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(-) Description

Title :  STRUCTURE OF BROAD SPECTRUM RACEMASE FROM AEROMONAS HYDROPHILA
 
Authors :  C. Carrasco-Lopez, J. A. Hermoso
Date :  15 Mar 13  (Deposition) - 15 Jan 14  (Release) - 09 Jul 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.45
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Isomerase, D-Amino Acids (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
    Atcc7966
    ChainsA, B
    EC Number5.1.1.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VectorPET28B
    Expression System Vector TypePLASMID
    Organism ScientificAEROMONAS HYDROPHILA SUBSP. HYDROPHILA
    Organism Taxid196023
    SynonymBROAD SPECTRUM RACEMASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 33)

Asymmetric/Biological Unit (4, 33)
No.NameCountTypeFull Name
1CL23Ligand/IonCHLORIDE ION
2GOL7Ligand/IonGLYCEROL
3NI1Ligand/IonNICKEL (II) ION
4PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE

(-) Sites  (28, 28)

Asymmetric Unit (28, 28)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:74 , TYR A:78 , HIS A:204 , SER A:245 , ARG A:260 , GLY A:262 , GLY A:263 , HOH A:2173 , HOH A:2291 , HOH A:2301BINDING SITE FOR RESIDUE PLP A1350
02AC2SOFTWAREHIS A:417 , HOH A:2403 , HOH A:2404 , LYS B:74 , TYR B:78 , VAL B:120 , ARG B:173 , HIS B:204 , SER B:245 , ARG B:260 , GLY B:262 , GLY B:263 , HOH B:2168 , HOH B:2255 , HOH B:2385BINDING SITE FOR RESIDUE PLP B1350
03AC3SOFTWARETYR A:24 , HOH A:2002 , ASN B:33 , GLY B:399 , TYR B:400 , ASN B:402 , LYS B:404 , HOH B:2108 , HOH B:2109 , HOH B:2426BINDING SITE FOR RESIDUE GOL B1418
04AC4SOFTWAREALA A:39 , SER A:40 , ASN A:41 , PRO A:403 , HOH A:2051 , ALA B:22 , SER B:101 , ASN B:102 , GLU B:103 , GLU B:127BINDING SITE FOR RESIDUE GOL B1419
05AC5SOFTWAREARG A:173 , ASN A:174 , HIS A:204BINDING SITE FOR RESIDUE CL A1418
06AC6SOFTWAREARG B:173 , ASN B:174 , HIS B:204BINDING SITE FOR RESIDUE CL B1420
07AC7SOFTWAREARG A:324BINDING SITE FOR RESIDUE CL A1419
08AC8SOFTWAREHOH A:2080BINDING SITE FOR RESIDUE CL A1421
09AC9SOFTWAREASP A:253BINDING SITE FOR RESIDUE CL A1422
10BC1SOFTWAREARG A:109BINDING SITE FOR RESIDUE CL A1423
11BC2SOFTWAREGLY A:337 , HOH A:2214 , HOH A:2218BINDING SITE FOR RESIDUE CL A1424
12BC3SOFTWAREASP B:253BINDING SITE FOR RESIDUE CL B1421
13BC4SOFTWARELYS B:210 , HOH B:2299BINDING SITE FOR RESIDUE CL B1422
14BC5SOFTWAREGLY A:49 , ARG A:408 , SER B:272BINDING SITE FOR RESIDUE CL B1423
15BC6SOFTWAREHIS B:414 , HIS B:416 , NI B:1430BINDING SITE FOR RESIDUE CL B1424
16BC7SOFTWAREGLU A:129 , GLN A:130BINDING SITE FOR RESIDUE CL A1425
17BC8SOFTWAREILE B:69 , HOH B:2076 , HOH B:2096BINDING SITE FOR RESIDUE CL B1426
18BC9SOFTWAREHOH B:2004BINDING SITE FOR RESIDUE CL A1426
19CC1SOFTWAREHOH B:2146BINDING SITE FOR RESIDUE CL B1427
20CC2SOFTWAREARG B:324 , TRP B:398 , GOL B:1432 , HOH B:2427BINDING SITE FOR RESIDUE CL B1428
21CC3SOFTWAREHOH B:2195BINDING SITE FOR RESIDUE CL B1429
22CC4SOFTWAREHIS B:414 , HIS B:416 , CL B:1424BINDING SITE FOR RESIDUE NI B1430
23CC5SOFTWAREALA A:22 , SER A:101 , ASN A:102 , GLU A:103 , GLU A:127 , HOH A:2499 , ALA B:39 , SER B:40 , ASN B:41 , PRO B:403BINDING SITE FOR RESIDUE GOL A1428
24CC6SOFTWAREVAL A:289 , TRP A:311 , VAL A:355 , LEU A:358 , LYS A:359 , GLY A:360 , VAL A:361 , HOH A:2500BINDING SITE FOR RESIDUE GOL A1430
25CC7SOFTWARETYR A:332 , LYS A:339 , ALA A:376 , GLU A:377 , HOH A:2501BINDING SITE FOR RESIDUE GOL A1431
26CC8SOFTWAREARG B:116BINDING SITE FOR RESIDUE CL B1431
27CC9SOFTWAREARG B:324 , ARG B:325 , ALA B:326 , ASN B:329 , MET B:394 , CL B:1428 , HOH B:2408BINDING SITE FOR RESIDUE GOL B1432
28DC1SOFTWARELYS B:359 , GLY B:360 , HOH B:2428BINDING SITE FOR RESIDUE GOL B1433

