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(-) Description

Title :  CRYSTAL STRUCTURE OF PSEUDOMONAS FLUORESCENS ALANINE RACEMASE
 
Authors :  H. Tsuge, K. Ohnishi, K. Yokoigawa
Date :  25 Dec 06  (Deposition) - 05 Feb 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Alanine Racemase, Plp, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Tsuge, K. Ohnishi, K. Yokoigawa
Crystal Structure Of Pseudomonas Fluorescens Alanine Racemase
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - ALANINE RACEMASE
    Chains: A, B, C, D
    EC Number: 5.1.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: PSEUDOMONAS FLUORESCENS
    Organism Taxid: 294
    Strain: TM5-2

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 12)

Asymmetric Unit (3, 12)
No.NameCountTypeFull Name
1ACT4Ligand/IonACETATE ION
2KCX4Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID
3LLP4Mod. Amino Acid2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)
Biological Unit 1 (3, 6)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2KCX2Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID
3LLP2Mod. Amino Acid2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)
Biological Unit 2 (3, 6)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2KCX2Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID
3LLP2Mod. Amino Acid2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:253 , TYR A:272 , SER A:300 , MET A:301 , LLP B:33 , ARG B:129BINDING SITE FOR RESIDUE ACT A 1400
2AC2SOFTWARELLP A:33 , ARG A:129 , TYR B:253 , TYR B:272 , SER B:300 , MET B:301 , HOH B:403BINDING SITE FOR RESIDUE ACT B 400
3AC3SOFTWARETYR C:253 , TYR C:272 , SER C:300 , MET C:301 , LLP D:33 , ARG D:129BINDING SITE FOR RESIDUE ACT C 3400
4AC4SOFTWAREARG C:129 , TYR D:253 , TYR D:272 , MET D:301BINDING SITE FOR RESIDUE ACT D 2400

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Val A:286 -Phe A:287
2Val B:286 -Phe B:287
3Val C:286 -Phe C:287
4Val D:286 -Phe D:287

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2ODO)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2ODO)

(-) Exons   (0, 0)

(no "Exon" information available for 2ODO)

(-) 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:356
 aligned with Q4ADX2_PSEFL | Q4ADX2 from UniProtKB/TrEMBL  Length:357

    Alignment length:356
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350      
         Q4ADX2_PSEFL     1 MRPARALIDLQALRHNYQLAREVTGAKALAVIKADAYGHGAVRCAQALEAEADGFAVACIEEALELRAAGIRAPILLLEGFFEADELPLIVEHDFWCVVHSLWQLDAIEQARLAKPIHVWLKLDSGMHRVGLHPNDYKAAYQRLQASANVAKIVLMSHFARADELDCTRSVEQVAVFLGARADLTAEISLRNSPAVLGWPRVPSDWVRPGLMLYGSSPFDEPQATASRLQPVMTLESKVICVRELPAGEPVGYGARFITPKPMRIGVVAMGYADGYPRQAPTGTPVFVDGVRSQLLGRVSMDMLCIDLTDVPQAGLGSTVELWGKNILASEVATAADTIPYQIFCNLKRVPRLYSG 356
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2odoA01  2odoA02 A:10-216 Alanine racemase                                                                                                                                                                              2odoA01 A:1-9,A:217-356 Lyase, Ornithine Decarboxylase; Chain A, domain 1                                                                    CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeehhhhhhhhhhhhhhhh.eeeeehhhhhhhhhhhhhhhhhhhhh.eeee.hhhhhhhhhh......eee.....hhhhhhhhhhh..eeee.hhhhhhhhhhh.....eeeeeee.........hhhhhhhhhhhhhh...eeeeeeee..........hhhhhhhhhhhhhhh....eee..hhhhhhhh......ee..hhhhhh.........hhhhh...eeeeeeeeeeeee......hhhhh......eeeeee..................ee..ee...........eeee...........eeeee....hhhhhhhhh..hhhhhhhh.....eeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2odo A   1 MRPARALIDLQALRHNYQLAREVTGAKALAVIkADAYGHGAVRCAQALEAEADGFAVACIEEALELRAAGIRAPILLLEGFFEADELPLIVEHDFWCVVHSLWQLDAIEQARLAKPIHVWLkLDSGMHRVGLHPNDYKAAYQRLQASANVAKIVLMSHFARADELDCTRSVEQVAVFLGARADLTAEISLRNSPAVLGWPRVPSDWVRPGLMLYGSSPFDEPQATASRLQPVMTLESKVICVRELPAGEPVGYGARFITPKPMRIGVVAMGYADGYPRQAPTGTPVFVDGVRSQLLGRVSMDMLCIDLTDVPQAGLGSTVELWGKNILASEVATAADTIPYQIFCNLKRVPRLYSG 356
                                    10        20        30  |     40        50        60        70        80        90       100       110       120 |     130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350      
                                                           33-LLP                                                                                  122-KCX                                                                                                                                                                                                                                      


