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(-) Description

Title :  RADIATION DAMAGE OF THE SCHIFF BASE IN PHOSPHOSERINE AMINOTRANSFERASE (STRUCTURE A)
 
Authors :  A. P. Dubnovitsky, R. B. G. Ravelli, A. N. Popov, A. C. Papageorgiou
Date :  20 Jan 05  (Deposition) - 19 May 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.68
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Transferase, Aminotransferase, Pyridoxal-5'-Phosphate, Radiation Damage (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. P. Dubnovitsky, R. B. G. Ravelli, A. N. Popov, A. C. Papageorgiou
Strain Relief At The Active Site Of Phosphoserine Aminotransferase Induced By Radiation Damage.
Protein Sci. V. 14 1498 2005
PubMed-ID: 15883191  |  Reference-DOI: 10.1110/PS.051397905

(-) Compounds

Molecule 1 - PHOSPHOSERINE AMINOTRANSFERASE
    Chains: A, B
    EC Number: 2.6.1.52
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PBALC-PSAT
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Organism Scientific: BACILLUS ALCALOPHILUS
    Organism Taxid: 1445
    Other Details: PYRIDOXAL-5'-PHOSPHATE LINKED TO 196

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 14)

Asymmetric/Biological Unit (5, 14)
No.NameCountTypeFull Name
11PE1Ligand/IonPENTAETHYLENE GLYCOL
2CL4Ligand/IonCHLORIDE ION
3MG4Ligand/IonMAGNESIUM ION
4PEG3Ligand/IonDI(HYDROXYETHYL)ETHER
5PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:256 , HOH A:2183 , HOH A:2185 , HOH A:2186 , GLU B:51 , HOH B:2064BINDING SITE FOR RESIDUE MG A1362
02AC2SOFTWAREASP A:344 , HOH A:2266 , HOH A:2268 , HOH A:2271 , ASP B:66 , HOH B:2185BINDING SITE FOR RESIDUE MG A1363
03AC3SOFTWARESER A:101 , TRP A:102 , ASN A:151 , THR A:152 , ILE A:153 , HOH A:2091BINDING SITE FOR RESIDUE CL A1364
04AC4SOFTWARETRP A:102 , THR A:152 , ARG A:334 , HOH A:2009BINDING SITE FOR RESIDUE CL A1365
05AC5SOFTWAREHOH A:2204 , HOH A:2205 , HOH B:2112 , HOH B:2251 , HOH B:2256 , HOH B:2257BINDING SITE FOR RESIDUE MG B1362
06AC6SOFTWAREASP B:256 , HOH B:2221 , HOH B:2227 , HOH B:2229BINDING SITE FOR RESIDUE MG B1363
07AC7SOFTWARESER B:101 , TRP B:102 , ASN B:151 , THR B:152 , ILE B:153 , HOH B:2152BINDING SITE FOR RESIDUE CL B1364
08AC8SOFTWARETRP B:102 , ILE B:153 , ARG B:334 , HOH B:2013BINDING SITE FOR RESIDUE CL B1365
09AC9SOFTWAREGLY A:75 , ALA A:76 , SER A:77 , TRP A:102 , THR A:152 , ASP A:172 , SER A:174 , GLN A:195 , LYS A:196 , HOH A:2138 , HOH A:2153 , HOH A:2278 , ASN B:237 , THR B:238 , HOH B:2214BINDING SITE FOR RESIDUE PLP A1361
10BC1SOFTWAREASP A:279 , LYS A:291 , HOH A:2279 , HOH A:2280 , GLU B:269 , ILE B:343 , HOH B:2244BINDING SITE FOR RESIDUE 1PE A1366
11BC2SOFTWAREASN A:237 , THR A:238 , HOH A:2174 , GLY B:75 , ALA B:76 , SER B:77 , PHE B:80 , TRP B:102 , THR B:152 , ASP B:172 , SER B:174 , GLN B:195 , LYS B:196 , HOH B:2191 , HOH B:2323 , HOH B:2324BINDING SITE FOR RESIDUE PLP B1361
12BC3SOFTWAREGLN A:159 , LYS A:291 , ARG A:294 , HOH A:2282BINDING SITE FOR RESIDUE PEG A1367
13BC4SOFTWAREGLU A:104 , LYS A:123BINDING SITE FOR RESIDUE PEG A1368
14BC5SOFTWAREGLN B:159 , TYR B:275 , LYS B:291 , GLY B:292 , ARG B:294 , LEU B:296BINDING SITE FOR RESIDUE PEG B1366

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2BHX)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gly A:10 -Pro A:11
2Gly B:10 -Pro B:11

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2BHX)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AA_TRANSFER_CLASS_5PS00595 Aminotransferases class-V pyridoxal-phosphate attachment site.SERC_BACAO188-207
 		  2A:187-206
B:187-206

(-) Exons   (0, 0)

(no "Exon" information available for 2BHX)

(-) 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:360
 aligned with SERC_BACAO | Q9RME2 from UniProtKB/Swiss-Prot  Length:361

