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(-) Description

Title :  THE CRYSTAL STRUCTURE OF MALONAMIDASE E2 COVALENTLY COMPLEXED WITH PYROPHOSPHATE FROM BRADYRHIZOBIUM JAPONICUM
 
Authors :  S. Shin, N. -C. Ha, T. -H. Lee, B. -H. Oh
Date :  08 Feb 03  (Deposition) - 25 Feb 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Amidase, Malonamidase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Shin, Y. S. Yun, H. M. Koo, Y. S. Kim, K. Y. Choi, B. -H. Oh
Characterization Of A Novel Ser-Cisser-Lys Catalytic Triad In Comparison With The Classical Ser-His-Asp Triad.
J. Biol. Chem. V. 278 24937 2003
PubMed-ID: 12711609  |  Reference-DOI: 10.1074/JBC.M302156200

(-) Compounds

Molecule 1 - MALONAMIDASE E2
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PUC18
    Expression System Strain: AD494(DE3)
    Expression System Taxid: 562
    Expression System Vector: ESCHERICHIA COLI
    Organism Scientific: BRADYRHIZOBIUM JAPONICUM
    Organism Taxid: 375
    Other Details: PYROPHOSPHATE COVALENTLY BONDED WITH RESIDUE 155 IN CHAIN A, B

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1POP2Ligand/IonPYROPHOSPHATE 2-

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:111 , ARG A:113 , SER A:131 , GLN A:151 , THR A:152 , GLY A:153 , GLY A:154 , SER A:155 , ARG A:158 , PRO A:359 , HOH A:2439 , HOH A:2440 , HOH A:2441BINDING SITE FOR RESIDUE POP A1155
2AC2SOFTWAREALA B:111 , ARG B:113 , SER B:131 , GLN B:151 , THR B:152 , GLY B:153 , GLY B:154 , SER B:155 , ARG B:158 , PRO B:359 , HOH B:2218 , HOH B:2260 , HOH B:2485 , HOH B:2486BINDING SITE FOR RESIDUE POP B1155

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gly A:130 -Ser A:131
2Gly B:130 -Ser B:131

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1OCM)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1OCM)

(-) 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:412
 aligned with Q9ZIV5_BRAJP | Q9ZIV5 from UniProtKB/TrEMBL  Length:414

    Alignment length:412
                                    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       360       370       380       390       400       410  
         Q9ZIV5_BRAJP     1 MISLADLQRRIETGELSPNAAIAQSHAAIEAREKEVHAFVRHDKSARAQASGPLRGIAVGIKDIIDTANMPTEMGSEIYRGWQPRSDAPVVMMLKRAGATIIGKTTTTAFASRDPTATLNPHNTGHSPGGSSSGSAAAVGAGMIPLALGTQTGGSVIRPAAYCGTAAIKPSFRMLPTVGVKCYSWALDTVGLFGARAEDLARGLLAMTGRSEFSGIVPAKAPRIGVVRQEFAGAVEPAAEQGLQAAIKAAERAGASVQAIDLPEAVHEAWRIHPIIQDFEAHRALAWEFSEHHDEIAPMLRASLDATVGLTPKEYDEARRIGRRGRRELGEVFEGVDVLLTYSAPGTAPAKALASTGDPRYNRLWTLMGNPCVNVPVLKVGGLPIGVQVIARFGNDAHALATAWFLEDALAK 412
               SCOP domains d1ocma_ A: Malonamidase E2                                                                                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 1ocmA00 A:1-412 Amidase signature (AS) enzymes                                                                                                                                                                                                                                                                                                                                                                               CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh.eeee...............eeeee.............hhhhh.......hhhhhhhhhh..eeeeee..hhhhh...................hhhhhhhhhh....eeeeee....hhhhhhhhh.eeee...................eeeeee.hhhhhhhhhhhhhhhhhhh........eeee..hhhhh..hhhhhhhhhhhhhhhhhh..eeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh....eeeee........hhhh.......hhhhhhhh..eeeeeeeee..eeeeeeeee...hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ocm A   1 MISLADLQRRIETGELSPNAAIAQSHAAIEAREKEVHAFVRHDKSARAQASGPLRGIAVGIKDIIDTANMPTEMGSEIYRGWQPRSDAPVVMMLKRAGATIIGKTTTTAFASRDPTATLNPHNTGHSPGGSSSGSAAAVGAGMIPLALGTQTGGSVIRPAAYCGTAAIKPSFRMLPTVGVKCYSWALDTVGLFGARAEDLARGLLAMTGRSEFSGIVPAKAPRIGVVRQEFAGAVEPAAEQGLQAAIKAAERAGASVQAIDLPEAVHEAWRIHPIIQDFEAHRALAWEFSEHHDEIAPMLRASLDATVGLTPKEYDEARRIGRRGRRELGEVFEGVDVLLTYSAPGTAPAKALASTGDPRYNRLWTLMGNPCVNVPVLKVGGLPIGVQVIARFGNDAHALATAWFLEDALAK 412
                                    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       360       370       380       390       400       410  


Chain B from PDB  Type:PROTEIN  Length:412
 aligned with Q9ZIV5_BRAJP | Q9ZIV5 from UniProtKB/TrEMBL  Length:414