Chain B from PDB  Type:PROTEIN  Length:356
 aligned with Q4ADX2_PSEFL | Q4ADX2 from UniProtKB/TrEMBL  Length:357

    Alignment length:356
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350      
         Q4ADX2_PSEFL     1 MRPARALIDLQALRHNYQLAREVTGAKALAVIKADAYGHGAVRCAQALEAEADGFAVACIEEALELRAAGIRAPILLLEGFFEADELPLIVEHDFWCVVHSLWQLDAIEQARLAKPIHVWLKLDSGMHRVGLHPNDYKAAYQRLQASANVAKIVLMSHFARADELDCTRSVEQVAVFLGARADLTAEISLRNSPAVLGWPRVPSDWVRPGLMLYGSSPFDEPQATASRLQPVMTLESKVICVRELPAGEPVGYGARFITPKPMRIGVVAMGYADGYPRQAPTGTPVFVDGVRSQLLGRVSMDMLCIDLTDVPQAGLGSTVELWGKNILASEVATAADTIPYQIFCNLKRVPRLYSG 356
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2odoB01  2odoB02 B:10-216 Alanine racemase                                                                                                                                                                              2odoB01 B:1-9,B:217-356 Lyase, Ornithine Decarboxylase; Chain A, domain 1                                                                    CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeehhhhhhhhhhhhhhhh.eeeeehhhhhhh.hhhhhhhhhhh...eeee.hhhhhhhhhhhh....eee.....hhhhhhhhhhhheeeee.hhhhhhhhhhh.....eeeeeee.........hhhhhhhhhhhhhh...eeeeeeee..........hhhhhhhhhhhhhhh....eee..hhhhhhhh......ee..hhhhhh........hhhhhh...eeeeeeeeeeeee....eehhhhhee....eeeeee..................ee..ee...........eeee...........eeeee....hhhhhhhhh..hhhhhhhh.....eeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2odo B   1 MRPARALIDLQALRHNYQLAREVTGAKALAVIkADAYGHGAVRCAQALEAEADGFAVACIEEALELRAAGIRAPILLLEGFFEADELPLIVEHDFWCVVHSLWQLDAIEQARLAKPIHVWLkLDSGMHRVGLHPNDYKAAYQRLQASANVAKIVLMSHFARADELDCTRSVEQVAVFLGARADLTAEISLRNSPAVLGWPRVPSDWVRPGLMLYGSSPFDEPQATASRLQPVMTLESKVICVRELPAGEPVGYGARFITPKPMRIGVVAMGYADGYPRQAPTGTPVFVDGVRSQLLGRVSMDMLCIDLTDVPQAGLGSTVELWGKNILASEVATAADTIPYQIFCNLKRVPRLYSG 356
                                    10        20        30  |     40        50        60        70        80        90       100       110       120 |     130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350      
                                                           33-LLP                                                                                  122-KCX                                                                                                                                                                                                                                      


Chain C from PDB  Type:PROTEIN  Length:356
 aligned with Q4ADX2_PSEFL | Q4ADX2 from UniProtKB/TrEMBL  Length:357

    Alignment length:356
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350      
         Q4ADX2_PSEFL     1 MRPARALIDLQALRHNYQLAREVTGAKALAVIKADAYGHGAVRCAQALEAEADGFAVACIEEALELRAAGIRAPILLLEGFFEADELPLIVEHDFWCVVHSLWQLDAIEQARLAKPIHVWLKLDSGMHRVGLHPNDYKAAYQRLQASANVAKIVLMSHFARADELDCTRSVEQVAVFLGARADLTAEISLRNSPAVLGWPRVPSDWVRPGLMLYGSSPFDEPQATASRLQPVMTLESKVICVRELPAGEPVGYGARFITPKPMRIGVVAMGYADGYPRQAPTGTPVFVDGVRSQLLGRVSMDMLCIDLTDVPQAGLGSTVELWGKNILASEVATAADTIPYQIFCNLKRVPRLYSG 356
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2odoC01  2odoC02 C:10-216 Alanine racemase                                                                                                                                                                              2odoC01 C:1-9,C:217-356 Lyase, Ornithine Decarboxylase; Chain A, domain 1                                                                    CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeehhhhhhhhhhhhhhhh.ee.eehhhhhhhhhhhhhhhhhhhhh..eee.hhhhhhhhhhh.....eee.....hhhhhhhhhhh..eeee.hhhhhhhhhhh.....eeeeeee.........hhhhhhhhhhhhhh...eeeeeeee..........hhhhhhhhhhhhhhh....eee..hhhhhhhh......ee..hhhhhh.........hhhhh...eeeeeeeeeeeee......hhhhh......eeeeee..................ee..ee...........eeee...........eeeee....hhhhhhhhh..hhhhhhhh.....eeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2odo C   1 MRPARALIDLQALRHNYQLAREVTGAKALAVIkADAYGHGAVRCAQALEAEADGFAVACIEEALELRAAGIRAPILLLEGFFEADELPLIVEHDFWCVVHSLWQLDAIEQARLAKPIHVWLkLDSGMHRVGLHPNDYKAAYQRLQASANVAKIVLMSHFARADELDCTRSVEQVAVFLGARADLTAEISLRNSPAVLGWPRVPSDWVRPGLMLYGSSPFDEPQATASRLQPVMTLESKVICVRELPAGEPVGYGARFITPKPMRIGVVAMGYADGYPRQAPTGTPVFVDGVRSQLLGRVSMDMLCIDLTDVPQAGLGSTVELWGKNILASEVATAADTIPYQIFCNLKRVPRLYSG 356
                                    10        20        30  |     40        50        60        70        80        90       100       110       120 |     130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350      
                                                           33-LLP                                                                                  122-KCX                                                                                                                                                                                                                                      


