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(-) Description

Title :  CRYSTAL STRUCTURE OF MJ0684 FROM METHANOCOCCUS JANNASCHII REVEALS ITS SIMILARITY IN THE ACTIVE SITE TO KYNURENINE AMINOTRANSFERASES
 
Authors :  J. K. Yang
Date :  21 Jul 07  (Deposition) - 03 Jun 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Amino Acid Aminotransferase, Kynurenine Aminotransferase, Mj0684, Cytoplasm, Pyridoxal Phosphate (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. K. Yang
Crystal Structure Of Mj0684 From Methanococcus Jannaschii, A Novel Archaeal Homolog Of Kynurenine Aminotransferase
Bull. Korean Chem. Soc. V. 29 173 2008
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROBABLE ASPARTATE AMINOTRANSFERASE 2
    Chains: A
    EC Number: 2.6.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET
    Expression System Strain: BL21(DE3)
    Expression System Vector Type: PLASMID
    Organism Scientific: METHANOCOCCUS JANNASCHII
    Synonym: MJ0684 PROTEIN, TRANSAMINASE A, ASPAT

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1LLP1Mod. Amino Acid2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1LLP2Mod. Amino Acid2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)

(-) Sites  (0, 0)

(no "Site" information available for 2Z61)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Z61)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Asn A:120 -Pro A:121
2Ser A:162 -Pro A:163
3Asn A:165 -Pro A:166

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Z61)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AA_TRANSFER_CLASS_1PS00105 Aminotransferases class-I pyridoxal-phosphate attachment site.MFNC_METJA219-232  1A:219-232
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AA_TRANSFER_CLASS_1PS00105 Aminotransferases class-I pyridoxal-phosphate attachment site.MFNC_METJA219-232  2A:219-232

(-) Exons   (0, 0)

(no "Exon" information available for 2Z61)

(-) 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:369
 aligned with MFNC_METJA | Q58097 from UniProtKB/Swiss-Prot  Length:370

    Alignment length:369
                                    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         
           MFNC_METJA     1 MLSKRLLNFESFEVMDILALAQKLESEGKKVIHLEIGEPDFNTPKPIVDEGIKSLKEGKTHYTDSRGILELREKISELYKDKYKADIIPDNIIITGGSSLGLFFALSSIIDDGDEVLIQNPCYPCYKNFIRFLGAKPVFCDFTVESLEEALSDKTKAIIINSPSNPLGEVIDREIYEFAYENIPYIISDEIYNGLVYEGKCYSAIEFDENLEKTILINGFSKLYAMTGWRIGYVISNDEIIEAILKLQQNLFISAPTISQYAALKAFEKETEREINSMIKEFDRRRRLVLKYVKDFGWEVNNPIGAYYVFPNIGEDGREFAYKLLKEKFVALTPGIGFGSKGKNYIRISYANSYENIKEGLERIKEFLN 369
               SCOP domains d2z61a_ A: automated matches                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 2z61A01 A:1-60,A:269-367                                    2z61A02 A:61-268 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                            2z61A01 A:1-60,A:269-367 Aspartate Aminotransferase, domain 1                                      -- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhh....hhhhhhhhhhhhhh....ee..........hhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhh....hhh.eeee.hhhhhhhhhhhhhh....eeeee....hhhhhhhhhh..eeeee..hhhhhhhhh...eeeeeee..........hhhhhhhhhhhh.eeeee.............hhhhh......eeeeee......hhhhh.eeee.hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........ee......hhhhhhhhhhhhhhee.ee.hhhhhhhh..eeee...hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AA_TRANSFER_CL----------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2z61 A   1 MLSKRLLNFESFEVMDILALAQKLESEGKKVIHLEIGEPDFNTPKPIVDEGIKSLKEGKTHYTDSRGILELREKISELYKDKYKADIIPDNIIITGGSSLGLFFALSSIIDDGDEVLIQNPCYPCYKNFIRFLGAKPVFCDFTVESLEEALSDKTKAIIINSPSNPLGEVIDREIYEFAYENIPYIISDEIYNGLVYEGKCYSAIEFDENLEKTILINGFSkLYAMTGWRIGYVISNDEIIEAILKLQQNLFISAPTISQYAALKAFEKETEREINSMIKEFDRRRRLVLKYVKDFGWEVNNPIGAYYVFPNIGEDGREFAYKLLKEKFVALTPGIGFGSKGKNYIRISYANSYENIKEGLERIKEFLN 369
                                    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         
                                                                                                                                                                                                                                                       222-LLP
   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  (0, 0)

(no "Pfam Domain" information available for 2Z61)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A   (MFNC_METJA | Q58097)
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: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: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.
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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  2z61
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