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(-) Description

Title :  2.37 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF AN ALANINE RACEMASE (ALR) FROM STAPHYLOCOCCUS AUREUS SUBSP. AUREUS COL
 
Authors :  A. S. Halavaty, L. Shuvalova, G. Minasov, J. Winsor, I. Dubrovska, K. Kw W. F. Anderson, Center For Structural Genomics Of Infectious D (Csgid)
Date :  30 Aug 10  (Deposition) - 06 Oct 10  (Release) - 06 Oct 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.37
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Alanine Racemase, Infectious Diseases, Center For Structural Genomics Of Infectious Diseases (Csgid), Alanine And Aspartate Metabolism And D-Alanine Metabolism, Biosynthesis And Degradation Of Murein Sacculus And Peptidoglycan, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. S. Halavaty, L. Shuvalova, G. Minasov, J. Winsor, I. Dubrovska, K. Kwon, W. F. Anderson, Center For Structural Genomics Of Infectious Diseases (Csgid)
2. 37 Angstrom Resolution Crystal Structure Of An Alanine Racemase (Alr) From Staphylococcus Aureus Subsp. Aureus Col
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - ALANINE RACEMASE 1
    Chains: A, B
    EC Number: 5.1.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21(DE3)/MAGIC
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: ALR, ALR1, SACOL2060
    Organism Scientific: STAPHYLOCOCCUS AUREUS SUBSP. AUREUS
    Organism Taxid: 93062
    Strain: COL

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric/Biological Unit (3, 7)
No.NameCountTypeFull Name
1BME3Ligand/IonBETA-MERCAPTOETHANOL
2NA2Ligand/IonSODIUM ION
3PO42Ligand/IonPHOSPHATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:154 , TYR A:157 , LEU A:160BINDING SITE FOR RESIDUE NA A 383
2AC2SOFTWAREALA A:170 , CYS A:171 , ASP A:173 , GLU A:174 , ARG B:309BINDING SITE FOR RESIDUE BME A 384
3AC3SOFTWARECYS A:311 , ARG B:138BINDING SITE FOR RESIDUE BME A 385
4AC4SOFTWARETYR A:43 , ASN A:203 , SER A:204 , GLY A:221 , ILE A:222 , TYR A:354BINDING SITE FOR RESIDUE PO4 A 386
5AC5SOFTWAREILE B:154 , TYR B:157 , LEU B:160 , HOH B:446BINDING SITE FOR RESIDUE NA B 383
6AC6SOFTWAREARG B:309 , CYS B:311BINDING SITE FOR RESIDUE BME B 384
7AC7SOFTWARETYR B:43 , ASN B:203 , SER B:204 , GLY B:221 , ILE B:222 , TYR B:354 , HOH B:402 , HOH B:409BINDING SITE FOR RESIDUE PO4 B 385

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:201 -A:215
2B:201 -B:215

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3OO2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3OO2)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ALANINE_RACEMASEPS00395 Alanine racemase pyridoxal-phosphate attachment site.ALR1_STAAC36-46
 		  2A:36-46
B:36-46

(-) Exons   (0, 0)

(no "Exon" information available for 3OO2)

(-) 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 ALR1_STAAC | Q5HED1 from UniProtKB/Swiss-Prot  Length:382

    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 
           ALR1_STAAC     2 SDKYYRSAYMNVDLNAVASNFKVFSTLHPNKTVMAVVKANAYGLGSVKVARHLMENGATFFAVATLDEAIELRMHGITAKILVLGVLPAKDIDKAIQHRVALTVPSKQWLKEAIKNISGEQEKKLWLHIKLDTGMGRLGIKDTKTYQEVIEIIQQYEQLVFEGVFTHFACADEPGDMTTEQYQRFKDMVNEAIKPEYIHCQNSAGSLLMDCQFCNAIRPGISLYGYYPSEYVQQKVKVHLKPSVQLIANVVQTKTLQAGESVSYGATYTATDPTTIALLPIGYADGYLRIMQGSFVNVNGHQCEVIGRVCMDQTIVKVPDQVKAGDSVILIDNHRESPQSVEVVAEKQHTINYEVLCNLSRRLPRIYHDGDQRFVTNELLK 382
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeehhhhhhhhhhhhhhh...eeeeehhhhhhh.hhhhhhhhhhhh...eeee.hhhhhhhhhh.....eeee....hhhhhhhhhhh.eeeee.hhhhhhhhhhh........eeeeee...........hhhhhhhhhhhhh....eeeeeee..........hhhhhhhhhhhhhhhh.....eeeeehhhhhhhh......ee..hhhhhh...hhhhhhhh.......eeeeee..eeeee.........--......eeeeee..hhhhh.hhhhh..eeee..eeeeee.......eeeee........eeeee........hhhhhhhhh..hhhhhhhhh.....eeeee..eeeeehhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------ALANINE_RAC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3oo2 A   2 SDKYYRSAYMNVDLNAVASNFKVFSTLHPNKTVMAVVKANAYGLGSVKVARHLMENGATFFAVATLDEAIELRMHGITAKILVLGVLPAKDIDKAIQHRVALTVPSKQWLKEAIKNISGEQEKKLWLHIKLDTGMGRLGIKDTKTYQEVIEIIQQYEQLVFEGVFTHFACADEPGDMTTEQYQRFKDMVNEAIKPEYIHCQNSAGSLLMDCQFCNAIRPGISLYGYYPSEYVQQKVKVHLKPSVQLIANVVQTKTLQAGESVSYG--YTATDPTTIALLPIGYADGYLRIMQGSFVNVNGHQCEVIGRVCMDQTIVKVPDQVKAGDSVILIDNHRESPQSVEVVAEKQHTINYEVLCNLSRRLPRIYHDGDQRFVTNELLK 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 
                                                                                                                                                                                                                                                                                                  266  |                                                                                                                 
                                                                                                                                                                                                                                                                                                     269                                                                                                                 


