Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit - manually
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit - manually
Asym./Biol. Unit - manually  (Jmol Viewer)
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF PHOSPHOSERINE AMINOTRANSFERASE FROM BACILLUS ALCALOPHILUS
 
Authors :  A. Dubnovitsky, E. G. Kapetaniou, A. C. Papageorgiou
Date :  25 Jun 04  (Deposition) - 22 Dec 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.08
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Aminotransferase, Pyridoxal-5'-Phosphate, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Dubnovitsky, E. G. Kapetaniou, A. C. Papageorgiou
Enzyme Adaptation To Alkaline Ph: Atomic Resolution (1. 08 A) Structure Of Phosphoserine Aminotransferase From Bacillus Alcalophilus
Protein Sci. V. 14 97 2005
PubMed-ID: 15608117  |  Reference-DOI: 10.1110/PS.041029805

(-) 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  (7, 16)

Asymmetric/Biological Unit (7, 16)
No.NameCountTypeFull Name
1CL4Ligand/IonCHLORIDE ION
2EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINEETHANESULFONIC ACID
3GOL1Ligand/IonGLYCEROL
4MG4Ligand/IonMAGNESIUM ION
5PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
6PGE3Ligand/IonTRIETHYLENE GLYCOL
7PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHOH B:2196 , HOH B:2197 , HOH B:2399 , HOH B:2400 , HOH B:2408BINDING SITE FOR RESIDUE MG A 503
02AC2SOFTWAREASP A:256 , HOH A:2141 , HOH A:2315 , HOH A:2316 , HOH A:2318 , HOH B:2120BINDING SITE FOR RESIDUE MG A1361
03AC3SOFTWAREASP A:344 , HOH A:2424 , HOH A:2425 , ASP B:66 , HOH B:2154 , HOH B:2329BINDING SITE FOR RESIDUE MG A1362
04AC4SOFTWARESER A:101 , TRP A:102 , ASN A:151 , THR A:152 , ILE A:153 , HOH A:2234BINDING SITE FOR RESIDUE CL A1365
05AC5SOFTWARETRP A:102 , ILE A:153 , ARG A:334 , HOH A:2020BINDING SITE FOR RESIDUE CL A1366
06AC6SOFTWARETYR B:127 , GLN B:128 , TYR B:154 , THR B:156 , VAL B:286 , GLY B:287 , HIS B:288 , ASN B:302 , HOH B:2436BINDING SITE FOR RESIDUE MG B1361
07AC7SOFTWARESER B:101 , TRP B:102 , ASN B:151 , THR B:152 , ILE B:153BINDING SITE FOR RESIDUE CL B1366
08AC8SOFTWARETRP B:102 , ILE B:153 , ARG B:334 , HOH B:2032 , HOH B:2476BINDING SITE FOR RESIDUE CL B1367
09AC9SOFTWAREGLU A:104 , ILE A:118 , LYS A:123BINDING SITE FOR RESIDUE PGE A1364
10BC1SOFTWAREGLY 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:2452 , HOH A:2453 , ASN B:237 , THR B:238 , HOH B:2354BINDING SITE FOR RESIDUE PLP A1367
11BC2SOFTWAREGLN B:159 , LYS B:291 , GLY B:292 , ARG B:294 , LEU B:296 , HOH B:2286 , HOH B:2424 , HOH B:2432 , HOH B:2519 , HOH B:2520BINDING SITE FOR RESIDUE PGE B1363
12BC3SOFTWAREGLU B:104 , LYS B:123BINDING SITE FOR RESIDUE PGE B1364
13BC4SOFTWAREGLN B:68 , LYS B:210 , ILE B:230 , LYS B:231 , ASP B:233 , HOH B:2343 , HOH B:2521BINDING SITE FOR RESIDUE EPE B1365
14BC5SOFTWAREASN A:237 , THR A:238 , HOH A:2301 , GLY B:75 , ALA B:76 , SER B:77 , TRP B:102 , THR B:152 , ASP B:172 , SER B:174 , GLN B:195 , LYS B:196 , HOH B:2523 , HOH B:2524BINDING SITE FOR RESIDUE PLP B1368
15BC6SOFTWAREGLN A:159 , LYS A:291 , GLY A:292 , ARG A:294 , HOH A:2367 , HOH A:2449 , HOH A:2450 , HOH A:2451BINDING SITE FOR RESIDUE PEG A1363
16BC7SOFTWAREILE A:230 , LYS A:231 , ASN B:139 , GLU B:140 , HOH B:2516 , HOH B:2517 , HOH B:2518BINDING SITE FOR RESIDUE GOL B1362

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1W23)

(-) 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 1W23)

(-) 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 1W23)

(-) 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 d1w23a_ A: Phosphoserine aminotransferase, PSAT                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains ---------------1w23A01 A:16-257 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                              1w23A02 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.....hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AA_TRANSFER_CLASS_5 ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1w23 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:357
 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 d1w23b_ B: Phosphoserine aminotransferase, PSAT                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains ---------------1w23B01 B:16-257 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                              1w23B02 B:258-360 Aspartate Aminotransferase, domain 1                                                  CATH domains
           Pfam domains (1) ---Aminotran_5-1w23B01 B:4-346                                                                                                                                                                                                                                                                                                                            -------------- Pfam domains (1)
           Pfam domains (2) ---Aminotran_5-1w23B02 B:4-346                                                                                                                                                                                                                                                                                                                            -------------- Pfam domains (2)
         Sec.struct. author ....ee........hhhhhhhhhhh.........hhhhh...hhhhhhhhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhheeeeeee.hhhh.....hhhhh.....eeeeeee.ee....ee...........eeee..........hhhhh.eeeee..........eeeeee.hhh---....hhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....ee..hhhh....eeeee..hhhhhhhhhhhhhhh.ee..........eeee.....hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AA_TRANSFER_CLASS_5 ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1w23 B   1 VKQVFNFNAGPSALPKPALERAQKELLNFNDTQMSVMELSHRSQSYEEVHEQAQNLLRELLQIPNDYQILFLQGGASLQFTMLPMNLLTKGTIGNYVLTGSWSEKALKEAKLLGETHIAASTKANSYQSIPDFSEFQLNENDAYLHITSNNTIYGTQYQNFPEINHAPLIADMSSDILSRPLKVNQFGMIYAGAQKNLGPSGVTVVIVKKDLL---VEQVPTMLQYATHIKSDSLYNTPPTFSIYMLRNVLDWIKDLGGAEAIAKQNEEKAKIIYDTIDESNGFYVGHAEKGSRSLMNVTFNLRNEELNQQFLAKAKEQGFVGLNGHRSVGGCRASIYNAVPIDACIALRELMIQFKENA 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
                                                                                                                                                                                                                                              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  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: PLP_aminotran (240)

(-) 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.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    EPE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PEG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PGE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PLP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
    BC4  [ RasMol ]  +environment [ RasMol ]
    BC5  [ RasMol ]  +environment [ RasMol ]
    BC6  [ RasMol ]  +environment [ RasMol ]
    BC7  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Gly A:10 - Pro A:11   [ RasMol ]  
    Gly B:10 - Pro B:11   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1w23
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  SERC_BACAO | Q9RME2
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  2.6.1.52
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  SERC_BACAO | Q9RME2
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

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

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1W23)