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(-) Description

Title :  STRUCTURE OF ORNITHINE CARBAMOYLTRANSFERASE FROM MYCOPLASMA PENETRANS WITH A P321 SPACE GROUP
 
Authors :  P. Gallego, J. Benach, R. Planell, E. Querol, J. A. Perez-Pons, D. Rever
Date :  13 Mar 12  (Deposition) - 28 Mar 12  (Release) - 31 Oct 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (3x)
Keywords :  Transferase, Ornithine Transcarbamoylase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Gallego, R. Planell, J. Benach, E. Querol, J. A. Perez-Pons, D. Reverter
Structural Characterization Of The Enzymes Composing The Arginine Deiminase Pathway In Mycoplasma Penetrans.
Plos One V. 7 47886 2012
PubMed-ID: 23082227  |  Reference-DOI: 10.1371/JOURNAL.PONE.0047886

(-) Compounds

Molecule 1 - ORNITHINE CARBAMOYLTRANSFERASE, CATABOLIC
    Chains: A, B, C, D
    EC Number: 2.1.3.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET19B
    Expression System Vector Type: PLASMID
    Organism Scientific: MYCOPLASMA PENETRANS
    Organism Taxid: 28227
    Synonym: ORNITHINE CARBAMOYLTRANSFERASE, OTCASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (3x): ABCD

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 4AMU)

(-) Sites  (0, 0)

(no "Site" information available for 4AMU)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4AMU)

(-) Cis Peptide Bonds  (5, 5)

Asymmetric Unit
No.Residues
1Leu A:277 -Pro A:278
2Leu B:277 -Pro B:278
3Leu C:277 -Pro C:278
4Leu D:240 -Gly D:241
5Leu D:277 -Pro D:278

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4AMU)

(-) PROSITE Motifs  (1, 4)

Asymmetric Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CARBAMOYLTRANSFERASEPS00097 Aspartate and ornithine carbamoyltransferases signature.OTCC_MYCPE55-62
 
 
 		  4A:55-62
B:55-62
C:55-62
D:55-62
Biological Unit 1 (1, 12)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CARBAMOYLTRANSFERASEPS00097 Aspartate and ornithine carbamoyltransferases signature.OTCC_MYCPE55-62
 
 
 		  12A:55-62
B:55-62
C:55-62
D:55-62

(-) Exons   (0, 0)

(no "Exon" information available for 4AMU)

(-) 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:344
 aligned with OTCC_MYCPE | Q8EVF5 from UniProtKB/Swiss-Prot  Length:342

    Alignment length:344
                              1                                                                                                                                                                                                                                                                                                                                                     
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338    
           OTCC_MYCPE     - --MPVNLKGRSLDSLLNFTTEEVQHLIDLSIDLKKAKYQGLHINNRPLVGKNIAILFQKDSTRTRCAFEVAASDLGAGVTYIGPSGSNMGKKESIEDTAKVLGRFYDGIEFRGFAQSDVDALVKYSGVPVWNGLTDDEHPTQIIADFMTMKEKFGNLKNKKIVFIGDYKNNVGVSTMIGAAFNGMHVVMCGPDNYKNEIDKNVLAKCIELFKRNGGSLRFSTDKILAAQDADVIYTDVWVSLGEPFELFDKRIGELKNFQVDMNMIKAAKNDVIFLHCLPAFHDDHTSFSKEVATTLGAKYPIVAKGEMEVTDEVFQSLHNKAFDQAENRMHSIKAIILSTIGY 342
               SCOP domains d4amua1 A:-1-153 automated matches                                                                                                                         d4amua2 A:154-342 automated matches                                                                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhhhhhhhhhhhhhhhhhhhhhh............eeeeee...hhhhhhhhhhhhhhhh.eeeeehhhhhh.....hhhhhhhhhhhhh.eeeee..hhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhh.....eeeee....hhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhhhhhhhhhhh.eeeee.hhhhhh....eeee........hhhhhhhhhhhhh....hhhhhhhh....eee..........hhhhhhhhhhh...hhhhhhh....hhhhhhh...hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------CARBAMOY---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4amu A  -1 KHMPVNLKGRSLDSLLNFTTEEVQHLIDLSIDLKKAKYQGLHINNRPLVGKNIAILFQKDSTRTRCAFEVAASDLGAGVTYIGPSGSNMGKKESIEDTAKVLGRFYDGIEFRGFAQSDVDALVKYSGVPVWNGLTDDEHPTQIIADFMTMKEKFGNLKNKKIVFIGDYKNNVGVSTMIGAAFNGMHVVMCGPDNYKNEIDKNVLAKCIELFKRNGGSLRFSTDKILAAQDADVIYTDVWVSLGEPFELFDKRIGELKNFQVDMNMIKAAKNDVIFLHCLPAFHDDHTSFSKEVATTLGAKYPIVAKGEMEVTDEVFQSLHNKAFDQAENRMHSIKAIILSTIGY 342
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338    


