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(-) Description

Title :  CRYSTAL STRUCTURE OF PUTATIVE AMINO-ACID AMINOTRANSFERASE (YP_265399.1) FROM PSYCHROBACTER ARCTICUM 273-4 AT 2.50 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  23 Jul 09  (Deposition) - 04 Aug 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Yp_265399. 1, Putative Amino-Acid Aminotransferase, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Aminotransferase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Putative Amino-Acid Aminotransferase (Yp_265399. 1) From Psychrobacter Arcticum 273-4 At 2. 50 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - AMINOTRANSFERASE
    Chains: A, B
    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: AVTA, PSYC_2118, YP_265399.1
    Organism Scientific: PSYCHROBACTER ARCTICUS 273-4
    Organism Taxid: 259536
    Strain: DSM 17307 / 273-4

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 25)

Asymmetric/Biological Unit (4, 25)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2GOL2Ligand/IonGLYCEROL
3MSE20Mod. Amino AcidSELENOMETHIONINE
4PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:113 , SER A:114 , GLN A:115 , PHE A:118 , TYR A:154 , ASN A:216 , ASP A:244 , ALA A:246 , TYR A:247 , SER A:272 , SER A:274 , LYS A:275 , ARG A:282 , TYR B:78BINDING SITE FOR RESIDUE PLP A 500
2AC2SOFTWAREARG A:323 , ASN A:330 , GLU A:331 , HOH A:549BINDING SITE FOR RESIDUE GOL A 444
3AC3SOFTWARETYR A:78 , GLY B:113 , SER B:114 , GLN B:115 , TYR B:154 , ASN B:216 , ASP B:244 , ALA B:246 , TYR B:247 , SER B:272 , SER B:274 , LYS B:275 , ARG B:282 , ACT B:444BINDING SITE FOR RESIDUE PLP B 500
4AC4SOFTWAREILE B:155 , ASN B:216 , ARG B:415 , PLP B:500 , HOH B:544BINDING SITE FOR RESIDUE ACT B 444
5AC5SOFTWARELYS A:338 , ARG B:323 , ASN B:330 , GLU B:331BINDING SITE FOR RESIDUE GOL B 445

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3IF2)

(-) Cis Peptide Bonds  (10, 10)

Asymmetric/Biological Unit
No.Residues
1Thr A:151 -Pro A:152
2Arg A:213 -Pro A:214
3Asn A:216 -Pro A:217
4Mse A:249 -Pro A:250
5Phe A:251 -Pro A:252
6Thr B:151 -Pro B:152
7Arg B:213 -Pro B:214
8Asn B:216 -Pro B:217
9Mse B:249 -Pro B:250
10Phe B:251 -Pro B:252

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3IF2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3IF2)

(-) Exons   (0, 0)

(no "Exon" information available for 3IF2)

(-) 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:437
 aligned with Q4FPU3_PSYA2 | Q4FPU3 from UniProtKB/TrEMBL  Length:443

    Alignment length:444
                             1                                                                                                                                                                                                                                                                                                                                                                                                                                                          
                             |       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       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439    
         Q4FPU3_PSYA2     - -MKFSKFGQKFTQPTGISQLMDDLGDALKSDQPVNMLGGGNPAKIDAVNELFLETYKALGNDNDTGKANSSAIISMANYSNPQGDSAFIDALVGFFNRHYDWNLTSENIALTNGSQNAFFYLFNLFGGAFVNEHSQDKESKSVDKSILLPLTPEYIGYSDVHVEGQHFAAVLPHIDEVTHDGEEGFFKYRVDFEALENLPALKEGRIGAICCSRPTNPTGNVLTDEEMAHLAEIAKRYDIPLIIDNAYGMPFPNIIYSDAHLNWDNNTILCFSLSKIGLPGMRTGIIVADAKVIEAVSAMNAVVNLAPTRFGAAIATPLVANDRIKQLSDNEIKPFYQKQATLAVKLLKQALGDYPLMIHKPEGAIFLWLWFKDLPISTLDLYERLKAKGTLIVPSEYFFPGVDVSDYQHAHECIRMSIAADEQTLIDGIKVIGEVVRELYDNK 443
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhhhhhh.hhhhhhhhhhhhhhhh....ee........hhhhhhhhhhhhhhhhh........hhhhhhhhh......hhhhhhhhhhhhhhhhh...hhh.eeee.hhhhhhhhhhhhh.eeee..-------.eeeeeeee.....hhhhh........eee...eeeeeee..eeeeeeee.hhhhhhhhhhhhh..eeeeeee..........hhhhhhhhhhhhhhh...eeee......................eeeeee.....hhhhh.eeee.hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeee......eeeeee.....hhhhhhhhhhhh.ee.ee.hhh.........hhhh.eeeee...hhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3if2 A   0 GmKFSKFGQKFTQPTGISQLmDDLGDALKSDQPVNmLGGGNPAKIDAVNELFLETYKALGNDNDTGKANSSAIISmANYSNPQGDSAFIDALVGFFNRHYDWNLTSENIALTNGSQNAFFYLFNLFGGAFVNE-------KSVDKSILLPLTPEYIGYSDVHVEGQHFAAVLPHIDEVTHDGEEGFFKYRVDFEALENLPALKEGRIGAICCSRPTNPTGNVLTDEEmAHLAEIAKRYDIPLIIDNAYGmPFPNIIYSDAHLNWDNNTILCFSLSKIGLPGmRTGIIVADAKVIEAVSAmNAVVNLAPTRFGAAIATPLVANDRIKQLSDNEIKPFYQKQATLAVKLLKQALGDYPLmIHKPEGAIFLWLWFKDLPISTLDLYERLKAKGTLIVPSEYFFPGVDVSDYQHAHECIRmSIAADEQTLIDGIKVIGEVVRELYDNK 443
                             |       9        19|       29     |  39        49        59        69     |  79        89        99       109       119       129  |      -|      149       159       169       179       189       199       209       219       229       239       249       259       269       279 |     289       299       309       319       329       339       349       359       369       379       389       399       409      |419       429       439    
                             |                 20-MSE         35-MSE                                  75-MSE                                                  132     140                                                                                    227-MSE               249-MSE                         281-MSE           299-MSE                                                   357-MSE                                                    416-MSE                       
                             1-MSE                                                                                                                                                                                                                                                                                                                                                                                                                                                      


