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(-) Description

Title :  ALANINE-GLYOXYLATE AMINOTRANSFERASE VARIANT S187F
 
Authors :  K. Fodor, E. Oppici, C. Williams, B. Cellini, M. Wilmanns
Date :  03 Dec 12  (Deposition) - 01 May 13  (Release) - 07 Aug 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Aminotransferase, Primary Hyperoxaluria Type 1, Peroxisome, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Oppici, K. Fodor, A. Paiardini, C. Williams, C. B. Voltattorni, M. Wilmanns, B. Cellini
Crystal Structure Of The S187F Variant Of Human Liver Alanine: Aminotransferase Associated With Primary Hyperoxaluria Type I And Its Functional Implications.
Proteins V. 81 1457 2013
PubMed-ID: 23589421  |  Reference-DOI: 10.1002/PROT.24300

(-) Compounds

Molecule 1 - SERINE-PYRUVATE AMINOTRANSFERASE
    Chains: A, B, C, D
    EC Number: 2.6.1.51, 2.6.1.44
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PETM11
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: AGXT, AGT1, SPAT
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: SPT, ALANINE-GLYOXYLATE AMINOTRANSFERASE, AGT

 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  (2, 17)

Asymmetric Unit (2, 17)
No.NameCountTypeFull Name
1GOL13Ligand/IonGLYCEROL
2LLP4Mod. Amino Acid2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2LLP2Mod. Amino Acid2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)
Biological Unit 2 (2, 11)
No.NameCountTypeFull Name
1GOL9Ligand/IonGLYCEROL
2LLP2Mod. Amino Acid2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:29 , LEU A:351 , ARG A:360 , SER B:48BINDING SITE FOR RESIDUE GOL A 401
02AC2SOFTWAREGLN A:110 , ARG A:111BINDING SITE FOR RESIDUE GOL A 402
03AC3SOFTWARELYS B:51BINDING SITE FOR RESIDUE GOL B 401
04AC4SOFTWAREMET A:49 , TYR A:260 , PRO B:28 , GLY B:29 , LEU B:351 , ARG B:360BINDING SITE FOR RESIDUE GOL B 402
05AC5SOFTWAREHIS C:133 , THR C:135BINDING SITE FOR RESIDUE GOL C 401
06AC6SOFTWAREPRO A:130 , PHE A:310 , LYS A:357 , HIS C:124 , PRO C:125 , HIS C:146BINDING SITE FOR RESIDUE GOL C 402
07AC7SOFTWAREMET C:348 , ARG C:360 , MET D:49 , TYR D:260BINDING SITE FOR RESIDUE GOL C 403
08AC8SOFTWAREGLY C:283 , GLU C:285 , ASN C:286BINDING SITE FOR RESIDUE GOL C 404
09AC9SOFTWAREARG D:122 , HIS D:124BINDING SITE FOR RESIDUE GOL D 401
10BC1SOFTWAREPRO D:73 , GOL D:404BINDING SITE FOR RESIDUE GOL D 402
11BC2SOFTWARELYS B:228 , ASP D:255 , GOL D:404BINDING SITE FOR RESIDUE GOL D 403
12BC3SOFTWARELYS D:227 , CYS D:253 , GOL D:402 , GOL D:403BINDING SITE FOR RESIDUE GOL D 404
13BC4SOFTWAREGLU D:138BINDING SITE FOR RESIDUE GOL D 405

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4I8A)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Gly A:29 -Pro A:30
2Gly B:29 -Pro B:30
3Gly C:29 -Pro C:30
4Gly D:29 -Pro D:30

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4I8A)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4I8A)

(-) Exons   (0, 0)

(no "Exon" information available for 4I8A)

(-) 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:387
                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains d4i8aa_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhh.......ee........hhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh.....eeee..hhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhh..eeeeee.......hhhhhhhhhhhhh..eeeee.ee....ee....hhhhhhhhh..eeeee..........hhhhhh..eeeeehhhhh......eeeeehhhhhhhhh...........hhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhh...eeeee.....hhhhhhhhhhhhhhee....hhhhh..eeeee.hhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4i8a A   6 LLVTPPKALLKPLSIPNQLLLGPGPSNLPPRIMAAGGLQMIGSMSKDMYQIMDEIKEGIQYVFQTRNPLTLVISGSGHCALEAALVNVLEPGDSFLVGANGIWGQRAVDIGERIGARVHPMTKDPGGHYTLQEVEEGLAQHKPVLLFLTHGESSTGVLQPLDGFGELCHRYKCLLLVDSVAFLGGTPLYMDRQGIDILYSGSQkALNAPPGTSLISFSDKAKKKMYSRKTKPFSFYLDIKWLANFWGCDDQPRMYHHTIPVISLYSLRESLALIAEQGLENSWRQHREAAAYLHGRLQALGLQLFVKDPALRLPTVTTVAVPAGYDWRDIVSYVIDHFDIEIMGGLGPSTGKVLRIGLLGCNATRENVDRVTEALRAALQHCPKKKL 392
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205   |   215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       
                                                                                                                                                                                                                                     209-LLP                                                                                                                                                                                   