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:70 -A:96
2B:70 -B:96

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ser A:410 -Gly A:411
2Gly A:411 -His A:412

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4BF5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4BF5)

(-) Exons   (0, 0)

(no "Exon" information available for 4BF5)

(-) 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:396
 aligned with A0KLG5_AERHH | A0KLG5 from UniProtKB/TrEMBL  Length:408

    Alignment length:396
                                                                                                                                                                                                                                                                                                                                                                                                                            408         
                                    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       371       381       391       401      |  -      
         A0KLG5_AERHH    22 APYLPLASDHRNGEVQTASNAWLEVDLGAFEHNIQTLKDRLGDKGPKICAIMKADAYGHGIDLLVPSVVKAGIPCIGIASNEEARVAREKGFTGRLMRVRAATPAEVEQALPYKMEELIGSLVSAQGIADIAQRHHTNIPVHIALNSAGMSRNGIDLRLADSKEDALAMLKLKGITPVGIMTHFPVEEKEDVKMGLAQFKLDSQWLLEAGKLDRSKITIHAANSFATLEVPDAYFDMVRPGGLLYGDSIPSYTEYKRVMAFKTQVASVNHYPAGNTVGYDRTFTLKRDSWLANLPLGYSDGYRRALSNKAYVLIQGQKVPVVGKTSMNTIMVDVTDLKGVKPGDEVVLFGRQGEAEVKQADLEEYNGALLADMYTIWGYTNPKKIKR---------   -
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....................eeeeeehhhhhhhhhhhhhhhh....eeeeehhhhhhh.hhhhhhhhhhhhh..eeee.hhhhhhhhhhh....eeee....hhhhhhhhhhhh..eee.hhhhhhhhhhhhhhh...eeeeee..............hhhhhhhhhhhhh...eeeeeee......hhhhhhhhhhhhhhhhhhhhhhh..hhhhheee..hhhhhhhhhhhh..ee..hhhhhh............eeeeee..eeeee....eehhhhhee....eeeeee..hhhhh.........eeee..eeeeee.......eeee...........eeeeeeee..eeehhhhhhhhhh..hhhhhhhhhhhh.eeee.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4bf5 A  22 APYLPLASDHRNGEVQTASNAWLEVDLGAFEHNIQTLKDRLGDKGPKICAIMKADAYGHGIDLLVPSVVKAGIPCIGIASNEEARVAREKGFTGRLMRVRAATPAEVEQALPYKMEELIGSLVSAQGIADIAQRHHTNIPVHIALNSAGMSRNGIDLRLADSKEDALAMLKLKGITPVGIMTHFPVEEKEDVKMGLAQFKLDSQWLLEAGKLDRSKITIHAANSFATLEVPDAYFDMVRPGGLLYGDSIPSYTEYKRVMAFKTQVASVNHYPAGNTVGYDRTFTLKRDSWLANLPLGYSDGYRRALSNKAYVLIQGQKVPVVGKTSMNTIMVDVTDLKGVKPGDEVVLFGRQGEAEVKQADLEEYNGALLADMYTIWGYTNPKKIKRSSGHHHHHH 417
                                    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       371       381       391       401       411      

