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(-) Description

Title :  ALANINE RACEMASE WITH BOUND PROPIONATE INHIBITOR
 
Authors :  A. A. Morollo, G. A. Petsko, D. Ringe
Date :  16 Feb 99  (Deposition) - 24 Feb 99  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Racemase, Isomerase, Alanine, Pyridoxal Phosphate (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. A. Morollo, G. A. Petsko, D. Ringe
Structure Of A Michaelis Complex Analogue: Propionate Binds In The Substrate Carboxylate Site Of Alanine Racemase.
Biochemistry V. 38 3293 1999
PubMed-ID: 10079072  |  Reference-DOI: 10.1021/BI9822729
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN (ALANINE RACEMASE)
    Chains: A, B
    EC Number: 5.1.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI STR. K12 SUBSTR. W3110
    Expression System Gene: ALR
    Expression System Plasmid: PMDALR3
    Expression System Strain: W3110
    Expression System Taxid: 316407
    Expression System Vector: PKK223-3
    Expression System Vector Type: PLASMID
    Organism Scientific: GEOBACILLUS STEAROTHERMOPHILUS
    Organism Taxid: 1422
    Other Details: PYRIDOXAL PHOSPHATE COFACTOR IN ALDIMINE LINKAGE WITH LYS39. CARBOXYLATED LYS129
    Strain: IFO 12550

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1KCX2Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID
2PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE
3PPI2Ligand/IonPROPANOIC ACID

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS 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:512 , HOH A:543 , HOH A:557 , PPI B:400BINDING SITE FOR RESIDUE PLP A 500
02AC2SOFTWARELYS A:39 , ARG A:136 , TYR A:354 , PLP A:500 , TYR B:265 , CYS B:311 , MET B:312 , HOH B:505 , HOH B:582BINDING SITE FOR RESIDUE PPI B 400
03AC3SOFTWAREPPI A:400 , LYS B:39 , TYR B:43 , ARG B:136 , HIS B:166 , SER B:204 , ARG B:219 , GLY B:221 , ILE B:222 , TYR B:354 , HOH B:537 , HOH B:551 , HOH B:581BINDING SITE FOR RESIDUE PLP B 500
04AC4SOFTWARETYR A:265 , TYR A:284 , CYS A:311 , MET A:312 , HOH A:569 , HOH A:570 , LYS B:39 , ARG B:136 , TYR B:354 , PLP B:500BINDING SITE FOR RESIDUE PPI A 400
05KC1AUTHORKCX A:129CARBAMYLATED LYSINE
06KC2AUTHORKCX B:129CARBAMYLATED LYSINE
07PL1AUTHORPLP A:500PYRIDOXAL-5-PHOSPHATE COFACTOR
08PL2AUTHORPLP B:500PYRIDOXAL-5-PHOSPHATE COFACTOR
09PP1AUTHORPPI B:400PROPIONATE INHIBITOR
10PP2AUTHORPPI A:400PROPIONATE INHIBITOR

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2SFP)

(-) 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 2SFP)

(-) 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 2SFP)

(-) 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:379
 aligned with ALR_GEOSE | P10724 from UniProtKB/Swiss-Prot  Length:388

    Alignment length:379
                                    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         
            ALR_GEOSE     3 DFHRDTWAEVDLDAIYDNVENLRRLLPDDTHIMAVVKANAYGHGDVQVARTALEAGASRLAVAFLDEALALREKGIEAPILVLGASRPADAALAAQQRIALTVFRSDWLEEASALYSGPFPIHFHLKMDTGMGRLGVKDEEETKRIVALIERHPHFVLEGLYTHFATADEVNTDYFSYQYTRFLHMLEWLPSRPPLVHCANSAASLRFPDRTFNMVRFGIAMYGLAPSPGIKPLLPYPLKEAFSLHSRLVHVKKLQPGEKVSYGATYTAQTEEWIGTIPIGYADGWLRRLQHFHVLVDGQKAPIVGRICMDQCMIRLPGPLPVGTKVTLIGRQGDEVISIDDVARHLETINYEVPCTISYRVPRIFFRHKRIMEVRNAI 381
               SCOP domains d2sfpa1  d2sfpa2 A:12-244 Alanine racemase                                                                                                                                                                                                        d2sfpa1 A:3-11,A:245-381 Alanine racemase                                                                                                 SCOP domains
               CATH domains 2sfpA02    2sfpA01 A:14-224 Alanine racemase                                                                                                                                                                                  -------------------2sfpA02 A:3-13,A:244-380 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..hhhhhhhhhh......eeeeee............hhhhhhhhhhhhh...eeeeeee...........hhhhhhhhhhhhhhhh......eee...hhhhhh.hhh...eeee.hhhh.....hhhhhh........eeeeeeeeeeeee.......hhh.......eeeeee...hhh...hhh...eeee..eeee.........eeeee........eeeeeeee..eee.hhhhhhh....hhhhhhh.....eeeeee..eeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------ALANINE_RAC----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2sfp A   3 DFHRDTWAEVDLDAIYDNVENLRRLLPDDTHIMAVVKANAYGHGDVQVARTALEAGASRLAVAFLDEALALREKGIEAPILVLGASRPADAALAAQQRIALTVFRSDWLEEASALYSGPFPIHFHLkMDTGMGRLGVKDEEETKRIVALIERHPHFVLEGLYTHFATADEVNTDYFSYQYTRFLHMLEWLPSRPPLVHCANSAASLRFPDRTFNMVRFGIAMYGLAPSPGIKPLLPYPLKEAFSLHSRLVHVKKLQPGEKVSYGATYTAQTEEWIGTIPIGYADGWLRRLQHFHVLVDGQKAPIVGRICMDQCMIRLPGPLPVGTKVTLIGRQGDEVISIDDVARHLETINYEVPCTISYRVPRIFFRHKRIMEVRNAI 381
                                    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         
                                                                                                                                                        129-KCX                                                                                                                                                                                                                                                        


