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(-) Description

Title :  THE MUTANT G127C-T313C OF DEINOCOCCUS RADIODURANS N-ACYLAMINO ACID RACEMASE
 
Authors :  W. C. Wang, W. C. Chiu
Date :  05 Jan 06  (Deposition) - 24 Jan 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (4x)
Biol. Unit 2:  B,D  (4x)
Keywords :  N-Acylamino Acid Racemase, Deinococcus Radiodurans, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. C. Wang, W. C. Chiu
Enhanced Thermoactivity In Covalently Cross-Linked N-Carbamoyl D-Amino Acid Amidohydrolase But Not In N-Acylamino Acid Racemase That Has Induced Fit Movements Upon Substrate Binding
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - N-ACYLAMINO ACID RACEMASE
    Chains: A, B, C, D
    EC Number: 5.1.1.10
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE30
    Expression System Strain: JM109
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: DEINOCOCCUS RADIODURANS
    Organism Taxid: 1299
    Strain: CCRC 12827

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (4x): A C 
Biological Unit 2 (4x):  B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2FKP)

(-) Sites  (0, 0)

(no "Site" information available for 2FKP)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Pro C:173 -Gly C:174

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2FKP)

(-) 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:360
 aligned with Q9RYA6_DEIRA | Q9RYA6 from UniProtKB/TrEMBL  Length:375

    Alignment length:370
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375
         Q9RYA6_DEIRA     6 RMFKIEAAEIVVARLPLKFRFETSFGVQTHKVVPLLILHGEGVQGVAEGTMEARPMYREETIAGALDLLRGTFLPAILGQTFANPEAVADALGSYRGNRMARAMVEMAAWDLWARTLGVPLGTLLGGHKEQVEVGVSLGIQAGEQATVDLVRKHVEQGYRRIKLKIKPGWDVQPVRATREAFPDIRLTVDANSAYTLADAGRLRQLDEYDLTYIEQPLAWDDLVDHAELARRIRTPLCLDESVASAADARKALALGAGGVINLKVARVGGHAESRRVHDVAQSFGAPVWCGGMLESGIGRAHNIHLSTLPNFRLPGDTSSASRYWERDLIQEPLEAVDGLMPVPQGPGTGVTLDREFLATVTEAQEEHRA 375
               SCOP domains d2fkpa2 A:6-132 N-          acylamino acid racemase                                                                            d2fkpa1 A:133-375 N-acylamino acid racemase                                                                                                                                                                                                         SCOP domains
               CATH domains 2fkpA01 A:6-123,A:          354-375 Enolase-like, N-terminal domain                                                   2fkpA02 A:124-353 Enolase superfamily                                                                                                                                                                                                 2fkpA01                CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee..eeeeeeeeee..----------.eeeeeeeeeee..eeeeee............hhhhhhhhhhhhhhhhhh..ee.hhhhhhhh......hhhhhhhhhhhhhhhhhhhhh.hhhhhhh....eee..eee....hhhhhhhhhhhhhhh....eeee.....hhhhhhhhhhhh....eeee.....hhhhhhhhhhhhhhh...ee.......hhhhhhhhhhh...eee.....hhhhhhhhhhh....eeee......hhhhhhhhhhhhhhh...eee.....hhhhhhhhhhhh............hhhhh...............eee...........hhhhhhhheeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2fkp A   6 RMFKIEAAEIVVARLPLK----------THKVVPLLILHGEGVQGVAEGTMEARPMYREETIAGALDLLRGTFLPAILGQTFANPEAVSDALGSYRGNRMARAMVEMAAWDLWARTLGVPLCTLLGGHKEQVEVGVSLGIQADEQATVDLVRRHVEQGYRRIKLKIKPGWDVQPVRATREAFPDIRLTVDANSAYTLADAGRLRQLDEYDLTYIEQPLAWDDLVDHAELARRIRTPLCLDESVASASDARKALALGAGGVINLKVARVGGHAESRRVHDVAQSFGAPVWCGGMLESGIGRAHNIHLSCLSNFRLPGDTSSASRYWERDLIQEPLEAVDGLMPVPQGPGTGVTLDREFLATVTEAQEEHRA 375
                                    15       | -        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375
                                            23         34                                                                                                                                                                                                                                                                                                                                                     


Chain B from PDB  Type:PROTEIN  Length:360
 aligned with Q9RYA6_DEIRA | Q9RYA6 from UniProtKB/TrEMBL  Length:375