Chain B from PDB  Type:PROTEIN  Length:396
 aligned with A0KLG5_AERHH | A0KLG5 from UniProtKB/TrEMBL  Length:408

    Alignment length:396
                                                                                                                                                                                                                                                                                                                                                                                                                            408         
                                    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       371       381       391       401      |  -      
         A0KLG5_AERHH    22 APYLPLASDHRNGEVQTASNAWLEVDLGAFEHNIQTLKDRLGDKGPKICAIMKADAYGHGIDLLVPSVVKAGIPCIGIASNEEARVAREKGFTGRLMRVRAATPAEVEQALPYKMEELIGSLVSAQGIADIAQRHHTNIPVHIALNSAGMSRNGIDLRLADSKEDALAMLKLKGITPVGIMTHFPVEEKEDVKMGLAQFKLDSQWLLEAGKLDRSKITIHAANSFATLEVPDAYFDMVRPGGLLYGDSIPSYTEYKRVMAFKTQVASVNHYPAGNTVGYDRTFTLKRDSWLANLPLGYSDGYRRALSNKAYVLIQGQKVPVVGKTSMNTIMVDVTDLKGVKPGDEVVLFGRQGEAEVKQADLEEYNGALLADMYTIWGYTNPKKIKR---------   -
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....................eeeeehhhhhhhhhhhhhhhhh....eeeeehhhhhhh.hhhhhhhhhhhh...eeee.hhhhhhhhhhh....eeee....hhhhhhhhhhhh..eee.hhhhhhhhhhhhhhh...eeeeee..............hhhhhhhhhhhhh...eeeeeee......hhhhhhhhhhhhhhhhhhhhhhh..hhhhheee..hhhhhhhhhhhh..ee..hhhhhh............eeeeee..eeeee....eehhhhhee....eeeeee..hhhhh.........eeee..eeeeee.......eeee...........eeeeeeee..eeehhhhhh.....hhhhhhhhhhhhh.eee.hhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4bf5 B  22 APYLPLASDHRNGEVQTASNAWLEVDLGAFEHNIQTLKDRLGDKGPKICAIMKADAYGHGIDLLVPSVVKAGIPCIGIASNEEARVAREKGFTGRLMRVRAATPAEVEQALPYKMEELIGSLVSAQGIADIAQRHHTNIPVHIALNSAGMSRNGIDLRLADSKEDALAMLKLKGITPVGIMTHFPVEEKEDVKMGLAQFKLDSQWLLEAGKLDRSKITIHAANSFATLEVPDAYFDMVRPGGLLYGDSIPSYTEYKRVMAFKTQVASVNHYPAGNTVGYDRTFTLKRDSWLANLPLGYSDGYRRALSNKAYVLIQGQKVPVVGKTSMNTIMVDVTDLKGVKPGDEVVLFGRQGEAEVKQADLEEYNGALLADMYTIWGYTNPKKIKRSSGHHHHHH 417
                                    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       371       381       391       401       411      

   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 4BF5)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4BF5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4BF5)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (A0KLG5_AERHH | A0KLG5)
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 Specified in the PDB File

4beq STRUCTURE OF VIBRIO CHOLERAE BROAD SPECTRUM RACEMASE DOUBLE MUTANT R173A, N174A
4beu STRUCTURE OF VIBRIO CHOLERAE BROAD SPECTRUM RACEMASE