SCOPe 2.05: Domain d1ypna1: 1ypn A:3-219

Lineage for d1ypna1 (1ypn A:3-219)

1. Root: SCOPe 2.05

2. Class c: Alpha and beta proteins (a/b) [51349] (148 folds)

3. Fold c.94: Periplasmic binding protein-like II [53849] (1 superfamily)
   consists of two similar intertwined domain with 3 layers (a/b/a) each: duplication
   mixed beta-sheet of 5 strands, order 21354; strand 5 is antiparallel to the rest

4. Superfamily c.94.1: Periplasmic binding protein-like II [53850] (4 families)
   Similar in architecture to the superfamily I but partly differs in topology

5. Family c.94.1.1: Phosphate binding protein-like [53851] (43 proteins)

6. Protein Porphobilinogen deaminase (hydroxymethylbilane synthase), N-terminal domain [53854] (1 species)

7. Species Escherichia coli [TaxId:562] [53855] (5 PDB entries)

8. Domain d1ypna1: 1ypn A:3-219 [35754]
   Other proteins in same PDB: d1ypna2
   complexed with dpm; mutant

Details for d1ypna1

PDB Entry: 1ypn, 2.3 Å

PDB Description: reduced form hydroxymethylbilane synthase (k59q mutant) crystal structure after 2 hours in a flow cell determined by time-resolved laue diffraction

PDB Compounds: (A:) hydroxymethylbilane synthase

SCOPe Domain Sequences for d1ypna1:

Sequence, based on SEQRES records:

>d1ypna1 c.94.1.1 (A:3-219) Porphobilinogen deaminase (hydroxymethylbilane synthase), N-terminal domain {Escherichia coli [TaxId: 562]}
dnvlriatrqsplalwqahyvkdklmashpglvvelvpmvtrgdvildtplakvggqglf
vkelevallenradiavhsmkdvpvefpqglglvticeredprdafvsnnydsldalpag
sivgtsslrrqcqlaerrpdliirslrgnvgtrlskldngeydaiilavaglkrlglesr
iraalppeislpavgqgavgiecrlddsrtrellaal

Sequence, based on observed residues (ATOM records):

>d1ypna1 c.94.1.1 (A:3-219) Porphobilinogen deaminase (hydroxymethylbilane synthase), N-terminal domain {Escherichia coli [TaxId: 562]}
dnvlriatrqsplalwqahyvkdklmashpglvvelvpmvtrgdvgqglfvkelevalle
nradiavhsmkdvpvefpqglglvticeredprdafvsnnydsldalpagsivgtsslrr
qcqlaerrpdliirslrgnvgtrlskldngeydaiilavaglkrlglesriraalppeis
lpavgqgavgiecrlddsrtrellaal

Timeline for d1ypna1:

• d1ypna1 first appeared (with stable ids) in SCOP 1.55, called d1ypn_1
  
• d1ypna1 appears in SCOPe 2.04
  
• d1ypna1 appears in SCOPe 2.06
  
• d1ypna1 appears in the current release, SCOPe 2.08