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(-) Description

Title :  CRYSTAL STRUCTURE OF PUTATIVE AMINOTRANSFERASE (YP_614685.1) FROM SILICIBACTER SP. TM1040 AT 1.80 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  22 Nov 08  (Deposition) - 13 Jan 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Yp_614685. 1, Putative Aminotransferase, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Aminotransferase, Pyridoxal Phosphate, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Putative Aminotransferase (Yp_614685. 1 From Silicibacter Sp. Tm1040 At 1. 80 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE AMINOTRANSFERASE
    Chains: A
    EC Number: 2.6.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Strain: HK100
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TM1040_2691, YP_614685.1
    Organism Scientific: SILICIBACTER SP. TM1040
    Organism Taxid: 292414

 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, 13)

Asymmetric Unit (4, 13)
No.NameCountTypeFull Name
1EDO5Ligand/Ion1,2-ETHANEDIOL
2LLP1Mod. Amino Acid2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)
3MSE6Mod. Amino AcidSELENOMETHIONINE
4PLP1Ligand/IonPYRIDOXAL-5'-PHOSPHATE
Biological Unit 1 (4, 26)
No.NameCountTypeFull Name
1EDO10Ligand/Ion1,2-ETHANEDIOL
2LLP2Mod. Amino Acid2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)
3MSE12Mod. Amino AcidSELENOMETHIONINE
4PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:118 , GLY A:119 , SER A:120 , TYR A:152 , HIS A:153 , GLY A:154 , GLU A:226 , ASP A:259 , VAL A:261 , VAL A:262 , LLP A:288 , TRP A:324 , THR A:325 , HOH A:464 , HOH A:469 , HOH A:504 , HOH A:568 , HOH A:646BINDING SITE FOR RESIDUE PLP A 458
2AC2SOFTWAREASN A:4 , LEU A:7 , ARG A:46 , GLU A:93BINDING SITE FOR RESIDUE EDO A 459
3AC3SOFTWARETHR A:37 , SER A:39 , PHE A:42 , GLU A:44 , LYS A:50BINDING SITE FOR RESIDUE EDO A 460
4AC4SOFTWARETRP A:10 , LYS A:100 , MSE A:101 , HOH A:567BINDING SITE FOR RESIDUE EDO A 461
5AC5SOFTWAREASP A:121 , TRP A:324 , HOH A:577BINDING SITE FOR RESIDUE EDO A 462
6AC6SOFTWAREASN A:135 , HIS A:169 , LYS A:171 , PHE A:172 , ASP A:173 , HOH A:611BINDING SITE FOR RESIDUE EDO A 463

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Leu A:174 -Pro A:175

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3FCR)

(-) 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 Q1GD43_RUEST | Q1GD43 from UniProtKB/TrEMBL  Length:457

    Alignment length:459
                                                                                                                                                                                                                                                                                                                            289                                                                                                                                                                        
                             1                                                                                                                                                                                                                                                                                            288 |                                                                                                                                                                        
                             |       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        |-|      298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448         
         Q1GD43_RUEST     - -MLKNDQLDQWDRDNFFHPSTHLAQHARGESANRVIKTASGVFIEDRDGTKLLDAFAGLYCVNVGYGRQEIAEAIADQARELAYYHSYVGHGTEASITLAKMILDRAPKNMSKVYFGLGGSDANETNVKLIWYYNNILGRPEKKKIISRWRGYHGSGLVTGSLTGLELFHKKFDLPVEQVIHTEAPYYFRREDLNQTEEQFVAHCVAELEALIEREGADTIAAFIGEPILGTGGIVPPPAGYWEAIQTVLNKHDILLVADEVVTGFGRLGTMFGSDHYGLEPDIITIAK-GLTSAYAPLSGSIVSDKVWKVLEQGTDENGPIGHGWTYSAHPIGAAAGVANLKLLDELNLVSNAGEVGAYLNATMAEALSQHANVGDVRGEGLLCAVEFVKDRDSRTFFDAADKIGPQISAKLLEQDKIIARAMPQGDILGFAPPFCLTRAEADQVVEGTLRAVKAVLG 457
               SCOP domains d3fcra_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhh.....hhhhhhh.......eeeee..eeee....eeee.hhhhhh......hhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhh...eeeeeee.hhhhhhhhhhhhhhhhhhhh......eeeee.......hhhhhhhh.hhhhh.........eeee...hhhhh.....hhhhhhhhhhhhhhhhhhhhh...eeeeee..............hhhhhhhhhhhhhh.eeeee............hhhhhhh....eeeehhhhhh......eeeeeehhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeee....eeeee..........hhhhhhhhhhhhhhhhhhhee.ee.....eeee......hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fcr A   0 GmLKNDQLDQWDRDNFFHPSTHLAQHARGESANRVIKTASGVFIEDRDGTKLLDAFAGLYCVNVGYGRQEIAEAIADQARELAYYHSYVGHGTEASITLAKmILDRAPKNmSKVYFGLGGSDANETNVKLIWYYNNILGRPEKKKIISRWRGYHGSGLVTGSLTGLELFHKKFDLPVEQVIHTEAPYYFRREDLNQTEEQFVAHCVAELEALIEREGADTIAAFIGEPILGTGGIVPPPAGYWEAIQTVLNKHDILLVADEVVTGFGRLGTmFGSDHYGLEPDIITIAkKGLTSAYAPLSGSIVSDKVWKVLEQGTDENGPIGHGWTYSAHPIGAAAGVANLKLLDELNLVSNAGEVGAYLNATmAEALSQHANVGDVRGEGLLCAVEFVKDRDSRTFFDAADKIGPQISAKLLEQDKIIARAmPQGDILGFAPPFCLTRAEADQVVEGTLRAVKAVLG 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       288       298       308       318       328       338       348       358    |  368       378       388       398       408       418   |   428       438       448         
                             |                                                                                                 101-MSE  110-MSE                                                                                                                                                          271-MSE          288-LLP                                                                     363-MSE                                                    422-MSE                               
                             1-MSE
   Legend:   → Mismatch (orange background)
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  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  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q1GD43_RUEST | Q1GD43)
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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