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(-) Description

Title :  STRUCTURE OF VIBRIO CHOLERAE BROAD SPECTRUM RACEMASE DOUBLE MUTANT R173A, N174A
 
Authors :  C. Carrasco-Lopez, J. A. Hermoso
Date :  12 Mar 13  (Deposition) - 15 Jan 14  (Release) - 09 Jul 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Espaillat, C. Carrasco-Lopez, N. Bernardo-Garcia, N. Pietrosemoli, L. H. Otero, L. Alvarez, M. A. De Pedro, F. Pazos, B. M. Davis, M. K. Waldor, J. A. Hermoso, F. Cava
Structural Basis For The Broad Specificity Of A New Family Of Amino-Acid Racemases.
Acta Crystallogr. , Sect. D V. 70 79 2014
PubMed-ID: 24419381  |  Reference-DOI: 10.1107/S1399004713024838

(-) Compounds

Molecule 1 - ALANINE RACEMASE 2
    Atcc: 39315
    Chains: A
    EC Number: 5.1.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: VIBRIO CHOLERAE
    Organism Taxid: 666

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1PLP1Ligand/IonPYRIDOXAL-5'-PHOSPHATE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:74 , TYR A:78 , VAL A:120 , HIS A:204 , SER A:245 , ARG A:260 , GLY A:262 , GLY A:263 , HOH A:2167 , HOH A:2264 , HOH A:2265 , HOH A:2299 , HOH A:2339 , HOH A:2397BINDING SITE FOR RESIDUE PLP A1350

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:70 -A:96

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4BEQ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ALANINE_RACEMASEPS00395 Alanine racemase pyridoxal-phosphate attachment site.ALR2_VIBCH56-66  1A:71-81
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ALANINE_RACEMASEPS00395 Alanine racemase pyridoxal-phosphate attachment site.ALR2_VIBCH56-66  2A:71-81

(-) Exons   (0, 0)

(no "Exon" information available for 4BEQ)

(-) Sequences/Alignments

Asymmetric 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:386
 aligned with ALR2_VIBCH | Q9KSE5 from UniProtKB/Swiss-Prot  Length:392

    Alignment length:386
                                                                                                                                                                                                                                                                                                                                                                                                                         392  
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388   |  
           ALR2_VIBCH     9 APLHIDTALPDAAQIQQSNSWLEISLGQFQSNIEQFKSHMNANTKICAIMKADAYGNGIRGLMPTIIAQGIPCVGVASNAEARAVRESGFKGELIRVRSASLSEMSSALDLNIEELIGTHQQALDLAELAKQSGKTLKVHIALNDGGMGRNGIDMTTEAGKKEAVSIATQPSLSVVGIMTHFPNYNADEVRAKLAQFKESSTWLMQQANLKREEITLHVANSYTALNVPEAQLDMVRPGGVLFGDLPTNPEYPSIVSFKTRVSSLHHLPKDSTVGYDSTFTTSRDSVLANLPVGYSDGYPRKMGNKAEVLINGQRAKVVGVTSMNTTVVDVTEIKGVLPGQEVVLFGQQQKQSIAVSEMENNAELIFPELYTLWGTSNPRFYVK--   -
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhh..eeeeeehhhhhhhhhhhhh......eeeeehhhhhhh.hhhhhhhhhhhh...eeee.hhhhhhhhhhh....eeee....hhhhhhhhhhh.eeeee.hhhhhhhhhhhhhhhh..eeeeee..............hhhhhhhhhhhhh...eeeeeee......hhhhhhhhhhhhhhhhhhhhhhh..hhhhheeeeehhhhhhhhhhhh..ee...................eeeeee..eeeee....eehhhhhee....eeeeee..hhhhh.hhhhh...eeee..eeee.........eeee...........eeeee.ee..ee.hhhhhhhhhh.hhhhhhhhhhhhh.eeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------ALANINE_RAC---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4beq A  24 APLHIDTALPDAAQIQQSNSWLEISLGQFQSNIEQFKSHMNANTKICAIMKADAYGNGIRGLMPTIIAQGIPCVGVASNAEARAVRESGFKGELIRVRSASLSEMSSALDLNIEELIGTHQQALDLAELAKQSGKTLKVHIALNDGGMGAAGIDMTTEAGKKEAVSIATQPSLSVVGIMTHFPNYNADEVRAKLAQFKESSTWLMQQANLKREEITLHVANSYTALNVPEAQLDMVRPGGVLFGDLPTNPEYPSIVSFKTRVSSLHHLPKDSTVGYDSTFTTSRDSVLANLPVGYSDGYPRKMGNKAEVLINGQRAKVVGVTSMNTTVVDVTEIKGVLPGQEVVLFGQQQKQSIAVSEMENNAELIFPELYTLWGTSNPRFYVKSS 409
                                    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       393       403
   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 4BEQ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A   (ALR2_VIBCH | Q9KSE5)
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.
    GO:0009252    peptidoglycan biosynthetic process    The chemical reactions and pathways resulting in the formation of peptidoglycans, any of a class of glycoconjugates found in bacterial cell walls.

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 Related Entries

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

UniProtKB/Swiss-Prot
        ALR2_VIBCH | Q9KSE5: 4beu

(-) Related Entries Specified in the PDB File

4be4 CLOSED CONFORMATION OF O. PICEAE STEROL ESTERASE
4be9 OPEN CONFORMATION OF O. PICEAE STEROL ESTERASE
4beu STRUCTURE OF VIBRIO CHOLERAE BROAD SPECTRUM RACEMASE