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(-) Description

Title :  STRUCTURE OF YGEW ENCODED PROTEIN FROM E. COLI
 
Authors :  Y. Li, Z. Jing, X. Yu, N. M. Allewell, M. Tuchman, D. Shi
Date :  07 Jan 11  (Deposition) - 04 May 11  (Release) - 14 Sep 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Keywords :  Rossmann Fold, Unknown Transcarbamylase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Li, Z. Jin, X. Yu, N. M. Allewell, M. Tuchman, D. Shi
The Ygew Encoded Protein From Escherichia Coli Is A Knotted Ancestral Catabolic Transcarbamylase.
Proteins V. 79 2327 2011
PubMed-ID: 21557323  |  Reference-DOI: 10.1002/PROT.23043

(-) Compounds

Molecule 1 - TRANSCARBAMYLASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: YGEW
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 15)

Asymmetric Unit (1, 15)
No.NameCountTypeFull Name
1MSE15Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 45)
No.NameCountTypeFull Name
1MSE45Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 3Q98)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3Q98)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Leu A:331 -Pro A:332

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3Q98)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3Q98)

(-) Exons   (0, 0)

(no "Exon" information available for 3Q98)

(-) 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:381
 aligned with Q1R7G1_ECOUT | Q1R7G1 from UniProtKB/TrEMBL  Length:396

    Alignment length:396
                                    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      
         Q1R7G1_ECOUT     1 MMKTVNELIKDINSLTSHLHEKDFLLTWEQTPDELKQVLDVAAALKALRAENISTKVFNSGLGISVFRDNSTRTRFSYASALNLLGLAQQDLDEGKSQIAHGETVRETANMISFCADAIGIRDDMYLGAGNAYMREVGAALDDGYKQGVLPQRPALVNLQCDIDHPTQSMADLAWLREHFGSLENLKGKKIAMTWAYSPSYGKPLSVPQGIIGLMTRFGMDVTLAHPEGYDLIPDVVEVAKNNAKASGGSFRQVTSMEEAFKDADIVYPKSWAPYKVMEERTELLRANDHEGLKALEKQCLAQNAQHKDWHCTEEMMELTRDGEALYMHCLPADISGVSCKEGEVTEGVFEKYRIATYKEASWKPYIIAAMILSRKYAKPGALLEQLLKEAQERVK 396
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ---------------------OTCace_N-3q98A02 A:22-179                                                                                                                                     -------OTCace-3q98A01 A:187-374                                                                                                                                                                    ---------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh...hhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh..........eeeeeee.-----.hhhhhhhhhhh.eeee..-------...hhhhhhhhh...eeeeeeee.....---hhhhhhhhhhhhhhhh.......eeeeee....hhhhhhhhhhhhhhhhh.hhhhh..eeeee..........hhhhhhhhhhhhhhh.eeeee.......hhhhhhhhhhhhhhhh.eeeee.hhhhhhh...eeee....hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhh.ee.......ee........eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3q98 A   1 mmKTVNELIKDINSLTSHLHEKDFLLTWEQTPDELKQVLDVAAALKALRAENISTKVFNSGLGISVFRD-----RFSYASALNLLGLAQQDLD-------HGETVRETANmISFCADAIGIRDDmYLG---AYmREVGAALDDGYKQGVLPQRPALVNLQCDIDHPTQSmADLAWLREHFGSLENLKGKKIAmTWAYSPSYGKPLSVPQGIIGLmTRFGmDVTLAHPEGYDLIPDVVEVAKNNAKASGGSFRQVTSmEEAFKDADIVYPKSWAPYKVmEERTELLRANDHEGLKALEKQCLAQNAQHKDWHCTEEmmELTRDGEALYmHCLPADISGVSCKEGEVTEGVFEKYRIATYKEASWKPYIIAAmILSRKYAKPGALLEQLLKEAQERVK 396
                            ||      10        20        30        40        50        60        |-    |   80        90  |      -|      110|      120    |  | - | |   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      
                            ||                                                                 69    75                93     101       111-MSE       125-MSE132 |                                 170-MSE                193-MSE               215-MSE|                                  257-MSE              278-MSE                               316-MSE     328-MSE                                    371-MSE                     
                            1-MSE                                                                                                                        128   134-MSE                                                                               220-MSE                                                                                          317-MSE                                                                           
                             2-MSE                                                                                                                                                                                                                                                                                                                                                                                                      