    Alignment length:370
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375
         Q9RYA6_DEIRA     6 RMFKIEAAEIVVARLPLKFRFETSFGVQTHKVVPLLILHGEGVQGVAEGTMEARPMYREETIAGALDLLRGTFLPAILGQTFANPEAVADALGSYRGNRMARAMVEMAAWDLWARTLGVPLGTLLGGHKEQVEVGVSLGIQAGEQATVDLVRKHVEQGYRRIKLKIKPGWDVQPVRATREAFPDIRLTVDANSAYTLADAGRLRQLDEYDLTYIEQPLAWDDLVDHAELARRIRTPLCLDESVASAADARKALALGAGGVINLKVARVGGHAESRRVHDVAQSFGAPVWCGGMLESGIGRAHNIHLSTLPNFRLPGDTSSASRYWERDLIQEPLEAVDGLMPVPQGPGTGVTLDREFLATVTEAQEEHRA 375
               SCOP domains d2fkpb1 B:6-132 N-          acylamino acid racemase                                                                            d2fkpb2 B:133-375 N-acylamino acid racemase                                                                                                                                                                                                         SCOP domains
               CATH domains 2fkpB01 B:6-123,B:          354-375 Enolase-like, N-terminal domain                                                   2fkpB02 B:124-353 Enolase superfamily                                                                                                                                                                                                 2fkpB01                CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee..eeeeeeeeee..----------.eeeeeeeeeee..eeeeee............hhhhhhhhhhhhhhhhhh..ee.hhhhhhhh......hhhhhhhhhhhhhhhhhhhhh.hhhhhhh....eee..eee....hhhhhhhhhhhhhhh....eeee.....hhhhhhhhhhhh....eeee.....hhhhhhhhhhhhhhh...ee.......hhhhhhhhhhh...eee.....hhhhhhhhhhh....eeee......hhhhhhhhhhhhhhh...eee.....hhhhhhhhhhhhh...........hhhhh...............eee...........hhhhhhhheeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2fkp B   6 RMFKIEAAEIVVARLPLK----------THKVVPLLILHGEGVQGVAEGTMEARPMYREETIAGALDLLRGTFLPAILGQTFANPEAVSDALGSYRGNRMARAMVEMAAWDLWARTLGVPLCTLLGGHKEQVEVGVSLGIQADEQATVDLVRRHVEQGYRRIKLKIKPGWDVQPVRATREAFPDIRLTVDANSAYTLADAGRLRQLDEYDLTYIEQPLAWDDLVDHAELARRIRTPLCLDESVASASDARKALALGAGGVINLKVARVGGHAESRRVHDVAQSFGAPVWCGGMLESGIGRAHNIHLSCLSNFRLPGDTSSASRYWERDLIQEPLEAVDGLMPVPQGPGTGVTLDREFLATVTEAQEEHRA 375
                                    15       | -        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375
                                            23         34                                                                                                                                                                                                                                                                                                                                                     


Chain C from PDB  Type:PROTEIN  Length:360
 aligned with Q9RYA6_DEIRA | Q9RYA6 from UniProtKB/TrEMBL  Length:375

    Alignment length:370
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375
         Q9RYA6_DEIRA     6 RMFKIEAAEIVVARLPLKFRFETSFGVQTHKVVPLLILHGEGVQGVAEGTMEARPMYREETIAGALDLLRGTFLPAILGQTFANPEAVADALGSYRGNRMARAMVEMAAWDLWARTLGVPLGTLLGGHKEQVEVGVSLGIQAGEQATVDLVRKHVEQGYRRIKLKIKPGWDVQPVRATREAFPDIRLTVDANSAYTLADAGRLRQLDEYDLTYIEQPLAWDDLVDHAELARRIRTPLCLDESVASAADARKALALGAGGVINLKVARVGGHAESRRVHDVAQSFGAPVWCGGMLESGIGRAHNIHLSTLPNFRLPGDTSSASRYWERDLIQEPLEAVDGLMPVPQGPGTGVTLDREFLATVTEAQEEHRA 375
               SCOP domains d2fkpc1 C:6-132 N-          acylamino acid racemase                                                                            d2fkpc2 C:133-375 N-acylamino acid racemase                                                                                                                                                                                                         SCOP domains
               CATH domains 2fkpC01 C:6-123,C:          354-375 Enolase-like, N-terminal domain                                                   2fkpC02 C:124-353 Enolase superfamily                                                                                                                                                                                                 2fkpC01                CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee..eeeeeeeeee..----------.eeeeeeeeeee..eeeeee............hhhhhhhhhhhhhhhhhh..ee.hhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh.hhhhhhh....eee..eee....hhhhhhhhhhhhhh.....eeee.....hhhhhhhhhhhh....eeee.....hhhhhhhhhhhhhhh...ee.......hhhhhhhhhhh...eee.....hhhhhhhhhhhh...eeee......hhhhhhhhhhhhhhh...eee.....hhhhhhhhhhhh............hhhhh...............eee...........hhhhhhhheeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2fkp C   6 RMFKIEAAEIVVARLPLK----------THKVVPLLILHGEGVQGVAEGTMEARPMYREETIAGALDLLRGTFLPAILGQTFANPEAVSDALGSYRGNRMARAMVEMAAWDLWARTLGVPLCTLLGGHKEQVEVGVSLGIQADEQATVDLVRRHVEQGYRRIKLKIKPGWDVQPVRATREAFPDIRLTVDANSAYTLADAGRLRQLDEYDLTYIEQPLAWDDLVDHAELARRIRTPLCLDESVASASDARKALALGAGGVINLKVARVGGHAESRRVHDVAQSFGAPVWCGGMLESGIGRAHNIHLSCLSNFRLPGDTSSASRYWERDLIQEPLEAVDGLMPVPQGPGTGVTLDREFLATVTEAQEEHRA 375
                                    15       | -        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375
                                            23         34                                                                                                                                                                                                                                                                                                                                                     


