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(-) Description

Title :  ALANINE RACEMASE COMPLEXED WITH ALANINE PHOSPHONATE
 
Authors :  G. F. Stamper, A. A. Morollo, D. Ringe
Date :  12 May 98  (Deposition) - 14 Oct 98  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Alanine, Isomerase, Pyridoxal Phosphate, Alanine Phosphonate (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. F. Stamper, A. A. Morollo, D. Ringe, C. G. Stamper
Reaction Of Alanine Racemase With 1-Aminoethylphosphonic Acid Forms A Stable External Aldimine.
Biochemistry V. 37 10438 1998
PubMed-ID: 9671513  |  Reference-DOI: 10.1021/BI980692S
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ALANINE RACEMASE
    Chains: A, B
    EC Number: 5.1.1.1
    Organism Scientific: GEOBACILLUS STEAROTHERMOPHILUS
    Organism Taxid: 1422
    Plasmid: PMDALR3
    Strain: XL-1 BLUE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1IN52Ligand/Ion{1-[(3-HYDROXY-METHYL-5-PHOSPHONOOXY-METHYL-PYRIDIN-4-YLMETHYL)-AMINO]-ETHYL}-PHOSPHONIC ACID

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:39 , TYR A:43 , ARG A:136 , HIS A:166 , ASN A:203 , SER A:204 , ARG A:219 , GLY A:221 , ILE A:222 , TYR A:354 , HOH A:433 , HOH A:450 , HOH A:459 , HOH A:461 , HOH A:490 , TYR B:265 , TYR B:284 , CYS B:311 , MET B:312BINDING SITE FOR RESIDUE IN5 A 389
2AC2SOFTWARETYR A:265 , TYR A:284 , CYS A:311 , MET A:312 , ASP A:313 , LYS B:39 , TYR B:43 , ARG B:136 , HIS B:166 , ASN B:203 , SER B:204 , ARG B:219 , GLY B:221 , ILE B:222 , TYR B:354 , HOH B:392 , HOH B:402 , HOH B:404 , HOH B:446 , HOH B:484BINDING SITE FOR RESIDUE IN5 B 389
3CICUNKNOWNLYS A:39 , TYR A:265LYS 39 AND TYR 265 (FROM THE OTHER SUBUNIT) ARE PROPOSED CATALYTIC RESIDUES IN THE ACTIVE SITE OF THE MOLECULE.

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1BD0)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gly A:120 -Pro A:121
2Gly B:120 -Pro B:121

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1BD0)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ALANINE_RACEMASEPS00395 Alanine racemase pyridoxal-phosphate attachment site.ALR_GEOSE36-46
 		  2A:36-46
B:36-46

(-) Exons   (0, 0)

(no "Exon" information available for 1BD0)

(-) 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:381
 aligned with ALR_GEOSE | P10724 from UniProtKB/Swiss-Prot  Length:388

    Alignment length:381
                                    11        21        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 
            ALR_GEOSE     2 NDFHRDTWAEVDLDAIYDNVENLRRLLPDDTHIMAVVKANAYGHGDVQVARTALEAGASRLAVAFLDEALALREKGIEAPILVLGASRPADAALAAQQRIALTVFRSDWLEEASALYSGPFPIHFHLKMDTGMGRLGVKDEEETKRIVALIERHPHFVLEGLYTHFATADEVNTDYFSYQYTRFLHMLEWLPSRPPLVHCANSAASLRFPDRTFNMVRFGIAMYGLAPSPGIKPLLPYPLKEAFSLHSRLVHVKKLQPGEKVSYGATYTAQTEEWIGTIPIGYADGWLRRLQHFHVLVDGQKAPIVGRICMDQCMIRLPGPLPVGTKVTLIGRQGDEVISIDDVARHLETINYEVPCTISYRVPRIFFRHKRIMEVRNAIG 382
               SCOP domains d1bd0a1   d1bd0a2 A:12-244 Alanine racemase                                                                                                                                                                                                        d1bd0a1 A:2-11,A:245-382 Alanine racemase                                                                                                  SCOP domains
               CATH domains 1bd0A02     1bd0A01 A:14-224 Alanine racemase                                                                                                                                                                                  -------------------1bd0A02 A:2-13,A:244-382 Lyase, Ornithine Decarboxylase; Chain A, domain 1                                                                  CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeehhhhhhhhhhhhhh.....eeeee.hhhhhh..hhhhhhhhhhh...eeee..hhhhhhhhh.....eeee.....hhhhhhhhh..eeeee..hhhhhhhh........eeeeee............hhhhhhhhhhhhh...eeeeeee...........hhhhhhhhhhhhhhhh......eee...hhhhhh.......eeee.hhhh........hhh........eeeeeeeeeeeee.......hhh.......eeeeee...hhh...hhhhh.eeee..eeee.........eeee.........eeeeeeee..eee.hhhhhhhh...hhhhhhh.....eeeeee..eeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------ALANINE_RAC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1bd0 A   2 NDFHRDTWAEVDLDAIYDNVENLRRLLPDDTHIMAVVKANAYGHGDVQVARTALEAGASRLAVAFLDEALALREKGIEAPILVLGASRPADAALAAQQRIALTVFRSDWLEEASALYSGPFPIHFHLKMDTGMGRLGVKDEEETKRIVALIERHPHFVLEGLYTHFATADEVNTDYFSYQYTRFLHMLEWLPSRPPLVHCANSAASLRFPDRTFNMVRFGIAMYGLAPSPGIKPLLPYPLKEAFSLHSRLVHVKKLQPGEKVSYGATYTAQTEEWIGTIPIGYADGWLRRLQHFHVLVDGQKAPIVGRICMDQCMIRLPGPLPVGTKVTLIGRQGDEVISIDDVARHLETINYEVPCTISYRVPRIFFRHKRIMEVRNAIG 382
                                    11        21        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 


