Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym.Unit - manually
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
(-)Biological Unit 3
collapse expand < >
Image Asym.Unit - manually
Asym.Unit - manually  (Jmol Viewer)
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)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)

(-) Description

Title :  THE PALA-LIGANDED ASPARTATE TRANSCARBAMOYLASE CATALYTIC SUBUNIT FROM PYROCOCCUS ABYSSI
 
Authors :  S. Van Boxstael, R. Cunin, D. Maes
Date :  30 Aug 02  (Deposition) - 25 Feb 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Biol. Unit 2:  A  (1x)
Biol. Unit 3:  A  (3x)
Keywords :  Beta Pleated Sheet, Protein Inhibitor Complex, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Van Boxstael, R. Cunin, S. Khan, D. Maes
Aspartate Transcarbamylase From The Hyperthermophilic Archaeon Pyrococcus Abyssi: Thermostability And 1. 8A Resolution Crystal Structure Of The Catalytic Subunit Complexed With The Bisubstrate Analogue N-Phosphonacetyl-L-Aspartate.
J. Mol. Biol. V. 326 203 2003
PubMed-ID: 12547202  |  Reference-DOI: 10.1016/S0022-2836(02)01228-7

(-) Compounds

Molecule 1 - ASPARTATE TRANSCARBAMOYLASE
    ChainsA
    EC Number2.1.3.2
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPTRC99A
    Expression System StrainC600ATC-
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GenePYRB
    Organism ScientificPYROCOCCUS ABYSSI
    Organism Taxid29292
    SynonymASPARTATE CARBAMOYLTRANSFERASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (3x)A
Biological Unit 2 (1x)A
Biological Unit 3 (3x)A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1PAL1Ligand/IonN-(PHOSPHONACETYL)-L-ASPARTIC ACID
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1PAL3Ligand/IonN-(PHOSPHONACETYL)-L-ASPARTIC ACID
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1PAL1Ligand/IonN-(PHOSPHONACETYL)-L-ASPARTIC ACID
Biological Unit 3 (1, 3)
No.NameCountTypeFull Name
1PAL3Ligand/IonN-(PHOSPHONACETYL)-L-ASPARTIC ACID

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:55 , THR A:56 , ARG A:57 , THR A:58 , SER A:83 , LYS A:86 , ARG A:107 , HIS A:135 , GLN A:138 , ARG A:168 , ARG A:229 , GLN A:231 , LEU A:268 , HOH A:394 , HOH A:395BINDING SITE FOR RESIDUE PAL A 385

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1ML4)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Leu A:268 -Pro A:269

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1ML4)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CARBAMOYLTRANSFERASEPS00097 Aspartate and ornithine carbamoyltransferases signature.PYRB_PYRAB51-58  1A:51-58
Biological Unit 1 (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CARBAMOYLTRANSFERASEPS00097 Aspartate and ornithine carbamoyltransferases signature.PYRB_PYRAB51-58  3A:51-58
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CARBAMOYLTRANSFERASEPS00097 Aspartate and ornithine carbamoyltransferases signature.PYRB_PYRAB51-58  1A:51-58
Biological Unit 3 (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CARBAMOYLTRANSFERASEPS00097 Aspartate and ornithine carbamoyltransferases signature.PYRB_PYRAB51-58  3A:51-58

(-) Exons   (0, 0)

(no "Exon" information available for 1ML4)

(-) 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:307
 aligned with PYRB_PYRAB | P77918 from UniProtKB/Swiss-Prot  Length:308

