Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF THE HEXAMERIC CATABOLIC ORNITHINE TRANSCARBAMYLASE FROM LACTOBACILLUS HILGARDII
 
Authors :  B. De Las Rivas, G. C. Fox, I. Angulo, H. Rodriguez, R. Munoz, J. M. Mancheno
Date :  06 Nov 08  (Deposition) - 17 Nov 09  (Release) - 17 Nov 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (2x)
Keywords :  Transcarbamylase, Metal Binding-Site, Hexamer, Cytoplasm, Ornithine, Transferase, Arginine Metabolism, Carbamoyl Phosphate (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. De Las Rivas, G. C. Fox, I. Angulo, M. M. Ripoll, H. Rodriguez, R. Munoz, J. M. Mancheno
Crystal Structure Of The Hexameric Catabolic Ornithine Transcarbamylase From Lactobacillus Hilgardii: Structural Insights Into The Oligomeric Assembly And Metal Binding.
J. Mol. Biol. V. 393 425 2009
PubMed-ID: 19666033  |  Reference-DOI: 10.1016/J.JMB.2009.08.002

(-) Compounds

Molecule 1 - ORNITHINE CARBAMOYLTRANSFERASE, CATABOLIC
    Chains: A, B, C
    EC Number: 2.1.3.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: JM109(DE3)
    Expression System Taxid: 562
    Organism Scientific: LACTOBACILLUS HILGARDII
    Organism Taxid: 1588
    Synonym: ORNITHINE TRANSCARBAMYLASE, OTCASE

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (2x): ABC

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1NI1Ligand/IonNICKEL (II) ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1NI-1Ligand/IonNICKEL (II) ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:79 , HOH A:2058 , HIS B:79 , HOH B:2048 , HIS C:79 , HOH C:2034BINDING SITE FOR RESIDUE NI A 1344

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2W37)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Leu A:279 -Pro A:280
2Leu B:279 -Pro B:280
3Leu C:279 -Pro C:280

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2W37)

(-) PROSITE Motifs  (1, 3)

Asymmetric Unit (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CARBAMOYLTRANSFERASEPS00097 Aspartate and ornithine carbamoyltransferases signature.OTCC_LACHI58-65
 
 		  3A:58-65
B:58-65
C:58-65
Biological Unit 1 (1, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CARBAMOYLTRANSFERASEPS00097 Aspartate and ornithine carbamoyltransferases signature.OTCC_LACHI58-65
 
 		  6A:58-65
B:58-65
C:58-65

(-) Exons   (0, 0)

(no "Exon" information available for 2W37)

(-) 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:341
 aligned with OTCC_LACHI | Q8G998 from UniProtKB/Swiss-Prot  Length:343

    Alignment length:341
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342 
           OTCC_LACHI     3 KDFRQNVFQGRSVLAEKDFSAAELEYLIDFGLHLKALKKAGIPHHYLEGKNIALLFEKSSTRTRSAFTTASIDLGAHPEYLGQNDIQLGKKESTSDTAKVLGSMFDGIEFRGFKQSDAEILARDSGVPVWNGLTDEWHPTQMLADFMTVKENFGKLQGLTLTFMGDGRNNVANSLLVTGAILGVNIHIVAPKALFPTEETQNIAKGFAEKSGAKLVITDDLDEGLKGSNVVYTDVWVSMGESNWEERVKELTPYQVNMEAMKKTGTPDDQLIFMHCLPAFHNTDTQYGKEIKEKYGITEMEVTDEVFTSKYARQFEEAENRMHSIKAMMAATLGNLFIPRV 343
               SCOP domains d2w37a1 A:3-156 automated matches                                                                                                                         d2w37a2 A:157-343 automated matches                                                                                                                                                         SCOP domains
               CATH domains 2w37A01 A:3-142  [code=3.40.50.1370, no name defined]                                                                                       2w37A02 A:143-322  [code=3.40.50.1370, no name defined]                                                                                                                             --------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....................hhhhhhhhhhhhhhhhhhhh..........eeeeeee...hhhhhhhhhhhhh...eeeee............hhhhhhhhhhh..eeeee...hhhhhhhhhh....eeeee.....hhhhhhhhhhhhhhh......eeeee.....hhhhhhhhhhhhh..eeeee........hhhhhhhhhhhhhh...eeee..hhhhh....eeee..........hhhhhhhh......hhhhhh........eeee..........hhhhhhhhhh........hhhh......hhhhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------CARBAMOY-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2w37 A   3 KDFRQNVFQGRSVLAEKDFSAAELEYLIDFGLHLKALKKAGIPHHYLEGKNIALLFEKSSTRTRSAFTTASIDLGAHPEYLGQNDIQLGKKESTSDTAKVLGSMFDGIEFRGFKQSDAEILARDSGVPVWNGLTDEWHPTQMLADFMTVKENFGKLQGLTLTFMGDGRNNVANSLLVTGAILGVNIHIVAPKALFPTEETQNIAKGFAEKSGAKLVITDDLDEGLKGSNVVYTDVWVSMGESNWEERVKELTPYQVNMEAMKKTGTPDDQLIFMHCLPAFHNTDTQYGKEIKEKYGITEMEVTDEVFTSKYARQFEEAENRMHSIKAMMAATLGNLFIPRV 343
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342 


Chain B from PDB  Type:PROTEIN  Length:341
 aligned with OTCC_LACHI | Q8G998 from UniProtKB/Swiss-Prot  Length:343