Chain B from PDB  Type:PROTEIN  Length:380
 aligned with ALR_GEOSE | P10724 from UniProtKB/Swiss-Prot  Length:388

    Alignment length:380
                                    11        21        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
            ALR_GEOSE     2 NDFHRDTWAEVDLDAIYDNVENLRRLLPDDTHIMAVVKANAYGHGDVQVARTALEAGASRLAVAFLDEALALREKGIEAPILVLGASRPADAALAAQQRIALTVFRSDWLEEASALYSGPFPIHFHLKMDTGMGRLGVKDEEETKRIVALIERHPHFVLEGLYTHFATADEVNTDYFSYQYTRFLHMLEWLPSRPPLVHCANSAASLRFPDRTFNMVRFGIAMYGLAPSPGIKPLLPYPLKEAFSLHSRLVHVKKLQPGEKVSYGATYTAQTEEWIGTIPIGYADGWLRRLQHFHVLVDGQKAPIVGRICMDQCMIRLPGPLPVGTKVTLIGRQGDEVISIDDVARHLETINYEVPCTISYRVPRIFFRHKRIMEVRNAI 381
               SCOP domains d1bd0b1   d1bd0b2 B:12-244 Alanine racemase                                                                                                                                                                                                        d1bd0b1 B:2-11,B:245-381 Alanine racemase                                                                                                 SCOP domains
               CATH domains 1bd0B02     1bd0B01 B:14-224 Alanine racemase                                                                                                                                                                                  -------------------1bd0B02 B:2-13,B:244-381 Lyase, Ornithine Decarboxylase; Chain A, domain 1                                                                 CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeehhhhhhhhhhhhhh.....eeeee.hhhhhh..hhhhhhhhhhh...eeee..hhhhhhhhhh....eeee.....hhhhhhhhh..eeeee..hhhhhhhhhh......eeeeee............hhhhhhhhhhhh....eeeeeee...........hhhhhhhhhhhhhhh.......eee...hhhhhh.......eeee.hhhh........hhh........eeeeeeeeeeeee.......hhh.......eeeeee...hhh...hhhhh.eeee..eeee.........eeee.........eeeeeeee..eee.hhhhhhhh...hhhhhhh.....eeeeee..eeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------ALANINE_RAC----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1bd0 B   2 NDFHRDTWAEVDLDAIYDNVENLRRLLPDDTHIMAVVKANAYGHGDVQVARTALEAGASRLAVAFLDEALALREKGIEAPILVLGASRPADAALAAQQRIALTVFRSDWLEEASALYSGPFPIHFHLKMDTGMGRLGVKDEEETKRIVALIERHPHFVLEGLYTHFATADEVNTDYFSYQYTRFLHMLEWLPSRPPLVHCANSAASLRFPDRTFNMVRFGIAMYGLAPSPGIKPLLPYPLKEAFSLHSRLVHVKKLQPGEKVSYGATYTAQTEEWIGTIPIGYADGWLRRLQHFHVLVDGQKAPIVGRICMDQCMIRLPGPLPVGTKVTLIGRQGDEVISIDDVARHLETINYEVPCTISYRVPRIFFRHKRIMEVRNAI 381
                                    11        21        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
   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  (0, 0)

(no "Pfam Domain" information available for 1BD0)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (ALR_GEOSE | P10724)
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/Swiss-Prot
        ALR_GEOSE | P10724: 1epv 1ftx 1l6f 1l6g 1niu 1sft 1xqk 1xql 2sfp 3uw6 4ils

(-) Related Entries Specified in the PDB File

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