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(-) Description

Title :  CRYSTAL STRUCTURE OF A PUTATIVE AMINOTRANSFERASE (MLL7127) FROM MESORHIZOBIUM LOTI MAFF303099 AT 1.55 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  09 Mar 09  (Deposition) - 17 Mar 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.55
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Pyridoxal Phosphate, Plp-Dependent Transferase-Like Fold, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Putative Aminotransferase (Np_107505. 1 From Mesorhizobium Loti At 1. 55 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE AMINOTRANSFERASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Strain: HK100
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: MLL7127, NP_107505.1
    Organism Scientific: MESORHIZOBIUM LOTI
    Organism Taxid: 266835
    Strain: MAFF303099

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 16)

Asymmetric Unit (4, 16)
No.NameCountTypeFull Name
1LLP1Mod. Amino Acid2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)
2MPD2Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
3MSE12Mod. Amino AcidSELENOMETHIONINE
4PLP1Ligand/IonPYRIDOXAL-5'-PHOSPHATE
Biological Unit 1 (4, 32)
No.NameCountTypeFull Name
1LLP2Mod. Amino Acid2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)
2MPD4Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
3MSE24Mod. Amino AcidSELENOMETHIONINE
4PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:119 , GLY A:120 , SER A:121 , TYR A:153 , HIS A:154 , GLY A:155 , GLU A:227 , ASP A:260 , VAL A:262 , VAL A:263 , LLP A:289 , THR A:326 , HOH A:465 , HOH A:491 , HOH A:513 , HOH A:530BINDING SITE FOR RESIDUE PLP A 460
2AC2SOFTWARELYS A:101 , GLU A:244 , LYS A:245 , HOH A:485BINDING SITE FOR RESIDUE MPD A 461
3AC3SOFTWARELYS A:109 , GLY A:110 , ASP A:305 , HOH A:509 , HOH A:702 , HOH A:774BINDING SITE FOR RESIDUE MPD A 462

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3GJU)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Leu A:175 -Pro A:176
2Ala A:178 -Pro A:179

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3GJU)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3GJU)

(-) Exons   (0, 0)

(no "Exon" information available for 3GJU)

(-) 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:459
 aligned with Q987B2_RHILO | Q987B2 from UniProtKB/TrEMBL  Length:459

    Alignment length:459
                                                                                                                                                                                                                                                                                                                             290                                                                                                                                                                       
                             1                                                                                                                                                                                                                                                                                             289 |                                                                                                                                                                       
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289 |     298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448         
         Q987B2_RHILO     - -MLNQSNELNAWDRDHFFHPSTHMGTHARGESPTRIMAGGEGVTVWDNNGRKSIDAFAGLYCVNVGYGRQKIADAIATQAKNLAYYHAYVGHGTEASITLAKMIIDRAPKGMSRVYFGLSGSDANETNIKLIWYYNNVLGRPEKKKIISRWRGYHGSGVMTGSLTGLDLFHNAFDLPRAPVLHTEAPYYFRRTDRSMSEEQFSQHCADKLEEMILAEGPETIAAFIGEPILGTGGIVPPPAGYWEKIQAVLKKYDVLLVADEVVTGFGRLGTMFGSDHYGIKPDLITIAK-GLTSAYAPLSGVIVADRVWQVLVQGSDKLGSLGHGWTYSAHPICVAAGVANLELIDEMDLVTNAGETGAYFRAELAKAVGGHKNVGEVRGDGMLAAVEFVADKDDRVFFDASQKIGPQVATALAASGVIGRAMPQGDILGFAPPLCLTREQADIVVSKTADAVKSVFA 457
               SCOP domains d3gjua_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhh.....hhhhhhh.......eeeee..eeee....eeee.hhhhhh......hhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhh...eeeeeee.hhhhhhhhhhhhhhhhhhhh......eeeee.......hhhhhhhh.hhhhh.........eeee...hhhhh.....hhhhhhhhhhhhhhhhhhhhh...eeeeee..............hhhhhhhhhhhhh..eeeee............hhhhhhh....eeeehhhhhh......eeeeeehhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeee..eeeeee..........hhhhhhhhhhhhhhhhh.ee.ee.....eeee......hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gju A   0 GmLNQSNELNAWDRDHFFHPSTHmGTHARGESPTRImAGGEGVTVWDNNGRKSIDAFAGLYCVNVGYGRQKIADAIATQAKNLAYYHAYVGHGTEASITLAKmIIDRAPKGmSRVYFGLSGSDANETNIKLIWYYNNVLGRPEKKKIISRWRGYHGSGVmTGSLTGLDLFHNAFDLPRAPVLHTEAPYYFRRTDRSmSEEQFSQHCADKLEEmILAEGPETIAAFIGEPILGTGGIVPPPAGYWEKIQAVLKKYDVLLVADEVVTGFGRLGTmFGSDHYGIKPDLITIAkKGLTSAYAPLSGVIVADRVWQVLVQGSDKLGSLGHGWTYSAHPICVAAGVANLELIDEmDLVTNAGETGAYFRAELAKAVGGHKNVGEVRGDGmLAAVEFVADKDDRVFFDASQKIGPQVATALAASGVIGRAmPQGDILGFAPPLCLTREQADIVVSKTADAVKSVFA 457
                             |       9        19   |    29      | 39        49        59        69        79        89        99  |    109 |     119       129       139       149       159       169       179       189      |199       209  |    219       229       239       249       259       269  |    279       289       298       308       318       328       338       348       358       368       378   |   388       398       408       418   |   428       438       448         
                             |                    23-MSE       36-MSE                                                           102-MSE  111-MSE                                         159-MSE                              196-MSE         212-MSE                                                     272-MSE          289-LLP                                                    347-MSE                            382-MSE                                 422-MSE                               
                             1-MSE
   Legend:   → Mismatch (orange background)
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  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  (0, 0)

(no "CATH Domain" information available for 3GJU)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3GJU)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q987B2_RHILO | Q987B2)
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.

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