Chain D from PDB  Type:PROTEIN  Length:360
 aligned with Q9RYA6_DEIRA | Q9RYA6 from UniProtKB/TrEMBL  Length:375

    Alignment length:370
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375
         Q9RYA6_DEIRA     6 RMFKIEAAEIVVARLPLKFRFETSFGVQTHKVVPLLILHGEGVQGVAEGTMEARPMYREETIAGALDLLRGTFLPAILGQTFANPEAVADALGSYRGNRMARAMVEMAAWDLWARTLGVPLGTLLGGHKEQVEVGVSLGIQAGEQATVDLVRKHVEQGYRRIKLKIKPGWDVQPVRATREAFPDIRLTVDANSAYTLADAGRLRQLDEYDLTYIEQPLAWDDLVDHAELARRIRTPLCLDESVASAADARKALALGAGGVINLKVARVGGHAESRRVHDVAQSFGAPVWCGGMLESGIGRAHNIHLSTLPNFRLPGDTSSASRYWERDLIQEPLEAVDGLMPVPQGPGTGVTLDREFLATVTEAQEEHRA 375
               SCOP domains d2fkpd1 D:6-132 N-          acylamino acid racemase                                                                            d2fkpd2 D:133-375 N-acylamino acid racemase                                                                                                                                                                                                         SCOP domains
               CATH domains 2fkpD01 D:6-123,D:          354-375 Enolase-like, N-terminal domain                                                   2fkpD02 D:124-353 Enolase superfamily                                                                                                                                                                                                 2fkpD01                CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee..eeeeeeeeee..----------.eeeeeeeeeee..eeeeee............hhhhhhhhhhhhhhhhhh..ee.hhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh.hhhhhhh....eee..eee....hhhhhhhhhhhhhh.....eeee.....hhhhhhhhhhhh....eeee.....hhhhhhhhhhhhhhh...ee.......hhhhhhhhhhh...eee.....hhhhhhhhhhhh...eeee......hhhhhhhhhhhhhhh...eee.....hhhhhhhhhhhh............hhhhh...............eee...........hhhhhhhheeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2fkp D   6 RMFKIEAAEIVVARLPLK----------THKVVPLLILHGEGVQGVAEGTMEARPMYREETIAGALDLLRGTFLPAILGQTFANPEAVSDALGSYRGNRMARAMVEMAAWDLWARTLGVPLCTLLGGHKEQVEVGVSLGIQADEQATVDLVRRHVEQGYRRIKLKIKPGWDVQPVRATREAFPDIRLTVDANSAYTLADAGRLRQLDEYDLTYIEQPLAWDDLVDHAELARRIRTPLCLDESVASASDARKALALGAGGVINLKVARVGGHAESRRVHDVAQSFGAPVWCGGMLESGIGRAHNIHLSCLSNFRLPGDTSSASRYWERDLIQEPLEAVDGLMPVPQGPGTGVTLDREFLATVTEAQEEHRA 375
                                    15       | -        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375
                                            23         34
   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, 8)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 8)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2FKP)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q9RYA6_DEIRA | Q9RYA6)
molecular function
    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:0016836    hydro-lyase activity    Catalysis of the cleavage of a carbon-oxygen bond by elimination of water.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0009234    menaquinone biosynthetic process    The chemical reactions and pathways resulting in the formation of any of the menaquinones. Structurally, menaquinones consist of a methylated naphthoquinone ring structure and side chains composed of a variable number of unsaturated isoprenoid residues. Menaquinones that have vitamin K activity and are known as vitamin K2.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.

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    Pro C:173 - Gly C:174   [ RasMol ]  
 
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  2fkp
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  5.1.1.10
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/TrEMBL
        Q9RYA6_DEIRA | Q9RYA6: 1r0m 1xpy 1xs2 2ggg 2ggh 2ggi 2ggj

(-) Related Entries Specified in the PDB File

1r0m STRUCTURE OF DEINOCOCCUS RADIODURANS N-ACYLAMINO ACID RACEMASE AT 1.3 A
2fkq THE SAME PROTEIN, THE MUTANT A68C-D72C
2fkr THE SAME PROTEIN, THE MUTANT A68C-D72C-NLQ
2fks THE SAME PROTEIN, THE MUTANT E149C-A182C
2fkt THE SAME PROTEIN, THE MUTANT Y218C