Chain B from PDB  Type:PROTEIN  Length:437
 aligned with Q4FPU3_PSYA2 | Q4FPU3 from UniProtKB/TrEMBL  Length:443

    Alignment length:444
                             1                                                                                                                                                                                                                                                                                                                                                                                                                                                          
                             |       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       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439    
         Q4FPU3_PSYA2     - -MKFSKFGQKFTQPTGISQLMDDLGDALKSDQPVNMLGGGNPAKIDAVNELFLETYKALGNDNDTGKANSSAIISMANYSNPQGDSAFIDALVGFFNRHYDWNLTSENIALTNGSQNAFFYLFNLFGGAFVNEHSQDKESKSVDKSILLPLTPEYIGYSDVHVEGQHFAAVLPHIDEVTHDGEEGFFKYRVDFEALENLPALKEGRIGAICCSRPTNPTGNVLTDEEMAHLAEIAKRYDIPLIIDNAYGMPFPNIIYSDAHLNWDNNTILCFSLSKIGLPGMRTGIIVADAKVIEAVSAMNAVVNLAPTRFGAAIATPLVANDRIKQLSDNEIKPFYQKQATLAVKLLKQALGDYPLMIHKPEGAIFLWLWFKDLPISTLDLYERLKAKGTLIVPSEYFFPGVDVSDYQHAHECIRMSIAADEQTLIDGIKVIGEVVRELYDNK 443
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhhhhhh.hhhhhhhhhhhhhhh.....ee........hhhhhhhhhhhhhhhhhh.......hhhhhhhhh......hhhhhhhhhhhhhhhhh...hhh.eeee.hhhhhhhhhhhhhheeee..-------.eeeeeeee.....hhhhh........eee...eeeeeee..eeeeeeee.hhhhhhhhhhhhh..eeeeeee..........hhhhhhhhhhhhhhh...eeee......................eeeeee.hhhhhhhhh.eeee.hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeee......eeeeee.....hhhhhhhhhhhh.ee.ee.hhh........hhhhh.eeeee...hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3if2 B   0 GmKFSKFGQKFTQPTGISQLmDDLGDALKSDQPVNmLGGGNPAKIDAVNELFLETYKALGNDNDTGKANSSAIISmANYSNPQGDSAFIDALVGFFNRHYDWNLTSENIALTNGSQNAFFYLFNLFGGAFVNE-------KSVDKSILLPLTPEYIGYSDVHVEGQHFAAVLPHIDEVTHDGEEGFFKYRVDFEALENLPALKEGRIGAICCSRPTNPTGNVLTDEEmAHLAEIAKRYDIPLIIDNAYGmPFPNIIYSDAHLNWDNNTILCFSLSKIGLPGmRTGIIVADAKVIEAVSAmNAVVNLAPTRFGAAIATPLVANDRIKQLSDNEIKPFYQKQATLAVKLLKQALGDYPLmIHKPEGAIFLWLWFKDLPISTLDLYERLKAKGTLIVPSEYFFPGVDVSDYQHAHECIRmSIAADEQTLIDGIKVIGEVVRELYDNK 443
                             |       9        19|       29     |  39        49        59        69     |  79        89        99       109       119       129  |      -|      149       159       169       179       189       199       209       219       229       239       249       259       269       279 |     289       299       309       319       329       339       349       359       369       379       389       399       409      |419       429       439    
                             1-MSE             20-MSE         35-MSE                                  75-MSE                                                  132     140                                                                                    227-MSE               249-MSE                         281-MSE           299-MSE                                                   357-MSE                                                    416-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  (0, 0)

(no "SCOP Domain" information available for 3IF2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3IF2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3IF2)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q4FPU3_PSYA2 | Q4FPU3)
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.

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