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(-) Description

Title :  THE CRYSTAL STRUCTURE OF ALANINE RACEMASE FROM BACILLUS ANTHRACIS (BA0252)
 
Authors :  K. Au, J. Ren, T. S. Walter, K. Harlos, J. E. Nettleship, R. J. Owens, D. I. R. M. Esnouf, Oxford Protein Production Facility (Oppf), Struct Proteomics In Europe (Spine)
Date :  01 Oct 07  (Deposition) - 20 May 08  (Release) - 06 May 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.47
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Pyridoxal 5'-Phosphate, Peptidoglycan Synthesis, Plp, Oppf, L-Alanine, Isomerase, D- Alanine, Pyridoxal Phosphate, Structural Genomics, Alanine Racemase, Spore Germination, Oxford Protein Production Facility, Structural Proteomics In Europe (Spine) (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Au, J. Ren, T. S. Walter, K. Harlos, J. E. Nettleship, R. J. Owens, D. I. Stuart, R. M. Esnouf
Structures Of An Alanine Racemase From Bacillus Anthracis (Ba0252) In The Presence And Absence Of (R)-1-Aminoethylphosphonic Acid (L-Ala-P).
Acta Crystallogr. , Sect. F V. 64 327 2008
PubMed-ID: 18453697  |  Reference-DOI: 10.1107/S1744309108007252

(-) Compounds

Molecule 1 - ALANINE RACEMASE
    Chains: A, B
    EC Number: 5.1.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: ROSETTA PLYSS
    Expression System Vector: POPINB
    Organism Scientific: BACILLUS ANTHRACIS
    Organism Taxid: 198094
    Other Details: PLP FORMS IMINO LINKAGE TO K41. ALL LYSINES DIMETHYLATED EXCEPT K41 AND K260
    Strain: AMES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 45)

Asymmetric/Biological Unit (4, 45)
No.NameCountTypeFull Name
1CL3Ligand/IonCHLORIDE ION
2MG4Ligand/IonMAGNESIUM ION
3MLY36Mod. Amino AcidN-DIMETHYL-LYSINE
4PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:161 , HOH A:2271 , HOH A:2273 , HOH A:2274 , HOH B:2218 , HOH B:2221BINDING SITE FOR RESIDUE MG B1001
2AC2SOFTWAREHOH A:2455 , GLY B:306 , ASP B:342 , GLU B:343 , HOH B:2406 , HOH B:2410BINDING SITE FOR RESIDUE MG B1002
3AC3SOFTWAREHOH A:2158 , HOH A:2159 , HOH A:2160 , HOH A:2404 , HOH A:2405BINDING SITE FOR RESIDUE MG B1003
4AC4SOFTWAREASP A:17 , HOH A:2033 , HOH A:2034 , HOH A:2035 , HOH A:2539 , HOH B:2388BINDING SITE FOR RESIDUE MG A1390
5AC5SOFTWAREARG A:144 , GLN A:216 , HOH A:2247 , HOH A:2249BINDING SITE FOR RESIDUE CL A1391
6AC6SOFTWAREASN A:131 , ARG A:138BINDING SITE FOR RESIDUE CL A1392
7AC7SOFTWAREASN B:131 , ARG B:138BINDING SITE FOR RESIDUE CL B1390

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2VD8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2VD8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2VD8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2VD8)

(-) Exons   (0, 0)

(no "Exon" information available for 2VD8)

(-) 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:387
 aligned with Q81VF6_BACAN | Q81VF6 from UniProtKB/TrEMBL  Length:389

