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(-) Description

Title :  CRYSTAL STRUCTURE OF PLP-BOUND PUTATIVE AMINOTRANSFERASE FROM CLOSTRIDIUM DIFFICILE 630
 
Authors :  I. G. Shabalin, O. Onopriyenko, M. Kudritska, M. Chruszcz, S. Grimshaw P. J. Porebski, D. R. Cooper, A. Savchenko, W. F. Anderson, W. Minor, Ce Structural Genomics Of Infectious Diseases (Csgid)
Date :  15 Feb 12  (Deposition) - 29 Feb 12  (Release) - 29 Feb 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Niaid, National Institute Of Allergy And Infectious Diseases, Center For Structural Genomics Of Infectious Diseases, Csgid, Internal Aldimine With Pyridoxalphosphate, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. G. Shabalin, O. Onopriyenko, M. Kudritska, S. Grimshaw, M. Chruszcz, P. J. Porebski, D. R. Cooper, A. Savchenko, W. F. Anderson W. Minor
Crystal Structures Of Putative Aminotransferase From Clostridium Difficile 630
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE PYRIDOXAL PHOSPHATE-DEPENDENT TRANSFERASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21-CODONPLUS(DE3)-RIPL
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: CD2733, CD630_27330
    Organism Scientific: CLOSTRIDIUM DIFFICILE
    Organism Taxid: 272563
    Strain: 630

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
1CL3Ligand/IonCHLORIDE ION
2PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:95 , VAL A:96 , ILE A:97 , PRO A:98 , TYR A:121 , CYS A:168 , ASN A:172 , ASP A:200 , ILE A:202 , HIS A:203 , LYS A:235 , HOH A:596 , HOH A:685 , HOH A:837 , HOH A:861 , HOH A:903 , HOH A:965 , TYR B:62 , ASP B:266BINDING SITE FOR RESIDUE PLP A 401
2AC2SOFTWAREASN A:145 , ASN A:147 , ASN B:145 , ASN B:147BINDING SITE FOR RESIDUE CL A 402
3AC3SOFTWAREMET A:311 , PRO A:312 , LYS A:313 , HOH A:844BINDING SITE FOR RESIDUE CL A 403
4AC4SOFTWARETYR A:62 , ASP A:266 , HOH A:778 , GLY B:95 , VAL B:96 , ILE B:97 , PRO B:98 , TYR B:121 , CYS B:168 , ASN B:172 , ASP B:200 , ILE B:202 , HIS B:203 , LYS B:235 , HOH B:617 , HOH B:764 , HOH B:794 , HOH B:812 , HOH B:871BINDING SITE FOR RESIDUE PLP B 401
5AC5SOFTWAREMET B:311 , PRO B:312 , LYS B:313BINDING SITE FOR RESIDUE CL B 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4DQ6)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Glu A:118 -Pro A:119
2Asn A:169 -Pro A:170
3Asn A:172 -Pro A:173
4Glu B:118 -Pro B:119
5Asn B:169 -Pro B:170
6Asn B:172 -Pro B:173

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4DQ6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4DQ6)

(-) Exons   (0, 0)

(no "Exon" information available for 4DQ6)

(-) 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:388
 aligned with Q183G9_PEPD6 | Q183G9 from UniProtKB/TrEMBL  Length:388

