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(-) Description

Title :  CRYSTAL STRUCTURE OF ALANINE RACEMASE FROM D-CYCLOSERINE PRODUCING STREPTOMYCES LAVENDULAE
 
Authors :  M. Noda, Y. Matoba, T. Kumagai, M. Sugiyama
Date :  13 Apr 04  (Deposition) - 14 Sep 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
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 T 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
    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

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1KCX1Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID
2PLP1Ligand/IonPYRIDOXAL-5'-PHOSPHATE
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1KCX2Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID
2PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:38 , TYR A:42 , TRP A:84 , ARG A:136 , TRP A:166 , HIS A:168 , SER A:209 , PRO A:210 , ARG A:224 , GLY A:226 , LEU A:227 , TYR A:361 , HOH A:508 , HOH A:526BINDING SITE FOR RESIDUE PLP A 401

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1VFH)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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  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: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 d1vfha1   d1vfha2 A:13-249 Alanine racemase                                                                                                                                                                                                            d1vfha1 A:3-12,A:250-384 Alanine racemase                                                                                               SCOP domains
               CATH domains 1vfhA01    1vfhA02 A:14-229 Alanine racemase                                                                                                                                                                                       -------------------1vfhA01 A:3-13,A:249-384 Lyase, Ornithine Decarboxylase; Chain A, domain 1                                                               CATH domains
               Pfam domains ---------Ala_racemase_N-1vfhA01 A:12-234                                                                                                                                                                                                --------------Ala_racemase_C-1vfhA02 A:249-376                                                                                                -------- Pfam domains
     Sec.struct. author (1) .....------hhhhhhhhhhhhhhh...eeeeehhhhhhhhhhhhhhhhhhhhhh.-----hhhhhhhhhhh....eeee.......hhhhhhhh..eeee.hhhhhhhhhhhhhhhh..eeeeee..........hhhhhhhhhhhhhhhhhh....eeeee..........hhhhhhhhhhhhhhhhhhhhh.....eee..hhhhhhhhhhhh..eeeehhhhhh...hhhhhhhhhhh....eeeeee..eeeee....eehhhhhee....eeeeee........hhhhh...eee....eeeee.......eeeeee........eeeee.hhhhh..hhhhhhhhh..hhhhhhhh......eeee..hhhhh. Sec.struct. author (1)
     Sec.struct. author (2) -----eeeeeeee--------------------------------------------eeeeee------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Sec.struct. author (2)
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vfh A   3 ETPTRVYAEIDLDAVRANVRALRARAPRSALMAVVKSNAYGHGAVPCARAAQEAGAAWLGTATPEEALELRAAGIQGRIMCWLWTPGGPWREAIETDIDVSVSGMWALDEVRAAARAAGRTARIQLkADTGLGRNGCQPADWAELVGAAVAAQAEGTVQVTGVWSHFACADEPGHPSIRLQLDAFRDMLAYAEKEGVDPEVRHIANSPATLTLPETHFDLVRTGLAVYGVSPSPELGTPAQLGLRPAMTLRASLALVKTVPAGHGVSYGHHYVTESETHLALVPAGYADGIPRNASGRGPVLVAGKIRRAAGRIAMDQFVVDLGEDLAEAGDEAVILGDAERGEPTAEDWAQAAHTIAYEIVTRIGGRVPRVYLGGLEHHHH 384
                                    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
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 Classification and Annotation

(-) SCOP Domains  (2, 2)

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

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (2, 2)

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

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A   (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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  1vfh
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 Related Entries

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

UniProtKB/TrEMBL
        Q65YW7_STRLA | Q65YW7: 1vfs 1vft

(-) Related Entries Specified in the PDB File

1vfs THE SAME PROTEIN, D-CYCLOSERINE-BOUND FORM
1vft THE SAME PROTEIN, L-CYCLOSERINE-BOUND FORM