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(-) Description

Title :  CRYSTAL STRUCTURE OF PUTATIVE PLP-DEPENDENT AMINOTRANSFERASE (NP_978343.1) FROM BACILLUS CEREUS ATCC 10987 AT 2.19 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  14 Sep 09  (Deposition) - 10 Nov 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.19
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Np_978343. 1, Putative Plp-Dependent Aminotransferase, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Pyridoxal Phosphate, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Putative Plp-Dependent Aminotransferas (Np_978343. 1) From Bacillus Cereus Atcc 10987 At 2. 19 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE PLP-DEPENDENT AMINOTRANSFERASE
    Atcc: 10987
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Strain: HK100
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: BCE_2027, NP_978343.1
    Organism Scientific: BACILLUS CEREUS ATCC 10987
    Organism Taxid: 222523
    Synonym: DEGT/DNRJ/ERYC1/STRS FAMILY PROTEIN

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 52)

Asymmetric/Biological Unit (6, 52)
No.NameCountTypeFull Name
1ACT5Ligand/IonACETATE ION
2CA4Ligand/IonCALCIUM ION
3LLP2Mod. Amino Acid2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)
4MSE32Mod. Amino AcidSELENOMETHIONINE
5PEG7Ligand/IonDI(HYDROXYETHYL)ETHER
6PGE2Ligand/IonTRIETHYLENE GLYCOL

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:19 , CA A:379 , HOH A:530 , HOH A:531BINDING SITE FOR RESIDUE CA A 377
02AC2SOFTWAREHOH A:533 , ARG B:329 , HOH B:521 , HOH B:535BINDING SITE FOR RESIDUE CA A 378
03AC3SOFTWAREASP A:19 , CA A:377 , HOH A:531 , HOH A:532 , HOH A:534 , ASN B:330BINDING SITE FOR RESIDUE CA A 379
04AC4SOFTWAREASN A:32 , PHE A:217 , ASN A:231 , LYS A:233 , HOH A:421 , HIS B:187 , LLP B:190BINDING SITE FOR RESIDUE ACT A 380
05AC5SOFTWAREARG A:223 , HOH A:396 , HOH A:398 , ARG B:315 , LEU B:316 , TYR B:317BINDING SITE FOR RESIDUE ACT A 381
06AC6SOFTWARELYS A:152BINDING SITE FOR RESIDUE ACT A 382
07AC7SOFTWARETHR A:221 , ASN A:222 , ARG A:223BINDING SITE FOR RESIDUE PEG A 383
08AC8SOFTWARETHR A:189 , LLP A:190 , GLN A:288 , HOH A:443 , ACT B:378BINDING SITE FOR RESIDUE PEG A 384
09AC9SOFTWARELYS A:264 , THR A:282 , GLU A:283 , GLN A:287BINDING SITE FOR RESIDUE PEG A 385
10BC1SOFTWARETRP A:141 , LEU A:144 , GLU A:145 , MSE A:172 , GLY A:175 , GLN A:176 , ASP A:177 , HOH A:527BINDING SITE FOR RESIDUE PGE A 386
11BC2SOFTWAREHOH A:528 , ASP B:19 , HOH B:520 , HOH B:534BINDING SITE FOR RESIDUE CA B 377
12BC3SOFTWAREHIS A:187 , LLP A:190 , PEG A:384 , ASN B:32 , PHE B:217 , ASN B:231 , LYS B:233 , HOH B:475BINDING SITE FOR RESIDUE ACT B 378
13BC4SOFTWAREARG A:315 , LEU A:316 , TYR A:317 , ARG B:223 , HOH B:405 , HOH B:461BINDING SITE FOR RESIDUE ACT B 379
14BC5SOFTWARETHR B:221 , ASN B:222BINDING SITE FOR RESIDUE PEG B 380
15BC6SOFTWARETHR B:189 , LLP B:190 , GLN B:288 , TYR B:317 , HOH B:517 , HOH B:531BINDING SITE FOR RESIDUE PEG B 381
16BC7SOFTWAREPHE B:48 , MSE B:168 , ASP B:250BINDING SITE FOR RESIDUE PEG B 382
17BC8SOFTWARELYS B:264 , GLN B:280 , THR B:282 , GLU B:283 , GLN B:287BINDING SITE FOR RESIDUE PEG B 383
18BC9SOFTWARETRP B:141 , ASN B:143 , LEU B:144 , GLU B:145 , TYR B:174 , GLY B:175 , ASP B:177BINDING SITE FOR RESIDUE PGE B 384

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3JU7)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Tyr A:317 -Phe A:318
2Ser A:319 -Pro A:320
3Tyr B:317 -Phe B:318
4Ser B:319 -Pro B:320

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3JU7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3JU7)

(-) Exons   (0, 0)

(no "Exon" information available for 3JU7)

(-) 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:368
 aligned with Q739W0_BACC1 | Q739W0 from UniProtKB/TrEMBL  Length:376

