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(-) Description

Title :  STRUCTURE OF DEINOCOCCUS RADIODURANS N-ACYLAMINO ACID RACEMASE AT 1.3 : INSIGHTS INTO A FLEXIBLE BINDING POCKET AND EVOLUTION OF ENZYMATIC ACTIVITY
 
Authors :  W. -C. Wang, W. -C. Chiu, S. -K. Hsu, C. -L. Wu, C. -Y. Chen, J. -S. Liu, W. - H. Hsu
Date :  22 Sep 03  (Deposition) - 22 Sep 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.30
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Racemase, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. -C. Wang, W. -C. Chiu, S. -K. Hsu, C. -L. Wu, C. -Y. Chen, J. -S. Liu, W. -H. Hsu
Structural Basis For Catalytic Racemization And Substrate Specificity Of An N-Acylamino Acid Racemase Homologue From Deinococcus Radiodurans
J. Mol. Biol. V. 342 155 2004
PubMed-ID: 15313614  |  Reference-DOI: 10.1016/J.JMB.2004.07.023
(for further references see the PDB file header)

(-) Compounds

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

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1R0M)

(-) Sites  (0, 0)

(no "Site" information available for 1R0M)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1R0M)

(-) 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 1R0M)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1R0M)

(-) Exons   (0, 0)

(no "Exon" information available for 1R0M)

