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(-) Description

Title :  STRUCTURE OF AN OMEGA-AMINOTRANSFERASE FROM PARACOCCUS DENITRIFICANS
 
Authors :  C. Rausch, A. Lerchner, A. Schiefner, A. Skerra
Date :  27 Aug 12  (Deposition) - 19 Dec 12  (Release) - 28 Aug 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Class Iii Transaminase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Rausch, A. Lerchner, A. Schiefner, A. Skerra
Crystal Structure Of The Omega-Aminotransferase From Paracoccus Denitrificans And Its Phylogenetic Relationship With Other Class Iii Aminotransferases That Have Biotechnological Potential.
Proteins V. 81 774 2013
PubMed-ID: 23239223  |  Reference-DOI: 10.1002/PROT.24233

(-) Compounds

Molecule 1 - AMINOTRANSFERASE
    Chains: A, B, C, D
    EC Number: 2.6.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL-21
    Expression System Taxid: 511693
    Expression System Vector: PASK-IBA5PLUS
    Gene: PDEN_3984
    Organism Scientific: PARACOCCUS DENITRIFICANS
    Organism Taxid: 318586
    Strain: PD1222

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 10)

Asymmetric Unit (3, 10)
No.NameCountTypeFull Name
1DAV2Ligand/IonDELTA-AMINO VALERIC ACID
2LLP4Mod. Amino Acid2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)
3NA4Ligand/IonSODIUM ION
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1DAV1Ligand/IonDELTA-AMINO VALERIC ACID
2LLP2Mod. Amino Acid2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)
3NA-1Ligand/IonSODIUM ION
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1DAV1Ligand/IonDELTA-AMINO VALERIC ACID
2LLP2Mod. Amino Acid2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)
3NA-1Ligand/IonSODIUM ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:101 , GLU A:102 , SER A:104 , PHE A:106 , HOH A:674BINDING SITE FOR RESIDUE NA A 501
2AC2SOFTWAREPHE A:19 , LLP A:285BINDING SITE FOR RESIDUE DAV A 502
3AC3SOFTWAREVAL B:101 , GLU B:102 , SER B:104 , PHE B:106 , HOH B:632 , HOH B:650BINDING SITE FOR RESIDUE NA B 501
4AC4SOFTWAREVAL C:101 , GLU C:102 , SER C:104 , PHE C:106 , HOH C:661 , HOH C:664BINDING SITE FOR RESIDUE NA C 501
5AC5SOFTWAREPHE C:19 , TYR C:150 , TYR C:165 , LLP C:285BINDING SITE FOR RESIDUE DAV C 502
6AC6SOFTWAREVAL D:101 , GLU D:102 , SER D:104 , PHE D:106 , HOH D:629 , HOH D:643BINDING SITE FOR RESIDUE NA D 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4GRX)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Leu A:171 -Pro A:172
2Leu B:171 -Pro B:172
3Leu C:171 -Pro C:172
4Leu D:171 -Pro D:172

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4GRX)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4GRX)

(-) Exons   (0, 0)

(no "Exon" information available for 4GRX)

(-) 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:449
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains d4grxa_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh.....hhhhhhhhh.eeeeeee..eeee....eeee.............hhhhhhhhhhhhhhh........eeehhhhhhhhhhhhhh.....eeeee.hhhhhhhhhhhhhhhhhhhh......eeeee.......hhhhhhhh.hhhhhhhh.....eeee...hhhhhh....hhhhhhhhhhhhhhhhhhhhh...eeeeee..............hhhhhhhhhhhhh...eeee............hhhhhh.....eeeehhhhhh.....eeeeehhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeee..eeeeee..........hhhhhhhhhhhhhhhhh.ee......eeee......hhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4grx A   5 QSWEARAETYSLYGFTDMPSVHQRGTVVVTHGEGPYIVDVHGRRYLDANSGLWNMVAGFDHKGLIEAAKAQYDRFPGYHAFFGRMSDQTVMLSEKLVEVSPFDNGRVFYTNSGSEANDTMVKMLWFLHAAEGKPQKRKILTRWNAYHGVTAVSASMTGKPYNSVFGLPLPGFIHLTCPHYWRYGEEGETEAQFVARLARELEDTITREGADTIAGFFAEPVMGAGGVIPPAKGYFQAILPILRKYDIPMISDEVICGFGRTGNTWGCLTYDFMPDAIISSkNLTAGFFPMGAVILGPDLAKRVEAAVEAIEEFPHGFTASGHPVGCAIALKAIDVVMNEGLAENVRRLAPRFEAGLKRIADRPNIGEYRGIGFMWALEAVKDKPTKTPFDANLSVSERIANTCTDLGLICRPLGQSIVLCPPFILTEAQMDEMFEKLEKALDKVFAEVA 453
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284|      294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444         
                                                                                                                                                                                                                                                                                                                  285-LLP                                                                                                                                                                    