Chain B from PDB  Type:PROTEIN  Length:344
 aligned with OTCC_MYCPE | Q8EVF5 from UniProtKB/Swiss-Prot  Length:342

    Alignment length:344
                              1                                                                                                                                                                                                                                                                                                                                                     
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338    
           OTCC_MYCPE     - --MPVNLKGRSLDSLLNFTTEEVQHLIDLSIDLKKAKYQGLHINNRPLVGKNIAILFQKDSTRTRCAFEVAASDLGAGVTYIGPSGSNMGKKESIEDTAKVLGRFYDGIEFRGFAQSDVDALVKYSGVPVWNGLTDDEHPTQIIADFMTMKEKFGNLKNKKIVFIGDYKNNVGVSTMIGAAFNGMHVVMCGPDNYKNEIDKNVLAKCIELFKRNGGSLRFSTDKILAAQDADVIYTDVWVSLGEPFELFDKRIGELKNFQVDMNMIKAAKNDVIFLHCLPAFHDDHTSFSKEVATTLGAKYPIVAKGEMEVTDEVFQSLHNKAFDQAENRMHSIKAIILSTIGY 342
               SCOP domains d4amub1 B:-1-153 automated matches                                                                                                                         d4amub2 B:154-342 automated matches                                                                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhhhhhhhhhhhhhhhhhhhhhh............eeeeee...hhhhhhhhhhhhhhhh.eeeeehhhhhh.....hhhhhhhhhhhhh.eeeee..hhhhhhhhhhhhh..eee......hhhhhhhhhhhhhhhhh.....eeeee....hhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhhhhhhhhhhh.eeeee.hhhhhh....eeee..........hhhhhhhhhhhhhh.hhhhhhh.....eee..........hhhhhhhhhhh...hhhhh......hhhhhh....hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------CARBAMOY---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4amu B  -1 KHMPVNLKGRSLDSLLNFTTEEVQHLIDLSIDLKKAKYQGLHINNRPLVGKNIAILFQKDSTRTRCAFEVAASDLGAGVTYIGPSGSNMGKKESIEDTAKVLGRFYDGIEFRGFAQSDVDALVKYSGVPVWNGLTDDEHPTQIIADFMTMKEKFGNLKNKKIVFIGDYKNNVGVSTMIGAAFNGMHVVMCGPDNYKNEIDKNVLAKCIELFKRNGGSLRFSTDKILAAQDADVIYTDVWVSLGEPFELFDKRIGELKNFQVDMNMIKAAKNDVIFLHCLPAFHDDHTSFSKEVATTLGAKYPIVAKGEMEVTDEVFQSLHNKAFDQAENRMHSIKAIILSTIGY 342
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338    


Chain C from PDB  Type:PROTEIN  Length:344
 aligned with OTCC_MYCPE | Q8EVF5 from UniProtKB/Swiss-Prot  Length:342

    Alignment length:344
                              1                                                                                                                                                                                                                                                                                                                                                     
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338    
           OTCC_MYCPE     - --MPVNLKGRSLDSLLNFTTEEVQHLIDLSIDLKKAKYQGLHINNRPLVGKNIAILFQKDSTRTRCAFEVAASDLGAGVTYIGPSGSNMGKKESIEDTAKVLGRFYDGIEFRGFAQSDVDALVKYSGVPVWNGLTDDEHPTQIIADFMTMKEKFGNLKNKKIVFIGDYKNNVGVSTMIGAAFNGMHVVMCGPDNYKNEIDKNVLAKCIELFKRNGGSLRFSTDKILAAQDADVIYTDVWVSLGEPFELFDKRIGELKNFQVDMNMIKAAKNDVIFLHCLPAFHDDHTSFSKEVATTLGAKYPIVAKGEMEVTDEVFQSLHNKAFDQAENRMHSIKAIILSTIGY 342
               SCOP domains d4amuc1 C:-1-153 automated matches                                                                                                                         d4amuc2 C:154-342 automated matches                                                                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhhhhhhhhhhhhhhhhhhhhhh............eeeeee...hhhhhhhhhhhhhhhh.eeeeehhhhhh.....hhhhhhhhhhhhh.eeeee..hhhhhhhhhhhhh..eee......hhhhhhhhhhhhhhhhh.....eeeee....hhhhhhhhhhhhhh..eeeee.hhhhhhh.hhhhhhhhhhhhhhhh.eeeee.hhhhhh....eeee........hhhhhhhhhhhhhhhh.hhhhhhhh....eee..........hhhhhhhhh.....hhhhh......hhhhhh....hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------CARBAMOY---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4amu C  -1 KHMPVNLKGRSLDSLLNFTTEEVQHLIDLSIDLKKAKYQGLHINNRPLVGKNIAILFQKDSTRTRCAFEVAASDLGAGVTYIGPSGSNMGKKESIEDTAKVLGRFYDGIEFRGFAQSDVDALVKYSGVPVWNGLTDDEHPTQIIADFMTMKEKFGNLKNKKIVFIGDYKNNVGVSTMIGAAFNGMHVVMCGPDNYKNEIDKNVLAKCIELFKRNGGSLRFSTDKILAAQDADVIYTDVWVSLGEPFELFDKRIGELKNFQVDMNMIKAAKNDVIFLHCLPAFHDDHTSFSKEVATTLGAKYPIVAKGEMEVTDEVFQSLHNKAFDQAENRMHSIKAIILSTIGY 342
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338    