Chain B from PDB  Type:PROTEIN  Length:364
 aligned with ALR1_STAAC | Q5HED1 from UniProtKB/Swiss-Prot  Length:382

    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 
           ALR1_STAAC     2 SDKYYRSAYMNVDLNAVASNFKVFSTLHPNKTVMAVVKANAYGLGSVKVARHLMENGATFFAVATLDEAIELRMHGITAKILVLGVLPAKDIDKAIQHRVALTVPSKQWLKEAIKNISGEQEKKLWLHIKLDTGMGRLGIKDTKTYQEVIEIIQQYEQLVFEGVFTHFACADEPGDMTTEQYQRFKDMVNEAIKPEYIHCQNSAGSLLMDCQFCNAIRPGISLYGYYPSEYVQQKVKVHLKPSVQLIANVVQTKTLQAGESVSYGATYTATDPTTIALLPIGYADGYLRIMQGSFVNVNGHQCEVIGRVCMDQTIVKVPDQVKAGDSVILIDNHRESPQSVEVVAEKQHTINYEVLCNLSRRLPRIYHDGDQRFVTNELLK 382
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----------Ala_racemase_N-3oo2B01 B:13-229                                                                                                                                                                                          --------------Ala_racemase_C-3             oo2B03 B:244-369                                                                                 ------------- Pfam domains (1)
           Pfam domains (2) -----------Ala_racemase_N-3oo2B02 B:13-229                                                                                                                                                                                          --------------Ala_racemase_C-3             oo2B04 B:244-369                                                                                 ------------- Pfam domains (2)
         Sec.struct. author .......eeeeeehhhhhhhhhhhhhhh...ee.eehhhhhhh.hhhhhhhhhhh....eeee.hhhhhhhhhhh....eeee....hhhhhhhhhhh...eee.hhhhhhhhh....----..eeeeee...........hhhhhhhhhhhhhhh..eeeeeee..........hhhhhhhhhhhhhhh......eeeeehhhhhhhh......ee..hhhhhh...hhhhhh.........eeeeee..eeeee..-------------..eeeeee..hhhhh.hhhhh..eeee..eeeeee.......eeeee........eeeee........hhhhhhhhh..hhhhhhhhh.....eeee....eeeehhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------ALANINE_RAC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3oo2 B   2 SDKYYRSAYMNVDLNAVASNFKVFSTLHPNKTVMAVVKANAYGLGSVKVARHLMENGATFFAVATLDEAIELRMHGITAKILVLGVLPAKDIDKAIQHRVALTVPSKQWLKEAIKNIS----KKLWLHIKLDTGMGRLGIKDTKTYQEVIEIIQQYEQLVFEGVFTHFACADEPGDMTTEQYQRFKDMVNEAIKPEYIHCQNSAGSLLMDCQFCNAIRPGISLYGYYPSEYVQQKVKVHLKPSVQLIANVVQTKTLQA-------------DPTTIALLPIGYADGYLRIMQGSFVNVNGHQCEVIGRVCMDQTIVKVPDQVKAGDSVILIDNHRESPQSVEVVAEKQHTINYEVLCNLSRRLPRIYHDGDQRFVTNELLK 382
                                    11        21        31        41        51        61        71        81        91       101       111       | -  |    131       141       151       161       171       181       191       201       211       221       231       241       251       | -         - |     281       291       301       311       321       331       341       351       361       371       381 
                                                                                                                                               119  124                                                                                                                                    259           273
   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 3OO2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3OO2)

(-) 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   (ALR1_STAAC | Q5HED1)
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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