Letunic et al. (2017) Nucleic Acids Res doi: 10.1093/nar/gkx922
Letunic et al. (2020) Nucleic Acids Res doi: 10.1093/nar/gkaa937

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Amb_all

SMART accession number:	SM00656
Description:	-
Interpro abstract (IPR002022):	Pectate lyase EC 4.2.2.2 is an enzyme involved in the maceration and soft rotting of plant tissue. Pectate lyase is responsible for the eliminative cleavage of pectate, yielding oligosaccharides with 4-deoxy-alpha-D-mann-4-enuronosyl groups at their non-reducing ends. The protein is maximally expressed late in pollen development. It has been suggested that the pollen expression of pectate lyase genes might relate to a requirement for pectin degradation during pollen tube growth [ (PUBMED:1983191) ]. The structure and the folding kinetics of one member of this family, pectate lyase C (pelC)1 from Erwinia chrysanthemi has been investigated in some detail [ (PUBMED:11926834) (PUBMED:8502994) ]. PelC contains a parallel beta-helix folding motif. The majority of the regular secondary structure is composed of parallel beta-sheets (about 30%). The individual strands of the sheets are connected by unordered loops of varying length. The backbone is then formed by a large helix composed of beta-sheets. There are two disulphide bonds in pelC and 12 proline residues. One of these prolines, Pro220, is involved in a cis peptide bond. he folding mechanism of pelC involves two slow phases that have been attributed to proline isomerization. Some of the proteins in this family are allergens [ (PUBMED:25978036) ].
Family alignment:	View or CHROMA formatHMM/Web logoCLUSTALW formatMSF formatFASTA formatPIR format

There are 8431 Amb_all domains in 8373 proteins in SMART's nrdb database.

Click on the following links for more information.

• Evolution (species in which this domain is found)

• Taxonomic distribution of proteins containing Amb_all domain.

  This tree includes only several representative species. The complete taxonomic breakdown of all proteins with Amb_all domain is also avaliable.

  Click on the protein counts, or double click on taxonomic names to display all proteins containing Amb_all domain in the selected taxonomic class.

• Metabolism (metabolic pathways involving proteins which contain this domain)

• Click the image to view the interactive version of the map in iPath

  % proteins involved KEGG pathway ID Description 88.46 map00040 Pentose and glucuronate interconversions 3.85 map00530 Aminosugars metabolism 3.85 map00220 Urea cycle and metabolism of amino groups 3.85 map00330 Arginine and proline metabolism This information is based on mapping of SMART genomic protein database to KEGG orthologous groups. Percentage points are related to the number of proteins with Amb_all domain which could be assigned to a KEGG orthologous group, and not all proteins containing Amb_all domain. Please note that proteins can be included in multiple pathways, ie. the numbers above will not always add up to 100%.

• Structure (3D structures containing this domain)

• 3D Structures of Amb_all domains in PDB

  PDB code	Main view	Title
  1air		PECTATE LYASE C FROM ERWINIA CHRYSANTHEMI (EC16) TO A RESOLUTION OF 2.2 ANGSTROMS WITH 128 WATERS
  1bn8		BACILLUS SUBTILIS PECTATE LYASE
  1idj		PECTIN LYASE A
  1idk		PECTIN LYASE A
  1jrg		Crystal Structure of the R3 form of Pectate Lyase A, Erwinia chrysanthemi
  1jta		Crystal Structure of Pectate Lyase A (C2 form)
  1o88		Pectate Lyase C From Erwinia Chrysanthemi at pH 11.2 with 30mM Ca2+
  1o8d		PECTATE LYASE C FROM ERWINIA CHRYSANTHEMI AT PH 11.2 WITH 5MM CA2+
  1o8e		PECTATE LYASE C FROM ERWINIA CHRYSANTHEMI AT PH 11.2 WITH 1MM CA2+
  1o8f		PECTATE LYASE C FROM ERWINIA CHRYSANTHEMI AT PH 9.5 WITH 30MM CA2+
  1o8g		PECTATE LYASE C FROM ERWINIA CHRYSANTHEMI AT PH 9.5 WITH 5MM CA2+
  1o8h		PECTATE LYASE C FROM ERWINIA CHRYSANTHEMI AT PH 9.5 WITH 0.3mM CA2+ added
  1o8i		PECTATE LYASE C FROM ERWINIA CHRYSANTHEMI AT PH 9.5 WITH no CA2+ added
  1o8j		PECTATE LYASE C FROM ERWINIA CHRYSANTHEMI AT PH 4.5 WITH 30MM CA2+
  1o8k		PECTATE LYASE C FROM ERWINIA CHRYSANTHEMI AT PH 4.5 WITH 20MM CA2+
  1o8l		PECTATE LYASE C FROM ERWINIA CHRYSANTHEMI AT PH 4.5 WITH 5MM CA2+
  1o8m		PECTATE LYASE C FROM ERWINIA CHRYSANTHEMI AT PH 4.5 WITH NO CA2+ ADDED
  1ooc		Mutations in the T1.5 loop of pectate lyase A
  1pcl		UNUSUAL STRUCTURAL FEATURES IN THE PARALLEL BETA-HELIX IN PECTATE LYASES
  1pe9		MUTATIONS IN THE T1.5 LOOP OF PECTATE LYASE A
  1plu		PECTATE LYASE C FROM ERWINIA CHRYSANTHEMI WITH 1 LU+3 ION IN THE PUTATIVE CALCIUM BINDING SITE
  1pxz		1.7 Angstrom Crystal Structure of jun a 1, the major allergen from cedar pollen
  1qcx		PECTIN LYASE B
  1vbl		Structure of the thermostable pectate lyase PL 47
  2bsp		BACILLUS SUBTILIS PECTATE LYASE R279K MUTANT
  2ewe		Crystal structure of Pectate Lyase C R218K mutant in complex with pentagalacturonic acid
  2nzm		Hexasaccharide I bound to Bacillus subtilis pectate lyase
  2o04		Pectate lyase bound to hexasaccharide compound II
  2o0v		Pectate lyase bound to hexasaccharide compound III
  2o0w		Pectate lyase bound to hexasaccharide compound IV
  2o17		Pectate lyase bound to hexasaccharide
  2o1d		Pectate lyase bound to trisaccharide
  2pec		THE REFINED THREE-DIMENSIONAL STRUCTURE OF PECTATE LYASE C FROM ERWINIA CHRYSANTHEMI AT 2.2 ANGSTROMS RESOLUTION: IMPLICATIONS FOR AN ENZYMATIC MECHANISM
  2qx3		Structure of pectate lyase II from Xanthomonas campestris pv. campestris str. ATCC 33913
  2qxz		pectate lyase R236F from Xanthomonas campestris
  2qy1		pectate lyase A31G/R236F from Xanthomonas campestris
  3krg		Structural insights into substrate specificity and the anti beta-elimination mechanism of pectate lyase
  3vmv		Crystal structure of pectate lyase Bsp165PelA from Bacillus sp. N165
  3vmw		Crystal structure of pectate lyase Bsp165PelA from Bacillus sp. N165 in complex with trigalacturonate
  3zpp		Structure of the Streptococcus pneumoniae surface protein and adhesin PfbA
  3zsc		Catalytic function and substrate recognition of the pectate lyase from Thermotoga maritima
  4hwv		Structure of Pectate Lyase from Acidovorax avenae subsp citrulli
  4mr0		Crystal structure of PfbA, a surface adhesin of Streptococcus pneumoniae
  5amv		5AMV

• Links (links to other resources describing this domain)

• INTERPRO	IPR002022
  PFAM	PF00544

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