    Alignment length:412
                                    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       360       370       380       390       400       410  
         Q9ZIV5_BRAJP     1 MISLADLQRRIETGELSPNAAIAQSHAAIEAREKEVHAFVRHDKSARAQASGPLRGIAVGIKDIIDTANMPTEMGSEIYRGWQPRSDAPVVMMLKRAGATIIGKTTTTAFASRDPTATLNPHNTGHSPGGSSSGSAAAVGAGMIPLALGTQTGGSVIRPAAYCGTAAIKPSFRMLPTVGVKCYSWALDTVGLFGARAEDLARGLLAMTGRSEFSGIVPAKAPRIGVVRQEFAGAVEPAAEQGLQAAIKAAERAGASVQAIDLPEAVHEAWRIHPIIQDFEAHRALAWEFSEHHDEIAPMLRASLDATVGLTPKEYDEARRIGRRGRRELGEVFEGVDVLLTYSAPGTAPAKALASTGDPRYNRLWTLMGNPCVNVPVLKVGGLPIGVQVIARFGNDAHALATAWFLEDALAK 412
               SCOP domains d1ocmb_ B: Malonamidase E2                                                                                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 1ocmB00 B:1-412 Amidase signature (AS) enzymes                                                                                                                                                                                                                                                                                                                                                                               CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh.eeee...............eeeee.............hhhhh.......hhhhhhhhhh..eeeeee..hhhhh...................hhhhhhhhhh....eeeeee....hhhhhhhhh.eeee...................eeeeee.hhhhhhhhhhhhhhhhhhh........eeee..hhhhh..hhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh....eeeee........hhhh.......hhhhhhhh..eeeeeeeee..eeeeeeeee...hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ocm B   1 MISLADLQRRIETGELSPNAAIAQSHAAIEAREKEVHAFVRHDKSARAQASGPLRGIAVGIKDIIDTANMPTEMGSEIYRGWQPRSDAPVVMMLKRAGATIIGKTTTTAFASRDPTATLNPHNTGHSPGGSSSGSAAAVGAGMIPLALGTQTGGSVIRPAAYCGTAAIKPSFRMLPTVGVKCYSWALDTVGLFGARAEDLARGLLAMTGRSEFSGIVPAKAPRIGVVRQEFAGAVEPAAEQGLQAAIKAAERAGASVQAIDLPEAVHEAWRIHPIIQDFEAHRALAWEFSEHHDEIAPMLRASLDATVGLTPKEYDEARRIGRRGRRELGEVFEGVDVLLTYSAPGTAPAKALASTGDPRYNRLWTLMGNPCVNVPVLKVGGLPIGVQVIARFGNDAHALATAWFLEDALAK 412
                                    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       360       370       380       390       400       410
   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  (1, 2)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1OCM)

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q9ZIV5_BRAJP | Q9ZIV5)
molecular function
    GO:0016884    carbon-nitrogen ligase activity, with glutamine as amido-N-donor    Catalysis of the transfer of the amide nitrogen of glutamine to a variety of substrates. GATases catalyze two separate reactions at two active sites, which are located either on a single polypeptide chain or on different subunits. In the glutaminase reaction, glutamine is hydrolyzed to glutamate and ammonia, which is added to an acceptor substrate in the synthase reaction.

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 Related Entries

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

UniProtKB/TrEMBL
        Q9ZIV5_BRAJP | Q9ZIV5: 1o9n 1o9o 1o9p 1o9q 1obi 1obj 1obk 1obl 1och 1ock 1ocl

(-) Related Entries Specified in the PDB File

1o9n CRYSTAL STRUCTURE OF THE K62A MUTANT OF MALONAMIDASE E2 FROM BRADYRHIZOBIUM JAPONICUM
1o9o CRYSTAL STRUCTURE OF THE S131A MUTANT OF MALONAMIDASE E2 COMPLEXED WITH MALONAMATE FROM BRADYRHIZOBIUM JAPONICUM
1o9p CRYSTAL STRUCTURE OF THE S131A MUTANT OF MALONAMIDASE E2 COMPLEXED WITH MALONATE FROM BRADYRHIZOBIUM JAPONICUM
1o9q CRYSTAL STRUCTURE OF THE S155C MUTANT OF MALONAMIDASE E2 FROM BRADYRHIZOBIUM JAPONICUM
1obi CRYSTAL STRUCTURE OF THE G130A MUTANT OF MALONAMIDASE E2 FROM BRADYRHIZOBIUM JAPONICUM
1obj CRYSTAL STRUCTURE OF THE T150A MUTANT OF MALONAMIDASE E2 FROM BRADYRHIZOBIUM JAPONICUM
1obk CRYSTAL STRUCTURE OF THE R158Q MUTANT OF MALONAMIDASE E2 FROM BRADYRHIZOBIUM JAPONICUM
1obl CRYSTAL STRUCTURE OF THE S133A MUTANT OF MALONAMIDASE E2 COMPLEXED WITH MALONATE FROM BRADYRHIZOBIUM JAPONICUM
1och CRYSTAL STRUCTURE OF THE S155C MUTANT OF MALONAMIDASE E2
1ock THE CRYSTAL STRUCTURE OF MALONAMIDASE E2 FROM BRADYRHIZOBIUM JAPONICUM
1ocl THE CRYSTAL STRUCTURE OF MALONAMIDASE E2 COMPLEXED WITH MALONATE FROM BRADYRHIZOBIUM JAPONICUM