Chain D from PDB  Type:PROTEIN  Length:344
 aligned with OTCC_MYCPE | Q8EVF5 from UniProtKB/Swiss-Prot  Length:342

    Alignment length:344
                              1                                                                                                                                                                                                                                                                                                                                                     
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338    
           OTCC_MYCPE     - --MPVNLKGRSLDSLLNFTTEEVQHLIDLSIDLKKAKYQGLHINNRPLVGKNIAILFQKDSTRTRCAFEVAASDLGAGVTYIGPSGSNMGKKESIEDTAKVLGRFYDGIEFRGFAQSDVDALVKYSGVPVWNGLTDDEHPTQIIADFMTMKEKFGNLKNKKIVFIGDYKNNVGVSTMIGAAFNGMHVVMCGPDNYKNEIDKNVLAKCIELFKRNGGSLRFSTDKILAAQDADVIYTDVWVSLGEPFELFDKRIGELKNFQVDMNMIKAAKNDVIFLHCLPAFHDDHTSFSKEVATTLGAKYPIVAKGEMEVTDEVFQSLHNKAFDQAENRMHSIKAIILSTIGY 342
               SCOP domains d4amud1 D:-1-153 automated matches                                                                                                                         d4amud2 D:154-342 automated matches                                                                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhhhhhhhhhhhhhhhhhhhhhh............eeeeee...hhhhhhhhhhhhhhhh.eeeeehhhhh......hhhhhhhhhhhhh.eeeee..hhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhh.....eeeee....hhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhhhhhhhhhhh.eeeee.hhhhhh....eeee........hhhhhhhhhhhhhhhh.hhhhhhhh....eee..........hhhhhhhhhhh...hhhhhhh....hhhhhh....hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------CARBAMOY---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4amu D  -1 KHMPVNLKGRSLDSLLNFTTEEVQHLIDLSIDLKKAKYQGLHINNRPLVGKNIAILFQKDSTRTRCAFEVAASDLGAGVTYIGPSGSNMGKKESIEDTAKVLGRFYDGIEFRGFAQSDVDALVKYSGVPVWNGLTDDEHPTQIIADFMTMKEKFGNLKNKKIVFIGDYKNNVGVSTMIGAAFNGMHVVMCGPDNYKNEIDKNVLAKCIELFKRNGGSLRFSTDKILAAQDADVIYTDVWVSLGEPFELFDKRIGELKNFQVDMNMIKAAKNDVIFLHCLPAFHDDHTSFSKEVATTLGAKYPIVAKGEMEVTDEVFQSLHNKAFDQAENRMHSIKAIILSTIGY 342
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338
   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, 8)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4AMU)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4AMU)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (OTCC_MYCPE | Q8EVF5)
molecular function
    GO:0016597    amino acid binding    Interacting selectively and non-covalently with an amino acid, organic acids containing one or more amino substituents.
    GO:0016743    carboxyl- or carbamoyltransferase activity    Catalysis of the transfer of a carboxyl- or carbamoyl group from one compound (donor) to another (acceptor).
    GO:0004585    ornithine carbamoyltransferase activity    Catalysis of the reaction: carbamoyl phosphate + L-ornithine = phosphate + L-citrulline.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0019547    arginine catabolic process to ornithine    The chemical reactions and pathways resulting in the breakdown of arginine into other compounds, including ornithine.
    GO:0019546    arginine deiminase pathway    The chemical reactions and pathways resulting in the breakdown of arginine into other compounds, including ornithine and CO2, using the enzyme arginine deiminase.
    GO:0006525    arginine metabolic process    The chemical reactions and pathways involving arginine, 2-amino-5-(carbamimidamido)pentanoic acid.
    GO:0006520    cellular amino acid metabolic process    The chemical reactions and pathways involving amino acids, carboxylic acids containing one or more amino groups, as carried out by individual cells.
    GO:0006591    ornithine metabolic process    The chemical reactions and pathways involving ornithine, an amino acid only rarely found in proteins, but which is important in living organisms as an intermediate in the reactions of the urea cycle and in arginine biosynthesis.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

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

UniProtKB/Swiss-Prot
        OTCC_MYCPE | Q8EVF5: 4anf

(-) Related Entries Specified in the PDB File

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