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(-) Description

Title :  CRYSTAL STRUCTURE OF A PUTATIVE AMINOTRANSFERASE FROM SILICIBACTER POMEROYI
 
Authors :  P. Sampathkumar, S. Atwell, S. Wasserman, S. Miller, K. Bain, M. Rutter J. M. Sauder, S. K. Burley, New York Sgx Research Center For Stru Genomics (Nysgxrc)
Date :  10 Apr 09  (Deposition) - 05 May 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Aminotransferase, Silicibacter Pomeroyi, Yp_167802. 1, Spo2589, Structural Genomics, Psi-2, Protein Structure Initiative, New York Structural Genomix Research Consortium, Nysgxrc, Pyridoxal Phosphate, Transferase, New York Sgx Research Center For Structural Genomics (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Sampathkumar
Crystal Structure Of A Putative Aminotransferase From Silicibacter Pomeroyi
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - AMINOTRANSFERASE, CLASSES I AND II
    Atcc: 700808
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: BC-PSGX3(BC), MODIFIED PET26B
    Expression System Strain: BL21(DE3)-CODON+RIL
    Expression System Taxid: 562
    Expression System Vector Type: PET
    Gene: SPO2589, YP_167802.1
    Organism Scientific: SILICIBACTER POMEROYI DSS-3
    Organism Taxid: 246200
    Strain: DSS-3 / DSM 15171

 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  (2, 13)

Asymmetric Unit (2, 13)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2MSE11Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (2, 13)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2MSE11Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (2, 26)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2MSE22Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:76 , LEU A:80 , GLU A:83 , TRP A:84 , PHE A:232 , LEU A:275 , ASP A:278 , HOH A:679BINDING SITE FOR RESIDUE GOL A 501
2AC2SOFTWAREILE A:120 , GLY A:121 , PRO A:123 , GLN A:151 , PRO A:152 , MSE A:166 , VAL A:167 , ALA A:168 , ALA A:171 , HOH A:698BINDING SITE FOR RESIDUE GOL A 502

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3H14)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Ala A:122 -Pro A:123
2Ser A:169 -Pro A:170
3Asn A:172 -Pro A:173

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3H14)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3H14)

(-) Exons   (0, 0)

(no "Exon" information available for 3H14)

(-) 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:370
 aligned with Q5LQA4_RUEPO | Q5LQA4 from UniProtKB/TrEMBL  Length:389

    Alignment length:380
                                    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       388
         Q5LQA4_RUEPO     9 VKNSSRSAVDPFIVMDVMEAARRAEEAGRRIIHMEVGQPGTGAPRGAVEALAKSLETDALGYTVALGLPALRQRIARLYGEWYGVDLDPGRVVITPGSSGGFLLAFTALFDSGDRVGIGAPGYPSYRQILRALGLVPVDLPTAPENRLQPVPADFAGLDLAGLMVASPANPTGTMLDHAAMGALIEAAQAQGASFISDEIYHGIEYEAKAVTALELTDECYVINSFSKYFSMTGWRVGWMVVPEDQVRVVERIAQNMFICAPHASQVAALAALDCDAELQANLDVYKANRKLMLERLPKAGFTRIAPPDGAFYVYADVSDLTDDSRAFAAEILEKAGVAVTPGLDFDPERGAGTLRFSYARATADIEEGLDRLEAFMQAR 388
               SCOP domains d3h14a_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhhhhhhhhhh....ee..........hhhhhhhhhhhhh----------.hhhhhhhhhhhhhhhhh...hhh.eeee.hhhhhhhhhhhhhh....eeeeee...hhhhhhhhhh..eeeeee.hhhhh...hhhhhh.....eeeee..........hhhhhhhhhhhhhhh..eeeee.............hhhhh....eeeee............eeee.hhhhhhhhhhhhhhh....hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh...........eeeee......hhhhhhhhhhhhhhee.ee.hhh...hhh.eeeee...hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3h14 A   3 LKNSSRSAVDPFIVmDVmEAARRAEEAGRRIIHmEVGQPGTGAPRGAVEALAKSLE----------GLPALRQRIARLYGEWYGVDLDPGRVVITPGSSGGFLLAFTALFDSGDRVGIGAPGYPSYRQILRALGLVPVDLPTAPENRLQPVPADFAGLDLAGLmVASPANPTGTmLDHAAmGALIEAAQAQGASFISDEIYHGIEYEAKAVTALELTDECYVINSFSKYFSmTGWRVGWmVVPEDQVRVVERIAQNmFICAPHASQVAALAALDCDAELQANLDVYKANRKLmLERLPKAGFTRIAPPDGAFYVYADVSDLTDDSRAFAAEILEKAGVAVTPGLDFDPERGAGTLRFSYARATADIEEGLDRLEAFmQAR 382
                                    12    |  |22        32   |    42        52     |   -      | 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
                                         17-MSE             36-MSE                58         69                                                                                              166-MSE    177-MSE |                                                234-MSE 242-MSE          259-MSE                             295-MSE                                                                             379-MSE
                                            20-MSE                                                                                                                                                            183-MSE
   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  (0, 0)

(no "CATH Domain" information available for 3H14)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3H14)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q5LQA4_RUEPO | Q5LQA4)
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:0008150    biological_process    Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
    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.

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