    Alignment length:307
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       
           PYRB_PYRAB     2 DWKGRDVISIRDFSKEDIETVLATAERLERELKEKGQLEYAKGKILATLFFEPSTRTRLSFESAMHRLGGAVIGFAEASTSSVKKGESLRDTIKTVEQYCDVIVIRHPKEGAARLAAEVAEVPVINAGDGSNQHPTQTLLDLYTIKKEFGRIDGLKIGLLGDLKYGRTVHSLAEALTFYDVELYLISPELLRMPRHIVEELREKGMKVVETTTLEDVIGKLDVLYVTRIQKERFPDEQEYLKVKGSYQVNLKVLEKAKDELRIMHPLPRVDEIHPEVDNTKHAIYFRQVFNGVPVRMALLALVLGVI 308
               SCOP domains d1ml4a1 A:2-151 Aspartate carbamoyltransferase catalytic subunit                                                                                      d1ml4a2 A:152-308 Aspartate carbamoyltransferase catalytic subunit                                                                                            SCOP domains
               CATH domains 1ml4A01 A:2-134,A:293-308  [code=3.40.50.1370, no name defined]                                                                      1ml4A02 A:135-292  [code=3.40.50.1370, no name defined]                                                                                                       1ml4A01          CATH domains
               Pfam domains ----OTCace_N-1ml4A02 A:6-149                                                                                                                        ----OTCace-1ml4A01 A:154-304                                                                                                                               ---- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhhhhhhhhhhhhhh........eeeeee....hhhhhhhhhhhhhh..eeeee.hhhhhhhhhh.hhhhhhhhhh....eeeeee...hhhhhhhhh....eeeeee....hhhhhhhhhhhhhhhh.....eeeeee.....hhhhhhhhhhhhhh.eeeeee.hhhhh.hhhhhhhhhhh...eeee..hhhhhh...eeee...hhhhh.hhhhhhh.........hhhhhh....eee.........hhhhhhh...hhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------CARBAMOY---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ml4 A   2 DWKGRDVISIRDFSKEDIETVLATAERLERELKEKGQLEYAKGKILATLFFEPSTRTRLSFESAMHRLGGAVIGFAEASTSSVKKGESLRDTIKTVEQYCDVIVIRHPKEGAARLAAEVAEVPVINAGDGSNQHPTQTLLDLYTIKKEFGRIDGLKIGLLGDLKYGRTVHSLAEALTFYDVELYLISPELLRMPRHIVEELREKGMKVVETTTLEDVIGKLDVLYVTRIQKERFPDEQEYLKVKGSYQVNLKVLEKAKDELRIMHPLPRVDEIHPEVDNTKHAIYFRQVFNGVPVRMALLALVLGVI 308
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       

   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 Unit

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (2, 2)

Asymmetric Unit

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A   (PYRB_PYRAB | P77918)
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:0004070    aspartate carbamoyltransferase activity    Catalysis of the reaction: L-aspartate + carbamoyl phosphate = N-carbamoyl-L-aspartate + H(+) + phosphate.
    GO:0016743    carboxyl- or carbamoyltransferase activity    Catalysis of the transfer of a carboxyl- or carbamoyl group from one compound (donor) to another (acceptor).
    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:0044205    'de novo' UMP biosynthetic process    The chemical reactions and pathways resulting in the formation of UMP, uridine monophosphate, starting with the synthesis of (S)-dihydroorotate from bicarbonate; UMP biosynthesis may either occur via reduction by quinone, NAD(+) or oxygen.
    GO:0006207    'de novo' pyrimidine nucleobase biosynthetic process    The chemical reactions and pathways resulting in the formation of pyrimidine nucleobases, 1,3-diazine, organic nitrogenous bases, beginning with the synthesis of a pyrimidine ring from simpler precursors.
    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:0006221    pyrimidine nucleotide biosynthetic process    The chemical reactions and pathways resulting in the formation of a pyrimidine nucleotide, a compound consisting of nucleoside (a pyrimidine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.

 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
    PAL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Leu A:268 - Pro A:269   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1ml4
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  PYRB_PYRAB | P77918
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  2.1.3.2
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  PYRB_PYRAB | P77918
    Protein Disorder PredictionDisEMBL | 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 1ML4)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1ML4)