    Alignment length:360
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361
           SERC_BACAO     2 VKQVFNFNAGPSALPKPALERAQKELLNFNDTQMSVMELSHRSQSYEEVHEQAQNLLRELLQIPNDYQILFLQGGASLQFTMLPMNLLTKGTIGNYVLTGSWSEKALKEAKLLGETHIAASTKANSYQSIPDFSEFQLNENDAYLHITSNNTIYGTQYQNFPEINHAPLIADMSSDILSRPLKVNQFGMIYAGAQKNLGPSGVTVVIVKKDLLNTKVEQVPTMLQYATHIKSDSLYNTPPTFSIYMLRNVLDWIKDLGGAEAIAKQNEEKAKIIYDTIDESNGFYVGHAEKGSRSLMNVTFNLRNEELNQQFLAKAKEQGFVGLNGHRSVGGCRASIYNAVPIDACIALRELMIQFKENA 361
               SCOP domains d2bhxa_ A: Phosphoserine aminotransferase, PSAT                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains ---------------2bhxA01 A:16-257 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                              2bhxA02 A:258-360 Aspartate Aminotransferase, domain 1                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....ee........hhhhhhhhhhh.........hhhhh...hhhhhhhhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhh..eeeeeee.hhhh.....hhhhh.....eeeeeee.ee....ee...........eeee..........hhhhh.eeeee..........eeeeeehhhhh......hhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....ee..hhhh....eeeee..hhhhhhhhhhhhhhh.ee..........eeee.....hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AA_TRANSFER_CLASS_5 ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2bhx A   1 VKQVFNFNAGPSALPKPALERAQKELLNFNDTQMSVMELSHRSQSYEEVHEQAQNLLRELLQIPNDYQILFLQGGASLQFTMLPMNLLTKGTIGNYVLTGSWSEKALKEAKLLGETHIAASTKANSYQSIPDFSEFQLNENDAYLHITSNNTIYGTQYQNFPEINHAPLIADMSSDILSRPLKVNQFGMIYAGAQKNLGPSGVTVVIVKKDLLNTKVEQVPTMLQYATHIKSDSLYNTPPTFSIYMLRNVLDWIKDLGGAEAIAKQNEEKAKIIYDTIDESNGFYVGHAEKGSRSLMNVTFNLRNEELNQQFLAKAKEQGFVGLNGHRSVGGCRASIYNAVPIDACIALRELMIQFKENA 360
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360


Chain B from PDB  Type:PROTEIN  Length:356
 aligned with SERC_BACAO | Q9RME2 from UniProtKB/Swiss-Prot  Length:361

    Alignment length:359
                                    12        22        32        42        52        62        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         
           SERC_BACAO     3 KQVFNFNAGPSALPKPALERAQKELLNFNDTQMSVMELSHRSQSYEEVHEQAQNLLRELLQIPNDYQILFLQGGASLQFTMLPMNLLTKGTIGNYVLTGSWSEKALKEAKLLGETHIAASTKANSYQSIPDFSEFQLNENDAYLHITSNNTIYGTQYQNFPEINHAPLIADMSSDILSRPLKVNQFGMIYAGAQKNLGPSGVTVVIVKKDLLNTKVEQVPTMLQYATHIKSDSLYNTPPTFSIYMLRNVLDWIKDLGGAEAIAKQNEEKAKIIYDTIDESNGFYVGHAEKGSRSLMNVTFNLRNEELNQQFLAKAKEQGFVGLNGHRSVGGCRASIYNAVPIDACIALRELMIQFKENA 361
               SCOP domains d2bhxb_ B: Phosphoserine aminotransferase, PSAT                                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains --------------2bhxB01 B:16-257 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                              2bhxB02 B:258-360 Aspartate Aminotransferase, domain 1                                                  CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee........hhhhhhhhhhh..hhhhh..hhhhh...hhhhhhhhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhheeeeeee.hhhh.....hhhhh.....eeeeeee.ee....ee...........eeee..........hhhhh.eeeee..........eeeeee.hhh---....hhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eee..hhhh....eeeeee.hhhhhhhhhhhhhhh.ee..........eeee.....hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AA_TRANSFER_CLASS_5 ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bhx B   2 KQVFNFNAGPSALPKPALERAQKELLNFNDTQMSVMELSHRSQSYEEVHEQAQNLLRELLQIPNDYQILFLQGGASLQFTMLPMNLLTKGTIGNYVLTGSWSEKALKEAKLLGETHIAASTKANSYQSIPDFSEFQLNENDAYLHITSNNTIYGTQYQNFPEINHAPLIADMSSDILSRPLKVNQFGMIYAGAQKNLGPSGVTVVIVKKDLL---VEQVPTMLQYATHIKSDSLYNTPPTFSIYMLRNVLDWIKDLGGAEAIAKQNEEKAKIIYDTIDESNGFYVGHAEKGSRSLMNVTFNLRNEELNQQFLAKAKEQGFVGLNGHRSVGGCRASIYNAVPIDACIALRELMIQFKENA 360
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211 |   | 221       231       241       251       261       271       281       291       301       311       321       331       341       351         
                                                                                                                                                                                                                                             213 217
   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, 2)

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

(-) CATH Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2BHX)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (SERC_BACAO | Q9RME2)
molecular function
    GO:0004648    O-phospho-L-serine:2-oxoglutarate aminotransferase activity    Catalysis of the reaction: O-phospho-L-serine + 2-oxoglutarate = 3-phosphonooxypyruvate + L-glutamate.
    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:0006564    L-serine biosynthetic process    The chemical reactions and pathways resulting in the formation of L-serine, the L-enantiomer of serine, i.e. (2S)-2-amino-3-hydroxypropanoic acid.
    GO:0008652    cellular amino acid biosynthetic process    The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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  2bhx
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  SERC_BACAO | Q9RME2
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  2.6.1.52
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 Related Entries

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

UniProtKB/Swiss-Prot
        SERC_BACAO | Q9RME2: 1w23 2bi1 2bi2 2bi3 2bi5 2bi9 2bia 2bie 2big 4azj 4azk

(-) Related Entries Specified in the PDB File

1w23 CRYSTAL STRUCTURE OF PHOSPHOSERINE AMINOTRANSFERASE FROM BACILLUS ALCALOPHILUS