    Alignment length:387
                                    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       362       372       382       
         Q81VF6_BACAN     3 EAPFYRDTWVEVDLDAIYNNVTHIKEFIPSDVEIFAVVKGNAYGHDYVPVAKIALEAGATRLAVAFLDEALVLRRAGITAPILVLGPSPPRDINVAAENDVALTVFQKEWVDEAIKLWDGSSTMKYHINFDSGMGRIGIRERKELKGFLKSLEGAPFLELEGVYTHFATADEVETSYFDKQYNTFLEQLSWLKEFGVDPKFVHTANSAATLRFQGITFNAVRIGIAMYGLSPSVEIRPFLPFKLEPALSLHTKVAHIKQVIKGDGISYNVTYRTKTEEWIATVAIGYADGWLRRLQGFEVLVNGKRVPIVGRVTMDQFMIHLPCEVPLGTKVTLIGRQGDEYISATEVAEYSGTINYEIITTISFRVPRIFIRNGKVVEVINYLNDI 389
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2vd8A01      2vd8A02 A:16-229 Alanine racemase                                                                                                                                                                                     -------------------2vd8A01 A:3-15,A:249-389 Lyase, Ornithine Decarboxylase; Chain A, domain 1                                                                    CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhhhhhhhhhhh....eeeeehhhhhhh.hhhhhhhhhhhh...eeee.hhhhhhhhhhh.....eee....hhhhhhhhhhh.eeee..hhhhhhhhhhhh.....eeeeee...........hhhhhhhhhhhhh....eeeeeee..........hhhhhhhhhhhhhhhhhhhhh......ee..hhhhhh........eeee............hhhhh.......eeeeeeeeeeeee....eehhhhhee....eeeeee..hhhhh.hhhhh..eeee..eeeeee.......eeeee........eeeeeeee..eeehhhhhhhhh..hhhhhhhh...................hhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vd8 A   3 EAPFYRDTWVEVDLDAIYNNVTHIkEFIPSDVEIFAVVKGNAYGHDYVPVAkIALEAGATRLAVAFLDEALVLRRAGITAPILVLGPSPPRDINVAAENDVALTVFQkEWVDEAIkLWDGSSTMkYHINFDSGMGRIGIRERkELkGFLkSLEGAPFLELEGVYTHFATADEVETSYFDkQYNTFLEQLSWLkEFGVDPkFVHTANSAATLRFQGITFNAVRIGIAMYGLSPSVEIRPFLPFkLEPALSLHTkVAHIKQVIkGDGISYNVTYRTkTEEWIATVAIGYADGWLRRLQGFEVLVNGkRVPIVGRVTMDQFMIHLPCEVPLGTkVTLIGRQGDEYISATEVAEYSGTINYEIITTISFRVPRIFIRNGkVVEVINYLNDI 389
                                    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       362       372     | 382       
                                                   27-MLY                     54-MLY                                                 110-MLY 118-MLY  127-MLY           145-MLY  |                           182-MLY      195-MLY  |                                        245-MLY   255-MLY  264-MLY      277-MLY                       307-MLY                   333-MLY                                      378-MLY       
                                                                                                                                                                           148-MLY                                               202-MLY                                                                                                                                                                                       
                                                                                                                                                                               152-MLY                                                                                                                                                                                                                                         


Chain B from PDB  Type:PROTEIN  Length:386
 aligned with Q81VF6_BACAN | Q81VF6 from UniProtKB/TrEMBL  Length:389