Chain D from PDB  Type:PROTEIN  Length:356
 aligned with Q4ADX2_PSEFL | Q4ADX2 from UniProtKB/TrEMBL  Length:357

    Alignment length:356
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350      
         Q4ADX2_PSEFL     1 MRPARALIDLQALRHNYQLAREVTGAKALAVIKADAYGHGAVRCAQALEAEADGFAVACIEEALELRAAGIRAPILLLEGFFEADELPLIVEHDFWCVVHSLWQLDAIEQARLAKPIHVWLKLDSGMHRVGLHPNDYKAAYQRLQASANVAKIVLMSHFARADELDCTRSVEQVAVFLGARADLTAEISLRNSPAVLGWPRVPSDWVRPGLMLYGSSPFDEPQATASRLQPVMTLESKVICVRELPAGEPVGYGARFITPKPMRIGVVAMGYADGYPRQAPTGTPVFVDGVRSQLLGRVSMDMLCIDLTDVPQAGLGSTVELWGKNILASEVATAADTIPYQIFCNLKRVPRLYSG 356
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2odoD01  2odoD02 D:10-216 Alanine racemase                                                                                                                                                                              2odoD01 D:1-9,D:217-356 Lyase, Ornithine Decarboxylase; Chain A, domain 1                                                                    CATH domains
           Pfam domains (1) -------Ala_racemase_N-2odoD01 D:8-218                                                                                                                                                                                     -------------Ala_racemase_C-2odoD05 D:232-355                                                                                            - Pfam domains (1)
           Pfam domains (2) -------Ala_racemase_N-2odoD02 D:8-218                                                                                                                                                                                     -------------Ala_racemase_C-2odoD06 D:232-355                                                                                            - Pfam domains (2)
           Pfam domains (3) -------Ala_racemase_N-2odoD03 D:8-218                                                                                                                                                                                     -------------Ala_racemase_C-2odoD07 D:232-355                                                                                            - Pfam domains (3)
           Pfam domains (4) -------Ala_racemase_N-2odoD04 D:8-218                                                                                                                                                                                     -------------Ala_racemase_C-2odoD08 D:232-355                                                                                            - Pfam domains (4)
         Sec.struct. author ....eeeeehhhhhhhhhhhhhhhh.ee.eehhhhhhh.hhhhhhhhhh.....eee.hhhhhhhhhhh.....eee.....hhhhhhhhhhh..eeee.hhhhhhhhhhh.....eeeeeee............hhhhhhhhhhh...eeeeeeee..........hhhhhhhhhhhhhhh.....ee..hhhhhhhh......ee..hhhhhh.........hhhhh...eeeeeeeeeeeee......hhhhh......eeeeee..................ee..ee...........eeee...........eeeee....hhhhhhhhh..hhhhhhhh.....eeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2odo D   1 MRPARALIDLQALRHNYQLAREVTGAKALAVIkADAYGHGAVRCAQALEAEADGFAVACIEEALELRAAGIRAPILLLEGFFEADELPLIVEHDFWCVVHSLWQLDAIEQARLAKPIHVWLkLDSGMHRVGLHPNDYKAAYQRLQASANVAKIVLMSHFARADELDCTRSVEQVAVFLGARADLTAEISLRNSPAVLGWPRVPSDWVRPGLMLYGSSPFDEPQATASRLQPVMTLESKVICVRELPAGEPVGYGARFITPKPMRIGVVAMGYADGYPRQAPTGTPVFVDGVRSQLLGRVSMDMLCIDLTDVPQAGLGSTVELWGKNILASEVATAADTIPYQIFCNLKRVPRLYSG 356
                                    10        20        30  |     40        50        60        70        80        90       100       110       120 |     130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350      
                                                           33-LLP                                                                                  122-KCX
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 2ODO)

(-) CATH Domains  (2, 8)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (2, 8)

Asymmetric Unit
(-)
Clan: TIM_barrel (694)
(-)
Clan: no clan defined [family: Ala_racemase_C] (18)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q4ADX2_PSEFL | Q4ADX2)
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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