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(-) Description

Title :  CRYSTAL STRUCTURE OF D-CYCLOSERINE-BOUND FORM OF ALANINE RACEMASE FROM D-CYCLOSERINE-PRODUCING STREPTOMYCES LAVENDULAE
 
Authors :  M. Noda, Y. Matoba, T. Kumagai, M. Sugiyama
Date :  19 Apr 04  (Deposition) - 14 Sep 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Tim-Barrel, Greek-Key Motief, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Noda, Y. Matoba, T. Kumagai, M. Sugiyama
Structural Evidence That Alanine Racemase From A D-Cycloserine-Producing Microorganism Exhibits Resistance To Its Own Product.
J. Biol. Chem. V. 279 46153 2004
PubMed-ID: 15302886  |  Reference-DOI: 10.1074/JBC.M404605200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ALANINE RACEMASE
    Chains: A, B
    EC Number: 5.1.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-ALR
    Expression System Strain: BL21(DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: ALR
    Organism Scientific: STREPTOMYCES LAVENDULAE
    Organism Taxid: 1914

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2DCS2Ligand/IonD-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-N,O-CYCLOSERYLAMIDE
3KCX2Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMET A:107BINDING SITE FOR RESIDUE CL A 656
2AC2SOFTWARELYS A:38 , TYR A:42 , TRP A:84 , ARG A:136 , HIS A:168 , ASN A:208 , SER A:209 , PRO A:210 , ARG A:224 , GLY A:226 , LEU A:227 , TYR A:361 , HOH A:516 , HOH A:532 , HOH A:559 , TYR B:1270 , TYR B:1289 , ALA B:1317 , MET B:1318BINDING SITE FOR RESIDUE DCS A 401
3AC3SOFTWARETYR A:270 , TYR A:289 , ALA A:317 , MET A:318 , HOH A:509 , HOH B:502 , HOH B:581 , LYS B:1038 , TYR B:1042 , ARG B:1136 , TRP B:1166 , HIS B:1168 , ASN B:1208 , SER B:1209 , PRO B:1210 , ARG B:1224 , GLY B:1226 , LEU B:1227 , TYR B:1361BINDING SITE FOR RESIDUE DCS B 1401

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1VFS)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1VFS)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1VFS)

(-) Exons   (0, 0)

(no "Exon" information available for 1VFS)

(-) 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:383
 aligned with Q65YW7_STRLA | Q65YW7 from UniProtKB/TrEMBL  Length:378

    Alignment length:383
                                                                                                                                                                                                                                                                                                                                                                                                                 378       
                                    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     |   -   
        Q65YW7_STRLA      3 ETPTRVYAEIDLDAVRANVRALRARAPRSALMAVVKSNAYGHGAVPCARAAQEAGAAWLGTATPEEALELRAAGIQGRIMCWLWTPGGPWREAIETDIDVSVSGMWALDEVRAAARAAGRTARIQLKADTGLGRNGCQPADWAELVGAAVAAQAEGTVQVTGVWSHFACADEPGHPSIRLQLDAFRDMLAYAEKEGVDPEVRHIANSPATLTLPETHFDLVRTGLAVYGVSPSPELGTPAQLGLRPAMTLRASLALVKTVPAGHGVSYGHHYVTESETHLALVPAGYADGIPRNASGRGPVLVAGKIRRAAGRIAMDQFVVDLGEDLAEAGDEAVILGDAERGEPTAEDWAQAAHTIAYEIVTRIGGRVPRVYLGG-------    -
               SCOP domains -d1vfsa1  d1vfsa2 A:13-249 Alanine racemase                                                                                                                                                                                                            d1vfsa1 A:4-12,A:250-385 Alanine racemase                                                                                                SCOP domains
               CATH domains 1vfsA01    1vfsA02 A:14-229 Alanine racemase                                                                                                                                                                                       -------------------1vfsA01 A:3-13,A:249-385 Lyase, Ornithine Decarboxylase; Chain A, domain 1                                                                CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeehhhhhhhhhhhhh.....eeeeehhhhhhh.hhhhhhhhhhhhh..eeee.hhhhhhhhhhh....eeee.......hhhhhhhh..eeee.hhhhhhhhhhhhhhhh..eeeeee..........hhhhhhhhhhhhhhhhhh..eeeeeee..........hhhhhhhhhhhhhhhhhhhhh.....eeeeehhhhhhhhhhhh..eeeehhhhhh...hhhhh..........eeeeee..eeeee....eehhhhhee....eeeeee........hhhhh...eeee..eeee.........eeeeee........eeeee.hhhhh..hhhhhhhhh..hhhhhhhh......eeee..hhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1vfs A    3 ETPTRVYAEIDLDAVRANVRALRARAPRSALMAVVKSNAYGHGAVPCARAAQEAGAAWLGTATPEEALELRAAGIQGRIMCWLWTPGGPWREAIETDIDVSVSGMWALDEVRAAARAAGRTARIQLkADTGLGRNGCQPADWAELVGAAVAAQAEGTVQVTGVWSHFACADEPGHPSIRLQLDAFRDMLAYAEKEGVDPEVRHIANSPATLTLPETHFDLVRTGLAVYGVSPSPELGTPAQLGLRPAMTLRASLALVKTVPAGHGVSYGHHYVTESETHLALVPAGYADGIPRNASGRGPVLVAGKIRRAAGRIAMDQFVVDLGEDLAEAGDEAVILGDAERGEPTAEDWAQAAHTIAYEIVTRIGGRVPRVYLGGLEHHHHH  385
                                    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   
                                                                                                                                                        129-KCX                                                                                                                                                                                                                                                            