(-) 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 d1r0ma2 A:6-132 N-          acylamino acid racemase                                                                            d1r0ma1 A:133-375 N-acylamino acid racemase                                                                                                                                                                                                         SCOP domains
               CATH domains 1r0mA01 A:6-123,A:          354-375 Enolase-like, N-terminal domain                                                   1r0mA02 A:124-353 Enolase superfamily                                                                                                                                                                                                 1r0mA01                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
                 1r0m A   6 RMFKIEAAEIVVARLPLK----------THKVVPLLILHGEGVQGVAEGTMEARPMYREETIAGALDLLRGTFLPAILGQTFANPEAVSDALGSYRGNRMARAMVEMAAWDLWARTLGVPLGTLLGGHKEQVEVGVSLGIQADEQATVDLVRRHVEQGYRRIKLKIKPGWDVQPVRATREAFPDIRLTVDANSAYTLADAGRLRQLDEYDLTYIEQPLAWDDLVDHAELARRIRTPLCLDESVASASDARKALALGAGGVINLKVARVGGHAESRRVHDVAQSFGAPVWCGGMLESGIGRAHNIHLSTLSNFRLPGDTSSASRYWERDLIQEPLEAVDGLMPVPQGPGTGVTLDREFLATVTEAQEEHRA 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 d1r0mb2 B:6-132 N-          acylamino acid racemase                                                                            d1r0mb1 B:133-375 N-acylamino acid racemase                                                                                                                                                                                                         SCOP domains
               CATH domains 1r0mB01 B:6-123,B:          354-375 Enolase-like, N-terminal domain                                                   1r0mB02 B:124-353 Enolase superfamily                                                                                                                                                                                                 1r0mB01                CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee..eeeeeeeeee..----------.eeeeeeeeeee..eeeeee............hhhhhhhhhhhhhhhhhh..ee.hhhhhhhh......hhhhhhhhhhhhhhhhhhhhh.hhhhhhh....eee..eee....hhhhhhhhhhhhhhhh...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
                 1r0m B   6 RMFKIEAAEIVVARLPLK----------THKVVPLLILHGEGVQGVAEGTMEARPMYREETIAGALDLLRGTFLPAILGQTFANPEAVSDALGSYRGNRMARAMVEMAAWDLWARTLGVPLGTLLGGHKEQVEVGVSLGIQADEQATVDLVRRHVEQGYRRIKLKIKPGWDVQPVRATREAFPDIRLTVDANSAYTLADAGRLRQLDEYDLTYIEQPLAWDDLVDHAELARRIRTPLCLDESVASASDARKALALGAGGVINLKVARVGGHAESRRVHDVAQSFGAPVWCGGMLESGIGRAHNIHLSTLSNFRLPGDTSSASRYWERDLIQEPLEAVDGLMPVPQGPGTGVTLDREFLATVTEAQEEHRA 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 d1r0mc2 C:6-132 N-          acylamino acid racemase                                                                            d1r0mc1 C:133-375 N-acylamino acid racemase                                                                                                                                                                                                         SCOP domains
               CATH domains 1r0mC01 C:6-123,C:          354-375 Enolase-like, N-terminal domain                                                   1r0mC02 C:124-353 Enolase superfamily                                                                                                                                                                                                 1r0mC01                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
                 1r0m C   6 RMFKIEAAEIVVARLPLK----------THKVVPLLILHGEGVQGVAEGTMEARPMYREETIAGALDLLRGTFLPAILGQTFANPEAVSDALGSYRGNRMARAMVEMAAWDLWARTLGVPLGTLLGGHKEQVEVGVSLGIQADEQATVDLVRRHVEQGYRRIKLKIKPGWDVQPVRATREAFPDIRLTVDANSAYTLADAGRLRQLDEYDLTYIEQPLAWDDLVDHAELARRIRTPLCLDESVASASDARKALALGAGGVINLKVARVGGHAESRRVHDVAQSFGAPVWCGGMLESGIGRAHNIHLSTLSNFRLPGDTSSASRYWERDLIQEPLEAVDGLMPVPQGPGTGVTLDREFLATVTEAQEEHRA 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 d1r0md2 D:6-132 N-          acylamino acid racemase                                                                            d1r0md1 D:133-375 N-acylamino acid racemase                                                                                                                                                                                                         SCOP domains
               CATH domains 1r0mD01 D:6-123,D:          354-375 Enolase-like, N-terminal domain                                                   1r0mD02 D:124-353 Enolase superfamily                                                                                                                                                                                                 1r0mD01                CATH domains
           Pfam domains (1) ---MR_MLE_N-1r0mD0          1 D:9-131                                                                                         -----------------------------------------------MR_MLE-1r0mD05 D:179-245                                           ---------------------------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ---MR_MLE_N-1r0mD0          2 D:9-131                                                                                         -----------------------------------------------MR_MLE-1r0mD06 D:179-245                                           ---------------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
           Pfam domains (3) ---MR_MLE_N-1r0mD0          3 D:9-131                                                                                         -----------------------------------------------MR_MLE-1r0mD07 D:179-245                                           ---------------------------------------------------------------------------------------------------------------------------------- Pfam domains (3)
           Pfam domains (4) ---MR_MLE_N-1r0mD0          4 D:9-131                                                                                         -----------------------------------------------MR_MLE-1r0mD08 D:179-245                                           ---------------------------------------------------------------------------------------------------------------------------------- Pfam domains (4)
         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
                 1r0m D   6 RMFKIEAAEIVVARLPLK----------THKVVPLLILHGEGVQGVAEGTMEARPMYREETIAGALDLLRGTFLPAILGQTFANPEAVSDALGSYRGNRMARAMVEMAAWDLWARTLGVPLGTLLGGHKEQVEVGVSLGIQADEQATVDLVRRHVEQGYRRIKLKIKPGWDVQPVRATREAFPDIRLTVDANSAYTLADAGRLRQLDEYDLTYIEQPLAWDDLVDHAELARRIRTPLCLDESVASASDARKALALGAGGVINLKVARVGGHAESRRVHDVAQSFGAPVWCGGMLESGIGRAHNIHLSTLSNFRLPGDTSSASRYWERDLIQEPLEAVDGLMPVPQGPGTGVTLDREFLATVTEAQEEHRA 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  (2, 8)

Asymmetric Unit
(-)
Clan: Enolase_N (69)
(-)
Clan: Enolase_TIM (82)
(-)
Family: MR_MLE (48)
(-)
Deinococcus radiodurans (3)
2aMR_MLE-1r0mD05D:179-245
2bMR_MLE-1r0mD06D:179-245
2cMR_MLE-1r0mD07D:179-245
2dMR_MLE-1r0mD08D:179-245

(-) 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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  1r0m
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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

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