Chain A from PDB  Type:PROTEIN  Length:381
 aligned with YGEW_ECOLI | Q46803 from UniProtKB/Swiss-Prot  Length:396

    Alignment length:396
                                    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      
           YGEW_ECOLI     1 MMKTVNELIKDINSLTSHLHEKDFLLTWEQTPDELKQVLDVAAALKALRAENISTKVFNSGLGISVFRDNSTRTRFSYASALNLLGLAQQDLDEGKSQIAHGETVRETANMISFCADAIGIRDDMYLGAGNAYMREVGAALDDGYKQGVLPQRPALVNLQCDIDHPTQSMADLAWLREHFGSLENLKGKKIAMTWAYSPSYGKPLSVPQGIIGLMTRFGMDVTLAHPEGYDLIPDVVEVAKNNAKASGGSFRQVTSMEEAFKDADIVYPKSWAPYKVMEERTELLRANDHEGLKALEKQCLAQNAQHKDWHCTEEMMELTRDGEALYMHCLPADISGVSCKEGEVTEGVFEKYRIATYKEASWKPYIIAAMILSRKYAKPGALLEQLLKEAQERVK 396
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ---------------------OTCace_N-3q98A02 A:22-179                                                                                                                                     -------OTCace-3q98A01 A:187-374                                                                                                                                                                    ---------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh...hhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh..........eeeeeee.-----.hhhhhhhhhhh.eeee..-------...hhhhhhhhh...eeeeeeee.....---hhhhhhhhhhhhhhhh.......eeeeee....hhhhhhhhhhhhhhhhh.hhhhh..eeeee..........hhhhhhhhhhhhhhh.eeeee.......hhhhhhhhhhhhhhhh.eeeee.hhhhhhh...eeee....hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhh.ee.......ee........eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3q98 A   1 mmKTVNELIKDINSLTSHLHEKDFLLTWEQTPDELKQVLDVAAALKALRAENISTKVFNSGLGISVFRD-----RFSYASALNLLGLAQQDLD-------HGETVRETANmISFCADAIGIRDDmYLG---AYmREVGAALDDGYKQGVLPQRPALVNLQCDIDHPTQSmADLAWLREHFGSLENLKGKKIAmTWAYSPSYGKPLSVPQGIIGLmTRFGmDVTLAHPEGYDLIPDVVEVAKNNAKASGGSFRQVTSmEEAFKDADIVYPKSWAPYKVmEERTELLRANDHEGLKALEKQCLAQNAQHKDWHCTEEmmELTRDGEALYmHCLPADISGVSCKEGEVTEGVFEKYRIATYKEASWKPYIIAAmILSRKYAKPGALLEQLLKEAQERVK 396
                            ||      10        20        30        40        50        60        |-    |   80        90  |      -|      110|      120    |  | - | |   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      
                            1-MSE                                                              69    75                93     101       111-MSE       125-MSE132 |                                 170-MSE                193-MSE               215-MSE|                                  257-MSE              278-MSE                               316-MSE     328-MSE                                    371-MSE                     
                             2-MSE                                                                                                                       128   134-MSE                                                                               220-MSE                                                                                          317-MSE
   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  (0, 0)

(no "SCOP Domain" information available for 3Q98)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3Q98)

(-) Pfam Domains  (2, 2)

Asymmetric Unit
(-)
Clan: no clan defined [family: OTCace] (48)
(-)
Clan: no clan defined [family: OTCace_N] (48)

(-) Gene Ontology  (9, 14)

Asymmetric Unit(hide GO term definitions)
Chain A   (YGEW_ECOLI | Q46803)
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).
biological process
    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:0044238    primary metabolic process    The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism.
    GO:0000050    urea cycle    The sequence of reactions by which arginine is synthesized from ornithine, then cleaved to yield urea and regenerate ornithine. The overall reaction equation is NH3 + CO2 + aspartate + 3 ATP + 2 H2O = urea + fumarate + 2 ADP + 2 phosphate + AMP + diphosphate.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Chain A   (Q1R7G1_ECOUT | Q1R7G1)
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: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.

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 Related Entries

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