Chain B from PDB  Type:PROTEIN  Length:379
 aligned with ALR_GEOSE | P10724 from UniProtKB/Swiss-Prot  Length:388

    Alignment length:379
                                    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         
            ALR_GEOSE     3 DFHRDTWAEVDLDAIYDNVENLRRLLPDDTHIMAVVKANAYGHGDVQVARTALEAGASRLAVAFLDEALALREKGIEAPILVLGASRPADAALAAQQRIALTVFRSDWLEEASALYSGPFPIHFHLKMDTGMGRLGVKDEEETKRIVALIERHPHFVLEGLYTHFATADEVNTDYFSYQYTRFLHMLEWLPSRPPLVHCANSAASLRFPDRTFNMVRFGIAMYGLAPSPGIKPLLPYPLKEAFSLHSRLVHVKKLQPGEKVSYGATYTAQTEEWIGTIPIGYADGWLRRLQHFHVLVDGQKAPIVGRICMDQCMIRLPGPLPVGTKVTLIGRQGDEVISIDDVARHLETINYEVPCTISYRVPRIFFRHKRIMEVRNAI 381
               SCOP domains d2sfpb1  d2sfpb2 B:12-244 Alanine racemase                                                                                                                                                                                                        d2sfpb1 B:3-11,B:245-381 Alanine racemase                                                                                                 SCOP domains
               CATH domains 2sfpB02    2sfpB01 B:14-224 Alanine racemase                                                                                                                                                                                  -------------------2sfpB02 B:3-13,B:244-380 Lyase, Ornithine Decarboxylase; Chain A, domain 1                                                               - CATH domains
           Pfam domains (1) ---------Ala_racemase_N-2sfpB01 B:12-229                                                                                                                                                                                           --------------Ala_racemase_C-2sfpB03 B:244-369                                                                                              ------------ Pfam domains (1)
           Pfam domains (2) ---------Ala_racemase_N-2sfpB02 B:12-229                                                                                                                                                                                           --------------Ala_racemase_C-2sfpB04 B:244-369                                                                                              ------------ Pfam domains (2)
         Sec.struct. author ......eeeeehhhhhhhhhhhhhh.....eeeee.hhhhhh..hhhhhhhhhhh...eeee..hhhhhhhhh.....eeee.....hhhhhhhhh..eeeee..hhhhhhhhhh........................hhhhhhhhhhhhh...eeeeeee...........hhhhhhhhhhhhhhhh......eee...hhhhhh.......eeee.hhhh........hhh........eeeeeeeeeeeee.......hhh.......eeeeee...hhh...hhh...eeee..eeee.........eeeee........eeeeeeee..eee.hhhhhhhh...hhhhhhh.....eeeeee..eeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------ALANINE_RAC----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2sfp B   3 DFHRDTWAEVDLDAIYDNVENLRRLLPDDTHIMAVVKANAYGHGDVQVARTALEAGASRLAVAFLDEALALREKGIEAPILVLGASRPADAALAAQQRIALTVFRSDWLEEASALYSGPFPIHFHLkMDTGMGRLGVKDEEETKRIVALIERHPHFVLEGLYTHFATADEVNTDYFSYQYTRFLHMLEWLPSRPPLVHCANSAASLRFPDRTFNMVRFGIAMYGLAPSPGIKPLLPYPLKEAFSLHSRLVHVKKLQPGEKVSYGATYTAQTEEWIGTIPIGYADGWLRRLQHFHVLVDGQKAPIVGRICMDQCMIRLPGPLPVGTKVTLIGRQGDEVISIDDVARHLETINYEVPCTISYRVPRIFFRHKRIMEVRNAI 381
                                    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         
                                                                                                                                                        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 1niu 1sft 1xqk 1xql 3uw6 4ils

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2SFP)