    Alignment length:341
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342 
           OTCC_LACHI     3 KDFRQNVFQGRSVLAEKDFSAAELEYLIDFGLHLKALKKAGIPHHYLEGKNIALLFEKSSTRTRSAFTTASIDLGAHPEYLGQNDIQLGKKESTSDTAKVLGSMFDGIEFRGFKQSDAEILARDSGVPVWNGLTDEWHPTQMLADFMTVKENFGKLQGLTLTFMGDGRNNVANSLLVTGAILGVNIHIVAPKALFPTEETQNIAKGFAEKSGAKLVITDDLDEGLKGSNVVYTDVWVSMGESNWEERVKELTPYQVNMEAMKKTGTPDDQLIFMHCLPAFHNTDTQYGKEIKEKYGITEMEVTDEVFTSKYARQFEEAENRMHSIKAMMAATLGNLFIPRV 343
               SCOP domains d2w37b1 B:3-156 automated matches                                                                                                                         d2w37b2 B:157-343 automated matches                                                                                                                                                         SCOP domains
               CATH domains 2w37B01 B:3-142  [code=3.40.50.1370, no name defined]                                                                                       2w37B02 B:143-322  [code=3.40.50.1370, no name defined]                                                                                                                             --------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....................hhhhhhhhhhhhhhhhhhhh..........eeeeeee...hhhhhhhhhhhhh...eeeee............hhhhhhhhhhh..eeeee...hhhhhhhhhh....eeeee.....hhhhhhhhhhhhhhh......eeeee.....hhhhhhhhhhhhh..eeeee........hhhhhhhhhhhhhh...eeee..hhhhh....eeee..........hhhhhhhh......hhhhhh........eeee..........hhhhhhhhhh........hhhh......hhhhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------CARBAMOY-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2w37 B   3 KDFRQNVFQGRSVLAEKDFSAAELEYLIDFGLHLKALKKAGIPHHYLEGKNIALLFEKSSTRTRSAFTTASIDLGAHPEYLGQNDIQLGKKESTSDTAKVLGSMFDGIEFRGFKQSDAEILARDSGVPVWNGLTDEWHPTQMLADFMTVKENFGKLQGLTLTFMGDGRNNVANSLLVTGAILGVNIHIVAPKALFPTEETQNIAKGFAEKSGAKLVITDDLDEGLKGSNVVYTDVWVSMGESNWEERVKELTPYQVNMEAMKKTGTPDDQLIFMHCLPAFHNTDTQYGKEIKEKYGITEMEVTDEVFTSKYARQFEEAENRMHSIKAMMAATLGNLFIPRV 343
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342 


Chain C from PDB  Type:PROTEIN  Length:341
 aligned with OTCC_LACHI | Q8G998 from UniProtKB/Swiss-Prot  Length:343

    Alignment length:341
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342 
           OTCC_LACHI     3 KDFRQNVFQGRSVLAEKDFSAAELEYLIDFGLHLKALKKAGIPHHYLEGKNIALLFEKSSTRTRSAFTTASIDLGAHPEYLGQNDIQLGKKESTSDTAKVLGSMFDGIEFRGFKQSDAEILARDSGVPVWNGLTDEWHPTQMLADFMTVKENFGKLQGLTLTFMGDGRNNVANSLLVTGAILGVNIHIVAPKALFPTEETQNIAKGFAEKSGAKLVITDDLDEGLKGSNVVYTDVWVSMGESNWEERVKELTPYQVNMEAMKKTGTPDDQLIFMHCLPAFHNTDTQYGKEIKEKYGITEMEVTDEVFTSKYARQFEEAENRMHSIKAMMAATLGNLFIPRV 343
               SCOP domains d2w37c1 C:3-156 automated matches                                                                                                                         d2w37c2 C:157-343 automated matches                                                                                                                                                         SCOP domains
               CATH domains 2w37C01 C:3-142  [code=3.40.50.1370, no name defined]                                                                                       2w37C02 C:143-322  [code=3.40.50.1370, no name defined]                                                                                                                             --------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....................hhhhhhhhhhhhhhhhhhhh..........eeeeeee...hhhhhhhhhhhhh...eeeee............hhhhhhhhhhh..eeeee...hhhhhhhhhh....eeeee.....hhhhhhhhhhhhhhh......eeeee.....hhhhhhhhhhhhh..eeeee........hhhhhhhhhhhhhh...eeee..hhhhh....eeee..........hhhhhhhh......hhhhhh........eeee..........hhhhhhhhhh........hhhh......hhhhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------CARBAMOY-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2w37 C   3 KDFRQNVFQGRSVLAEKDFSAAELEYLIDFGLHLKALKKAGIPHHYLEGKNIALLFEKSSTRTRSAFTTASIDLGAHPEYLGQNDIQLGKKESTSDTAKVLGSMFDGIEFRGFKQSDAEILARDSGVPVWNGLTDEWHPTQMLADFMTVKENFGKLQGLTLTFMGDGRNNVANSLLVTGAILGVNIHIVAPKALFPTEETQNIAKGFAEKSGAKLVITDDLDEGLKGSNVVYTDVWVSMGESNWEERVKELTPYQVNMEAMKKTGTPDDQLIFMHCLPAFHNTDTQYGKEIKEKYGITEMEVTDEVFTSKYARQFEEAENRMHSIKAMMAATLGNLFIPRV 343
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342
   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, 6)

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

(-) CATH Domains  (1, 6)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2W37)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (OTCC_LACHI | Q8G998)
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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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: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.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    NI  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Leu A:279 - Pro A:280   [ RasMol ]  
    Leu B:279 - Pro B:280   [ RasMol ]  
    Leu C:279 - Pro C:280   [ RasMol ]  
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2w37
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  OTCC_LACHI | Q8G998
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  2.1.3.3
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  OTCC_LACHI | Q8G998
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 2W37)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2W37)