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(-) Description

Title :  ALANINE RACEMASE WITH BOUND INHIBITOR DERIVED FROM L-CYCLOSERINE
 
Authors :  T. D. Fenn, G. F. Stamper, A. A. Morollo, D. Ringe
Date :  26 Dec 02  (Deposition) - 16 Sep 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Tim Barrel, Plp-Containing, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. D. Fenn, G. F. Stamper, A. A. Morollo, D. Ringe
A Side Reaction Of Alanine Racemase: Transamination Of Cycloserine.
Biochemistry V. 42 5775 2003
PubMed-ID: 12741835  |  Reference-DOI: 10.1021/BI027022D
(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 Taxid: 562
    Gene: ALR OR DAL
    Organism Scientific: GEOBACILLUS STEAROTHERMOPHILUS
    Organism Taxid: 1422

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

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

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:39 , TYR A:43 , LEU A:85 , 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:518 , HOH A:530 , HOH A:571 , HOH A:615 , TYR B:265 , TYR B:284 , CYS B:311 , MET B:312 , HOH B:605BINDING SITE FOR RESIDUE DCS A 800
2AC2SOFTWARETYR A:265 , TYR A:284 , CYS A:311 , MET A:312 , LYS B:39 , TYR B:43 , LEU B:85 , ARG B:136 , ASN B:203 , SER B:204 , ARG B:219 , GLY B:221 , ILE B:222 , TYR B:354 , HOH B:401 , HOH B:481 , HOH B:539 , HOH B:572 , HOH B:611BINDING SITE FOR RESIDUE DCS B 900

(-) SS Bonds  (0, 0)

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

(-) 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 1NIU)

(-) 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 1NIU)

(-) 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:382
 aligned with ALR_GEOSE | P10724 from UniProtKB/Swiss-Prot  Length:388

    Alignment length: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  
            ALR_GEOSE     2 NDFHRDTWAEVDLDAIYDNVENLRRLLPDDTHIMAVVKANAYGHGDVQVARTALEAGASRLAVAFLDEALALREKGIEAPILVLGASRPADAALAAQQRIALTVFRSDWLEEASALYSGPFPIHFHLKMDTGMGRLGVKDEEETKRIVALIERHPHFVLEGLYTHFATADEVNTDYFSYQYTRFLHMLEWLPSRPPLVHCANSAASLRFPDRTFNMVRFGIAMYGLAPSPGIKPLLPYPLKEAFSLHSRLVHVKKLQPGEKVSYGATYTAQTEEWIGTIPIGYADGWLRRLQHFHVLVDGQKAPIVGRICMDQCMIRLPGPLPVGTKVTLIGRQGDEVISIDDVARHLETINYEVPCTISYRVPRIFFRHKRIMEVRNAIGR 383
               SCOP domains d1niua1   d1niua2 A:12-244 Alanine racemase                                                                                                                                                                                                        d1niua1 A:2-11,A:245-383 Alanine racemase                                                                                                   SCOP domains
               CATH domains 1niuA02     1niuA01 A:14-224 Alanine racemase                                                                                                                                                                                  -------------------1niuA02 A:2-13,A:244-382 Lyase, Ornithine Decarboxylase; Chain A, domain 1                                                                 - CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeehhhhhhhhhhhhhhh....eeeeehhhhhhhhhhhhhhhhhhhhh..eeee.hhhhhhhhhhh.....eee....hhhhhhhhhhh.eeeee.hhhhhhhhhh.......eeeee............hhhhhhhhhhhhhhh..eeeeeee..........hhhhhhhhhhhhhhhh.......eee..hhhhhhhhhhhh..eeeehhhhhh......hhhhh.......eeeeee..eeeee....eehhhhhee....eeeeee..hhhhh.hhhhhh.eeee..eeeeee.......eeeee........eeeeeeee..eeehhhhhhhhhh...hhhhhhh.....eeeee..eeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------ALANINE_RAC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1niu A   2 NDFHRDTWAEVDLDAIYDNVENLRRLLPDDTHIMAVVKANAYGHGDVQVARTALEAGASRLAVAFLDEALALREKGIEAPILVLGASRPADAALAAQQRIALTVFRSDWLEEASALYSGPFPIHFHLkMDTGMGRLGVKDEEETKRIVALIERHPHFVLEGLYTHFATADEVNTDYFSYQYTRFLHMLEWLPSRPPLVHCANSAASLRFPDRTFNMVRFGIAMYGLAPSPGIKPLLPYPLKEAFSLHSRLVHVKKLQPGEKVSYGATYTAQTEEWIGTIPIGYADGWLRRLQHFHVLVDGQKAPIVGRICMDQCMIRLPGPLPVGTKVTLIGRQGDEVISIDDVARHLETINYEVPCTISYRVPRIFFRHKRIMEVRNAIGR 383
                                    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  
                                                                                                                                                         129-KCX                                                                                                                                                                                                                                                          


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 d1niub1   d1niub2 B:12-244 Alanine racemase                                                                                                                                                                                                        d1niub1 B:2-11,B:245-381 Alanine racemase                                                                                                 SCOP domains
               CATH domains 1niuB02     1niuB01 B:14-224 Alanine racemase                                                                                                                                                                                  -------------------1niuB02 B:2-13,B:244-380 Lyase, Ornithine Decarboxylase; Chain A, domain 1                                                               - CATH domains
           Pfam domains (1) ----------Ala_racemase_N-1niuB01 B:12-229                                                                                                                                                                                           --------------Ala_racemase_C-1niuB03 B:244-369                                                                                              ------------ Pfam domains (1)
           Pfam domains (2) ----------Ala_racemase_N-1niuB02 B:12-229                                                                                                                                                                                           --------------Ala_racemase_C-1niuB04 B:244-369                                                                                              ------------ Pfam domains (2)
         Sec.struct. author ......eeeeeehhhhhhhhhhhhhhh....eeeeehhhhhhhhhhhhhhhhhhhhh..eeee.hhhhhhhhhhh.....eee....hhhhhhhhhhh.eeeee.hhhhhhhhhhhh.....eeeee............hhhhhhhhhhhhhhh..eeeeeee..........hhhhhhhhhhhhhhhhhh.....eee..hhhhhhhh......eeeehhhhhh......hhhhh.......eeeeee..eeeee....eehhhhhee....eeeeee..hhhhh.hhhhhh.eeee..eeeeee.......eeee.........eeeeeeee..eeehhhhhhhhhh...hhhhhhh.....eeeee..eeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------ALANINE_RAC----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1niu 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
                                                                                                                                                         129-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   (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: 1bd0 1epv 1ftx 1l6f 1l6g 1sft 1xqk 1xql 2sfp 3uw6 4ils

(-) Related Entries Specified in the PDB File

1bd0 1epv 1sft