    Alignment length:388
                                    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       370       380        
         Q183G9_PEPD6     1 MNYNFNEIVDRSNNFSSKWSEMEKKYGTNDLLPMWVADMDFKAAPCIIDSLKNRLEQEIYGYTTRPDSYNESIVNWLYRRHNWKIKSEWLIYSPGVIPAISLLINELTKANDKIMIQEPVYSPFNSVVKNNNRELIISPLQKLENGNYIMDYEDIENKIKDVKLFILCNPHNPVGRVWTKDELKKLGDICLKHNVKIISDEIHSDIILKKHKHIPMASISKEFEKNTITCMAPTKTFNIAGLQSSYVVLPDEKDYKLLDDAFTRIDIKRNNCFSLVATEASYNNGESWLESFLEYLESNIDFAIKYINENMPKLKVRKPEGTYLLWVDFSALGLSDEELESILVQKGKVALNQGNSFGIGGSGYQRINLACPRSMLEEALIRIKNAIN 388
               SCOP domains d4dq6a_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhhhhhhhhhhh....ee..........hhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhh...hhh.eeee.hhhhhhhhhhhhhh....eeee.....hhhhhhhhhh..eeee...ee.....ee.hhhhhhhhh..eeeeeee..........hhhhhhhhhhhhhhh..eeeee..............hhhhhhhhhhhheeeee.hhhhhhhhhhh.eeee..hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...ee.......eeeee.hhhh.hhhhhhhhhhhh..ee.ee.hhhh.....eeeee...hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4dq6 A   1 MNYNFNEIVDRSNNFSSKWSEMEKKYGTNDLLPMWVADMDFKAAPCIIDSLKNRLEQEIYGYTTRPDSYNESIVNWLYRRHNWKIKSEWLIYSPGVIPAISLLINELTKANDKIMIQEPVYSPFNSVVKNNNRELIISPLQKLENGNYIMDYEDIENKIKDVKLFILCNPHNPVGRVWTKDELKKLGDICLKHNVKIISDEIHSDIILKKHKHIPMASISKEFEKNTITCMAPTKTFNIAGLQSSYVVLPDEKDYKLLDDAFTRIDIKRNNCFSLVATEASYNNGESWLESFLEYLESNIDFAIKYINENMPKLKVRKPEGTYLLWVDFSALGLSDEELESILVQKGKVALNQGNSFGIGGSGYQRINLACPRSMLEEALIRIKNAIN 388
                                    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       370       380        


Chain B from PDB  Type:PROTEIN  Length:388
 aligned with Q183G9_PEPD6 | Q183G9 from UniProtKB/TrEMBL  Length:388

    Alignment length:388
                                    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       370       380        
         Q183G9_PEPD6     1 MNYNFNEIVDRSNNFSSKWSEMEKKYGTNDLLPMWVADMDFKAAPCIIDSLKNRLEQEIYGYTTRPDSYNESIVNWLYRRHNWKIKSEWLIYSPGVIPAISLLINELTKANDKIMIQEPVYSPFNSVVKNNNRELIISPLQKLENGNYIMDYEDIENKIKDVKLFILCNPHNPVGRVWTKDELKKLGDICLKHNVKIISDEIHSDIILKKHKHIPMASISKEFEKNTITCMAPTKTFNIAGLQSSYVVLPDEKDYKLLDDAFTRIDIKRNNCFSLVATEASYNNGESWLESFLEYLESNIDFAIKYINENMPKLKVRKPEGTYLLWVDFSALGLSDEELESILVQKGKVALNQGNSFGIGGSGYQRINLACPRSMLEEALIRIKNAIN 388
               SCOP domains d4dq6b_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhhhhhhhhhhh....ee..........hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhh...hhh.eeee.hhhhhhhhhhhhhh....eeee.....hhhhhhhhhh..eeee...ee.....ee.hhhhhhhhh..eeeeeee..........hhhhhhhhhhhhhhhh.eeeee..............hhhhhhhhhhhheeeee.hhhhhhhhhhh.eeee..hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...ee.......eeeee.hhhh.hhhhhhhhhhhh..ee.ee.hhhh.....eeeee...hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4dq6 B   1 MNYNFNEIVDRSNNFSSKWSEMEKKYGTNDLLPMWVADMDFKAAPCIIDSLKNRLEQEIYGYTTRPDSYNESIVNWLYRRHNWKIKSEWLIYSPGVIPAISLLINELTKANDKIMIQEPVYSPFNSVVKNNNRELIISPLQKLENGNYIMDYEDIENKIKDVKLFILCNPHNPVGRVWTKDELKKLGDICLKHNVKIISDEIHSDIILKKHKHIPMASISKEFEKNTITCMAPTKTFNIAGLQSSYVVLPDEKDYKLLDDAFTRIDIKRNNCFSLVATEASYNNGESWLESFLEYLESNIDFAIKYINENMPKLKVRKPEGTYLLWVDFSALGLSDEELESILVQKGKVALNQGNSFGIGGSGYQRINLACPRSMLEEALIRIKNAIN 388
                                    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       370       380
   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  (0, 0)

(no "CATH Domain" information available for 4DQ6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4DQ6)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q183G9_PEPD6 | Q183G9)
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: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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 Related Entries

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

UniProtKB/TrEMBL
        Q183G9_PEPD6 | Q183G9: 4dgt

(-) Related Entries Specified in the PDB File

4dgt THE SAME PROTEIN CRYSTALLIZED WITH MAGNESIUM RELATED ID: CSGID-IDP05302 RELATED DB: TARGETTRACK RELATED ID: IDP05302 RELATED DB: TARGETTRACK