Chain B from PDB  Type:PROTEIN  Length:449
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains d4grxb_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh.....hhhhhh....eeeeeee..eeee....eeee.............hhhhhhhhhhhhh..........eeehhhhhhhhhhhhhh.....eeeee.hhhhhhhhhhhhhhhhhhhh......eeeee.......hhhhhhhh.hhhhhhhh.....eeee...hhhhhh....hhhhhhhhhhhhhhhhhhhhh...eeeeee..............hhhhhhhhhhhhh...eeee............hhhhhh.....eeeee.hhhh.....eeeeehhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeee..eeeeee..........hhhhhhhhhhhhhhhhh.ee.eee..eeee......hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4grx B   5 QSWEARAETYSLYGFTDMPSVHQRGTVVVTHGEGPYIVDVHGRRYLDANSGLWNMVAGFDHKGLIEAAKAQYDRFPGYHAFFGRMSDQTVMLSEKLVEVSPFDNGRVFYTNSGSEANDTMVKMLWFLHAAEGKPQKRKILTRWNAYHGVTAVSASMTGKPYNSVFGLPLPGFIHLTCPHYWRYGEEGETEAQFVARLARELEDTITREGADTIAGFFAEPVMGAGGVIPPAKGYFQAILPILRKYDIPMISDEVICGFGRTGNTWGCLTYDFMPDAIISSkNLTAGFFPMGAVILGPDLAKRVEAAVEAIEEFPHGFTASGHPVGCAIALKAIDVVMNEGLAENVRRLAPRFEAGLKRIADRPNIGEYRGIGFMWALEAVKDKPTKTPFDANLSVSERIANTCTDLGLICRPLGQSIVLCPPFILTEAQMDEMFEKLEKALDKVFAEVA 453
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284|      294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444         
                                                                                                                                                                                                                                                                                                                  285-LLP                                                                                                                                                                    


Chain C from PDB  Type:PROTEIN  Length:449
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains d4grxc_ C: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh.....hhhhhhhhh.eeeeeee..eeee....eeee.............hhhhhhhhhhhhhhh........eeehhhhhhhhhhhhhh.....eeeee.hhhhhhhhhhhhhhhhhhhh......eeeee.......hhhhhhhh.hhhhhhhh.....eeee...hhhhhh....hhhhhhhhhhhhhhhhhhhhh...eeeeee..............hhhhhhhhhhhhh...eeee............hhhhhh.....eeeehhhhhh.....eeeeehhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeee..eeeeee..........hhhhhhhhhhhhhhhhh.ee......eeee......hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4grx C   5 QSWEARAETYSLYGFTDMPSVHQRGTVVVTHGEGPYIVDVHGRRYLDANSGLWNMVAGFDHKGLIEAAKAQYDRFPGYHAFFGRMSDQTVMLSEKLVEVSPFDNGRVFYTNSGSEANDTMVKMLWFLHAAEGKPQKRKILTRWNAYHGVTAVSASMTGKPYNSVFGLPLPGFIHLTCPHYWRYGEEGETEAQFVARLARELEDTITREGADTIAGFFAEPVMGAGGVIPPAKGYFQAILPILRKYDIPMISDEVICGFGRTGNTWGCLTYDFMPDAIISSkNLTAGFFPMGAVILGPDLAKRVEAAVEAIEEFPHGFTASGHPVGCAIALKAIDVVMNEGLAENVRRLAPRFEAGLKRIADRPNIGEYRGIGFMWALEAVKDKPTKTPFDANLSVSERIANTCTDLGLICRPLGQSIVLCPPFILTEAQMDEMFEKLEKALDKVFAEVA 453
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284|      294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444         
                                                                                                                                                                                                                                                                                                                  285-LLP                                                                                                                                                                    


Chain D from PDB  Type:PROTEIN  Length:449
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains d4grxd_ D: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh......hhhhhh...eeeeeee..eeee....eeee.............hhhhhhhhhhhhhhh........eeehhhhhhhhhhhhhh.....eeeee.hhhhhhhhhhhhhhhhhhhh......eeeee.......hhhhhhhh.hhhhhhhh.....eeee...hhhhhh....hhhhhhhhhhhhhhhhhhhhh...eeeeee..............hhhhhhhhhhhhh...eeee............hhhhhh.....eeeehhhhhh.....eeeeehhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeee..eeeeee..........hhhhhhhhhhhhhhhhh.ee......eeee......hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4grx D   5 QSWEARAETYSLYGFTDMPSVHQRGTVVVTHGEGPYIVDVHGRRYLDANSGLWNMVAGFDHKGLIEAAKAQYDRFPGYHAFFGRMSDQTVMLSEKLVEVSPFDNGRVFYTNSGSEANDTMVKMLWFLHAAEGKPQKRKILTRWNAYHGVTAVSASMTGKPYNSVFGLPLPGFIHLTCPHYWRYGEEGETEAQFVARLARELEDTITREGADTIAGFFAEPVMGAGGVIPPAKGYFQAILPILRKYDIPMISDEVICGFGRTGNTWGCLTYDFMPDAIISSkNLTAGFFPMGAVILGPDLAKRVEAAVEAIEEFPHGFTASGHPVGCAIALKAIDVVMNEGLAENVRRLAPRFEAGLKRIADRPNIGEYRGIGFMWALEAVKDKPTKTPFDANLSVSERIANTCTDLGLICRPLGQSIVLCPPFILTEAQMDEMFEKLEKALDKVFAEVA 453
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284|      294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444         
                                                                                                                                                                                                                                                                                                                  285-LLP
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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, 4)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4GRX)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4GRX)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)

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