Chain B from PDB  Type:PROTEIN  Length:386
                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains d4i8ab_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhh.......ee........hhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh.....eeee..hhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhh..eeeeee.......hhhhhhhhhhhhh..eeeee.ee....ee....hhhhhhhhh..eeeee..........hhhhhh..eeeeehhhhh......eeeeehhhhhhhhh...........hhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhh...eeeee.....hhhhhhhhhhhhhhee....hhhhh..eeeee.hhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4i8a B   5 KLLVTPPKALLKPLSIPNQLLLGPGPSNLPPRIMAAGGLQMIGSMSKDMYQIMDEIKEGIQYVFQTRNPLTLVISGSGHCALEAALVNVLEPGDSFLVGANGIWGQRAVDIGERIGARVHPMTKDPGGHYTLQEVEEGLAQHKPVLLFLTHGESSTGVLQPLDGFGELCHRYKCLLLVDSVAFLGGTPLYMDRQGIDILYSGSQkALNAPPGTSLISFSDKAKKKMYSRKTKPFSFYLDIKWLANFWGCDDQPRMYHHTIPVISLYSLRESLALIAEQGLENSWRQHREAAAYLHGRLQALGLQLFVKDPALRLPTVTTVAVPAGYDWRDIVSYVIDHFDIEIMGGLGPSTGKVLRIGLLGCNATRENVDRVTEALRAALQHCPKK 390
                                    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      
                                                                                                                                                                                                                                      209-LLP                                                                                                                                                                                 


Chain C from PDB  Type:PROTEIN  Length:385
                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains d4i8ac_ C: automated matches                                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhh.......ee........hhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh.....eeee..hhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhh..eeeeee.......hhhhhhhhhhhhh..eeeee.ee....ee....hhhhhhhhh..eeeee..........hhhhhh..eeeeehhhhh......eeeeehhhhhhhhh...........hhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhh...eeeee.....hhhhhhhhhhhhhhee....hhhhh..eeeee.hhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4i8a C   6 LLVTPPKALLKPLSIPNQLLLGPGPSNLPPRIMAAGGLQMIGSMSKDMYQIMDEIKEGIQYVFQTRNPLTLVISGSGHCALEAALVNVLEPGDSFLVGANGIWGQRAVDIGERIGARVHPMTKDPGGHYTLQEVEEGLAQHKPVLLFLTHGESSTGVLQPLDGFGELCHRYKCLLLVDSVAFLGGTPLYMDRQGIDILYSGSQkALNAPPGTSLISFSDKAKKKMYSRKTKPFSFYLDIKWLANFWGCDDQPRMYHHTIPVISLYSLRESLALIAEQGLENSWRQHREAAAYLHGRLQALGLQLFVKDPALRLPTVTTVAVPAGYDWRDIVSYVIDHFDIEIMGGLGPSTGKVLRIGLLGCNATRENVDRVTEALRAALQHCPKK 390
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205   |   215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385     
                                                                                                                                                                                                                                     209-LLP                                                                                                                                                                                 


Chain D from PDB  Type:PROTEIN  Length:386
                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains d4i8ad_ D: automated matches                                                                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhh.......ee........hhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh.....eeee..hhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhh..eeeeee.......hhhhhhhhhhhhh..eeeee.ee....ee....hhhhhhhhh..eeeee..........hhhhhh..eeeeehhhhh......eeeeehhhhhhhhh...........hhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhh...eeeee.....hhhhhhhhhhhhhhee....hhhhh..eeeee.hhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4i8a D   5 KLLVTPPKALLKPLSIPNQLLLGPGPSNLPPRIMAAGGLQMIGSMSKDMYQIMDEIKEGIQYVFQTRNPLTLVISGSGHCALEAALVNVLEPGDSFLVGANGIWGQRAVDIGERIGARVHPMTKDPGGHYTLQEVEEGLAQHKPVLLFLTHGESSTGVLQPLDGFGELCHRYKCLLLVDSVAFLGGTPLYMDRQGIDILYSGSQkALNAPPGTSLISFSDKAKKKMYSRKTKPFSFYLDIKWLANFWGCDDQPRMYHHTIPVISLYSLRESLALIAEQGLENSWRQHREAAAYLHGRLQALGLQLFVKDPALRLPTVTTVAVPAGYDWRDIVSYVIDHFDIEIMGGLGPSTGKVLRIGLLGCNATRENVDRVTEALRAALQHCPKK 390
                                    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      
                                                                                                                                                                                                                                      209-LLP
   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, 4)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4I8A)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4I8A)

(-) Gene Ontology  (26, 26)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

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        SPYA_HUMAN | P21549: 1h0c 1j04 2yob 3r9a 4cbr 4cbs 4kxk 4kyo 5f9s 5hhy

(-) Related Entries Specified in the PDB File

1h0c 1jo4