hhhhhhhhhh..eeeee...........hhhhhhhhhh....eeeeee............hhhhhhhhhhhhhh..eeeeee.........hhhhhhhhhhhhhh...eeeeee............eeeeeee..hhhhhhhhhhhhhhhhh......hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhh...eeeee...hhhhhhhhhhheee....eeeee....hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AA_TRANSFER_CL--------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1aka B   3 SSWWSHVEMGPPDPILGVTEAFKRDTNSKKMNLGVGAYRDDNGKPYVLNCVRKAEAMIAAKKMDKEYLPIAGLADFTRASAELALGENSEAFKSGRYVTVQGISGTGSLRVGANFLQRFFKFSRDVYLPKPSWGNHTPIFRDAGLQLQAYRYYDPKTCSLDFTGAMEDISKIPEKSIILLHACAHNPTGVDPRQEQWKELASVVKKRNLLAYFDMAYQGFASGDINRDAWALRHFIEQGIDVVLSQSYAHNMGLYGERAGAFTVICRDAEEAKRVESQLKILIRPMYSNPPMNGARIASLILNTPELRKEWLVEVKGMADRIISMRTQLVSNLKKEGSSHNWQHITDQIGMFCFTGLKPEQVERLTKEFSIYMTKDGRISVAGVASSNVGYLAHAIHQVTK 410
                                    12        22        32        42        52        62 ||     73        83        93       103       113       123  |||| 137       147    || 158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       409 
                                                                                        64|                                                         126|||                152|                                                                                                                                                                                                                                                         406|  
                                                                                         66                                                          129||                 154                                                                                                                                                                                                                                                          408  
                                                                                                                                                      130|                                                                                                                                                                                                                                                                                   
                                                                                                                                                       133
   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  (0, 0)

(no "Pfam Domain" information available for 1AKA)

(-) Gene Ontology  (18, 18)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (AATM_CHICK | P00508)
molecular function
    GO:0004069    L-aspartate:2-oxoglutarate aminotransferase activity    Catalysis of the reaction: L-aspartate + 2-oxoglutarate = oxaloacetate + L-glutamate.
    GO:0080130    L-phenylalanine:2-oxoglutarate aminotransferase activity    Catalysis of the reaction: L-phenylalanine + 2-oxoglutarate = phenylpyruvate + 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:0016212    kynurenine-oxoglutarate transaminase activity    Catalysis of the reaction: L-kynurenine + 2-oxoglutarate = 4-(2-aminophenyl)-2,4-dioxobutanoate + L-glutamate.
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    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:0006103    2-oxoglutarate metabolic process    The chemical reactions and pathways involving oxoglutarate, the dianion of 2-oxoglutaric acid. It is a key constituent of the TCA cycle and a key intermediate in amino-acid metabolism.
    GO:0097052    L-kynurenine metabolic process    The chemical reactions and pathways involving L-kynurenine, the L-enantiomer of the amino acid kynurenine (3-(2-aminobenzoyl)-alanine).
    GO:0006533    aspartate catabolic process    The chemical reactions and pathways resulting in the breakdown of aspartate, the anion derived from aspartic acid, 2-aminobutanedioic acid.
    GO:0006531    aspartate metabolic process    The chemical reactions and pathways involving aspartate, the anion derived from aspartic acid, 2-aminobutanedioic acid.
    GO:0009058    biosynthetic process    The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.
    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:0006094    gluconeogenesis    The formation of glucose from noncarbohydrate precursors, such as pyruvate, amino acids and glycerol.
    GO:0006536    glutamate metabolic process    The chemical reactions and pathways involving glutamate, the anion of 2-aminopentanedioic acid.
cellular component
    GO:0005759    mitochondrial matrix    The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    PLP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    ACT  [ RasMol ]  +environment [ RasMol ]
    BCT  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Asn A:194 - Pro A:195   [ RasMol ]  
    Asn B:194 - Pro B:195   [ RasMol ]  
    Lys A:137 - Pro A:138   [ RasMol ]  
    Lys B:137 - Pro B:138   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1aka
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  AATM_CHICK | P00508
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  2.6.1.1
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  AATM_CHICK | P00508
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        AATM_CHICK | P00508: 1akb 1akc 1ama 1ivr 1map 1maq 1oxo 1oxp 1tar 1tas 1tat 7aat 8aat 9aat

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1AKA)