    Alignment length:368
                                    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        
         Q739W0_BACC1     2 ENIPFLRASTVPVIEYLDELKEIDASHIYTNYGPINQRFEQTIMSGFFQNRGAVTTVANATLGLMAAIQLKKRKKGKYALMPSFTFPATPLAAIWCGLEPYFIDISIDDWYMDKTVLWDKIEELKEEVAIVVPYATFGSWMNLEEYEELEKKGVPVVVDAAPGFGLMNGGMHYGQDFSGMIIYSFHATKPFGIGEGGLIYSKNEEDIQRIKRMGNFGFDTNRECTMMGFNCKMSEYAAAIGIATMKKWDDKLKERTRISEWYKQLLQSNGLMKKGWQLQKTEAVIQQFMPILCPEEVRNKQVIEDLKKQKIEARLYFSPSCHQQVLFRNYKSTDLTRTNKIAKRIVSLPLWEGMTKEIVEQIVICLGQ 369
               SCOP domains d3ju7a_ A: automated matches                                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh.....eeeee.hhhhhhhhhhhhhh.....eeeee....hhhhhhhhhh..eeeee.........hhhhhhhhhhhhh..eeee...hhhhh...hhhhhhhhhh....eee.......ee..ee.......eeeee............eeeee.hhhhhhhhhhhh...................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...................eeee.....hhhhhhhhhhh...........hhhhhhhhh......hhhhhhhhhheeee......hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ju7 A   2 ENIPFLRASTVPVIEYLDELKEIDASHIYTNYGPINQRFEQTImSGFFQNRGAVTTVANATLGLmAAIQLKKRKKGKYALmPSFTFPATPLAAIWCGLEPYFIDISIDDWYmDKTVLWDKIEELKEEVAIVVPYATFGSWmNLEEYEELEKKGVPVVVDAAPGFGLmNGGmHYGQDFSGmIIYSFHATkPFGIGEGGLIYSKNEEDIQRIKRmGNFGFDTNRECTmmGFNCKmSEYAAAIGIATmKKWDDKLKERTRISEWYKQLLQSNGLmKKGWQLQKTEAVIQQFmPILCPEEVRNKQVIEDLKKQKIEARLYFSPSCHQQVLFRNYKSTDLTRTNKIAKRIVSLPLWEGmTKEIVEQIVICLGQ 369
                                    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        
                                                                      45-MSE               66-MSE          82-MSE                        113-MSE                      142-MSE                   168-MSE      181-MSE  190-LLP                 214-MSE      227-MSE  |         246-MSE                    273-MSE          290-MSE                                                          355-MSE          
                                                                                                                                                                                                    172-MSE                                                 228-MSE |                                                                                                                                       
                                                                                                                                                                                                                                                                  234-MSE                                                                                                                                   


Chain B from PDB  Type:PROTEIN  Length:368
 aligned with Q739W0_BACC1 | Q739W0 from UniProtKB/TrEMBL  Length:376

    Alignment length:368
                                    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        
         Q739W0_BACC1     2 ENIPFLRASTVPVIEYLDELKEIDASHIYTNYGPINQRFEQTIMSGFFQNRGAVTTVANATLGLMAAIQLKKRKKGKYALMPSFTFPATPLAAIWCGLEPYFIDISIDDWYMDKTVLWDKIEELKEEVAIVVPYATFGSWMNLEEYEELEKKGVPVVVDAAPGFGLMNGGMHYGQDFSGMIIYSFHATKPFGIGEGGLIYSKNEEDIQRIKRMGNFGFDTNRECTMMGFNCKMSEYAAAIGIATMKKWDDKLKERTRISEWYKQLLQSNGLMKKGWQLQKTEAVIQQFMPILCPEEVRNKQVIEDLKKQKIEARLYFSPSCHQQVLFRNYKSTDLTRTNKIAKRIVSLPLWEGMTKEIVEQIVICLGQ 369
               SCOP domains d3ju7b_ B: automated matches                                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh.....eeeee.hhhhhhhhhhhhhh.....eeeee....hhhhhhhhhh..eeeee.........hhhhhhhhhhhhh..eeee...........hhhhhhhhhhh...eee.......ee..ee.......eeeee............eeeee.hhhhhhhhhhhh...................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...................eeee.....hhhhhhhhhhhh..........hhhhhhhhh......hhhhhhhhhheeee......hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ju7 B   2 ENIPFLRASTVPVIEYLDELKEIDASHIYTNYGPINQRFEQTImSGFFQNRGAVTTVANATLGLmAAIQLKKRKKGKYALmPSFTFPATPLAAIWCGLEPYFIDISIDDWYmDKTVLWDKIEELKEEVAIVVPYATFGSWmNLEEYEELEKKGVPVVVDAAPGFGLmNGGmHYGQDFSGmIIYSFHATkPFGIGEGGLIYSKNEEDIQRIKRmGNFGFDTNRECTmmGFNCKmSEYAAAIGIATmKKWDDKLKERTRISEWYKQLLQSNGLmKKGWQLQKTEAVIQQFmPILCPEEVRNKQVIEDLKKQKIEARLYFSPSCHQQVLFRNYKSTDLTRTNKIAKRIVSLPLWEGmTKEIVEQIVICLGQ 369
                                    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        
                                                                      45-MSE               66-MSE          82-MSE                        113-MSE                      142-MSE                   168-MSE      181-MSE  190-LLP                 214-MSE      227-MSE  |         246-MSE                    273-MSE          290-MSE                                                          355-MSE          
                                                                                                                                                                                                    172-MSE                                                 228-MSE |                                                                                                                                       
                                                                                                                                                                                                                                                                  234-MSE
   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 3JU7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3JU7)

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q739W0_BACC1 | Q739W0)
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.

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 Related Entries

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