Chain B from PDB  Type:PROTEIN  Length:382
 aligned with Q65YW7_STRLA | Q65YW7 from UniProtKB/TrEMBL  Length:378

    Alignment length:382
                                                                                                                                                                                                                                                                                                                                                                                                                 378      
                                    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     |   -  
        Q65YW7_STRLA      3 ETPTRVYAEIDLDAVRANVRALRARAPRSALMAVVKSNAYGHGAVPCARAAQEAGAAWLGTATPEEALELRAAGIQGRIMCWLWTPGGPWREAIETDIDVSVSGMWALDEVRAAARAAGRTARIQLKADTGLGRNGCQPADWAELVGAAVAAQAEGTVQVTGVWSHFACADEPGHPSIRLQLDAFRDMLAYAEKEGVDPEVRHIANSPATLTLPETHFDLVRTGLAVYGVSPSPELGTPAQLGLRPAMTLRASLALVKTVPAGHGVSYGHHYVTESETHLALVPAGYADGIPRNASGRGPVLVAGKIRRAAGRIAMDQFVVDLGEDLAEAGDEAVILGDAERGEPTAEDWAQAAHTIAYEIVTRIGGRVPRVYLGG------    -
               SCOP domains d1vfsb1   d1vfsb2 B:1013-1249 Alanine racemase                                                                                                                                                                                                         d1vfsb1 B:1003-1012,B:1250-1384 Alanine racemase                                                                                        SCOP domains
               CATH domains 1vfsB01    1vfsB02 B:1014-1229 Alanine racemase                                                                                                                                                                                    -------------------1vfsB01 B:1003-1013,B:1249-1384 Lyase, Ornithine Decarboxylase; Chain A, domain 1                                                        CATH domains
           Pfam domains (1) ---------Ala_racemase_N-1vfsB01 B:1012-1234                                                                                                                                                                                             --------------Ala_racemase_C-1vfsB03 B:1249-1376                                                                                              -------- Pfam domains (1)
           Pfam domains (2) ---------Ala_racemase_N-1vfsB02 B:1012-1234                                                                                                                                                                                             --------------Ala_racemase_C-1vfsB04 B:1249-1376                                                                                              -------- Pfam domains (2)
         Sec.struct. author .....eeeeeehhhhhhhhhhhhhhh...eeeeehhhhhhh.hhhhhhhhhhhhh..eeee.hhhhhhhhhhh....eeee.......hhhhhhhh..eeee.hhhhhhhhhhhhhhhh..eeeeee..........hhhhhhhhhhhhhhhhhh..eeeeeee..........hhhhhhhhhhhhhhhhhhhhh.....eee..hhhhhhhhhhhh..eeeehhhhhh........hhhhhh....eeeeee..eeeee....eehhhhhee....eeeeee..hhhhh.hhhhh...eeee..eeee.........eeeeee........eeeee.hhhhh..hhhhhhhhh..hhhhhhhh......eeee..hhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1vfs B 1003 ETPTRVYAEIDLDAVRANVRALRARAPRSALMAVVKSNAYGHGAVPCARAAQEAGAAWLGTATPEEALELRAAGIQGRIMCWLWTPGGPWREAIETDIDVSVSGMWALDEVRAAARAAGRTARIQLkADTGLGRNGCQPADWAELVGAAVAAQAEGTVQVTGVWSHFACADEPGHPSIRLQLDAFRDMLAYAEKEGVDPEVRHIANSPATLTLPETHFDLVRTGLAVYGVSPSPELGTPAQLGLRPAMTLRASLALVKTVPAGHGVSYGHHYVTESETHLALVPAGYADGIPRNASGRGPVLVAGKIRRAAGRIAMDQFVVDLGEDLAEAGDEAVILGDAERGEPTAEDWAQAAHTIAYEIVTRIGGRVPRVYLGGLEHHHH 1384
                                  1012      1022      1032      1042      1052      1062      1072      1082      1092      1102      1112      1122      1132      1142      1152      1162      1172      1182      1192      1202      1212      1222      1232      1242      1252      1262      1272      1282      1292      1302      1312      1322      1332      1342      1352      1362      1372      1382  
                                                                                                                                                       1129-KCX
   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  (2, 4)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) 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   (Q65YW7_STRLA | Q65YW7)
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
        Q65YW7_STRLA | Q65YW7: 1vfh 1vft

(-) Related Entries Specified in the PDB File

1vfh THE SAME PROTEIN WITH PYRIDOXAL-5'-PHOSPHATE
1vft THE SAME PROTEIN, L-CYCLOSERINE-BOUND FORM