    Alignment length:386
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383      
         Q81VF6_BACAN     4 APFYRDTWVEVDLDAIYNNVTHIKEFIPSDVEIFAVVKGNAYGHDYVPVAKIALEAGATRLAVAFLDEALVLRRAGITAPILVLGPSPPRDINVAAENDVALTVFQKEWVDEAIKLWDGSSTMKYHINFDSGMGRIGIRERKELKGFLKSLEGAPFLELEGVYTHFATADEVETSYFDKQYNTFLEQLSWLKEFGVDPKFVHTANSAATLRFQGITFNAVRIGIAMYGLSPSVEIRPFLPFKLEPALSLHTKVAHIKQVIKGDGISYNVTYRTKTEEWIATVAIGYADGWLRRLQGFEVLVNGKRVPIVGRVTMDQFMIHLPCEVPLGTKVTLIGRQGDEYISATEVAEYSGTINYEIITTISFRVPRIFIRNGKVVEVINYLNDI 389
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2vd8B01     2vd8B02 B:16-229 Alanine racemase                                                                                                                                                                                     -------------------2vd8B01 B:4-15,B:249-389 Lyase, Ornithine Decarboxylase; Chain A, domain 1                                                                    CATH domains
           Pfam domains (1) ----------Ala_racemase_N-2vd8B01 B:14-234                                                                                                                                                                                              --------------Ala_racemase_C-2vd8B03 B:249-374                                                                                              --------------- Pfam domains (1)
           Pfam domains (2) ----------Ala_racemase_N-2vd8B02 B:14-234                                                                                                                                                                                              --------------Ala_racemase_C-2vd8B04 B:249-374                                                                                              --------------- Pfam domains (2)
         Sec.struct. author .......eeeeehhhhhhhhhhhhhhh....eeeeehhhhhhh.hhhhhhhhhhhhh..eeee.hhhhhhhhhhh.....eee....hhhhhhhhhhh..eee..hhhhhhhhhhhh.....eeeeee...........hhhhhhhhhhhhh....eeeeeee..........hhhhhhhhhhhhhhhhhhhhh......ee..hhhhhhhh......eeee............hhhhh.......eeeeeeeeeeeee....eehhhhhee............hhhhh.hhhhh..................................eeeeeeee..eeehhhhhhhhhh.hhhhhhhh......eeeee..eeeeeehhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vd8 B   4 APFYRDTWVEVDLDAIYNNVTHIkEFIPSDVEIFAVVKGNAYGHDYVPVAkIALEAGATRLAVAFLDEALVLRRAGITAPILVLGPSPPRDINVAAENDVALTVFQkEWVDEAIkLWDGSSTMkYHINFDSGMGRIGIRERkELkGFLkSLEGAPFLELEGVYTHFATADEVETSYFDkQYNTFLEQLSWLkEFGVDPkFVHTANSAATLRFQGITFNAVRIGIAMYGLSPSVEIRPFLPFkLEPALSLHTkVAHIKQVIkGDGISYNVTYRTkTEEWIATVAIGYADGWLRRLQGFEVLVNGkRVPIVGRVTMDQFMIHLPCEVPLGTkVTLIGRQGDEYISATEVAEYSGTINYEIITTISFRVPRIFIRNGkVVEVINYLNDI 389
                                    13        23   |    33        43        53|       63        73        83        93       103      |113    |  123   |   133       143 |  |  153       163       173       183       193 |     203       213       223       233       243 |     253 |     263|      273   |   283       293       303   |   313       323       333       343       353       363       373    |  383      
                                                  27-MLY                     54-MLY                                                 110-MLY 118-MLY  127-MLY           145-MLY  |                           182-MLY      195-MLY  |                                        245-MLY   255-MLY  264-MLY      277-MLY                       307-MLY                   333-MLY                                      378-MLY       
                                                                                                                                                                          148-MLY                                               202-MLY                                                                                                                                                                                       
                                                                                                                                                                              152-MLY
   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  (0, 0)

(no "SCOP Domain" information available for 2VD8)

(-) CATH Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: TIM_barrel (694)
(-)
Clan: no clan defined [family: Ala_racemase_C] (18)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q81VF6_BACAN | Q81VF6)
molecular function
    GO:0008784    alanine racemase activity    Catalysis of the reaction: L-alanine = D-alanine.
    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:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
    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.
biological process
    GO:0030632    D-alanine biosynthetic process    The chemical reactions and pathways resulting in the formation of D-alanine, the D-enantiomer of the amino acid alanine, i.e (2R)-2-aminopropanoic acid.
    GO:0006522    alanine metabolic process    The chemical reactions and pathways involving alanine, 2-aminopropanoic acid.

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 Related Entries

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

UniProtKB/TrEMBL
        Q81VF6_BACAN | Q81VF6: 2vd9 3ha1

(-) Related Entries Specified in the PDB File

2vd9 THE CRYSTAL STRUCTURE OF ALANINE RACEMASE FROM BACILLUS ANTHRACIS (BA0252) WITH BOUND L-ALA-P