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723  structures 8519  species 0  interactions 69610  sequences 380  architectures

Family: PALP (PF00291)

Summary: Pyridoxal-phosphate dependent enzyme

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

The Pfam group coordinates the annotation of Pfam families in Wikipedia, but we have not yet assigned a Wikipedia article to this family. If you think that a particular Wikipedia article provides good annotation, please let us know.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

Pyridoxal-phosphate dependent enzyme Provide feedback

Members of this family are all pyridoxal-phosphate dependent enzymes. This family includes: serine dehydratase EC:4.2.1.13 P20132, threonine dehydratase EC:4.2.1.16 P04968 tryptophan synthase beta chain EC:4.2.1.20 P00932 threonine synthase EC:4.2.99.2 P04990 cysteine synthase EC:4.2.99.8 P11096, cystathionine beta-synthase EC:4.2.1.22 P35520 1-aminocyclopropane-1-carboxylate deaminase EC:4.1.99.4 P76316.

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001926

This entry represent a domain found in a group of proteins of the PLP-dependent enzymes superfamily represented by the beta subunit of tryptophan synthase [ PUBMED:10673430 ]. It is a group of diverse proteins, including threonine dehydratase, cysteine synthase, pyridoxal phosphate-dependent deaminase, etc.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan NADP_Rossmann (CL0063), which has the following description:

A class of redox enzymes are two domain proteins. One domain, termed the catalytic domain, confers substrate specificity and the precise reaction of the enzyme. The other domain, which is common to this class of redox enzymes, is a Rossmann-fold domain. The Rossmann domain binds nicotinamide adenine dinucleotide (NAD+) and it is this cofactor that reversibly accepts a hydride ion, which is lost or gained by the substrate in the redox reaction. Rossmann domains have an alpha/beta fold, which has a central beta sheet, with approximately five alpha helices found surrounding the beta sheet.The strands forming the beta sheet are found in the following characteristic order 654123. The inter sheet crossover of the stands in the sheet form the NAD+ binding site [1]. In some more distantly relate Rossmann domains the NAD+ cofactor is replaced by the functionally similar cofactor FAD.

The clan contains the following 206 members:

2-Hacid_dh_C 3Beta_HSD 3HCDH_N 3HCDH_RFF adh_short adh_short_C2 ADH_zinc_N ADH_zinc_N_2 AdoHcyase_NAD AdoMet_MTase AlaDh_PNT_C Amino_oxidase ApbA AviRa B12-binding Bac_GDH Bin3 Bmt2 CbiJ CheR CMAS CmcI CoA_binding CoA_binding_2 CoA_binding_3 Cons_hypoth95 CoV_ExoN CoV_Methyltr_2 DAO DapB_N DFP DNA_methylase DOT1 DRE2_N DREV DUF1442 DUF1611_N DUF166 DUF1776 DUF2431 DUF268 DUF2855 DUF3410 DUF364 DUF43 DUF5129 DUF5130 DUF6094 DUF938 DXP_reductoisom DXPR_C Eco57I ELFV_dehydrog Eno-Rase_FAD_bd Eno-Rase_NADH_b Enoyl_reductase Epimerase F420_oxidored FAD_binding_2 FAD_binding_3 FAD_oxidored Fibrillarin FMO-like FmrO FtsJ fvmX7 G6PD_N GCD14 GDI GDP_Man_Dehyd GFO_IDH_MocA GIDA GidB GLF Glu_dehyd_C Glyco_hydro_4 Glyco_tran_WecG GMC_oxred_N Gp_dh_N GRAS GRDA HcgC HI0933_like HIM1 IlvN ISPD_C K_oxygenase KR LCM Ldh_1_N LpxI_N Lycopene_cycl Malic_M Mannitol_dh MCRA Met_10 Methyltr_RsmB-F Methyltr_RsmF_N Methyltrans_Mon Methyltrans_SAM Methyltransf_10 Methyltransf_11 Methyltransf_12 Methyltransf_14 Methyltransf_15 Methyltransf_16 Methyltransf_17 Methyltransf_18 Methyltransf_19 Methyltransf_2 Methyltransf_20 Methyltransf_21 Methyltransf_22 Methyltransf_23 Methyltransf_24 Methyltransf_25 Methyltransf_28 Methyltransf_29 Methyltransf_3 Methyltransf_30 Methyltransf_31 Methyltransf_32 Methyltransf_33 Methyltransf_34 Methyltransf_4 Methyltransf_5 Methyltransf_7 Methyltransf_8 Methyltransf_9 Methyltransf_PK MethyltransfD12 MetW Mg-por_mtran_C MOLO1 Mqo MT-A70 MTS Mur_ligase N2227 N6-adenineMlase N6_Mtase N6_N4_Mtase NAD_binding_10 NAD_binding_2 NAD_binding_3 NAD_binding_4 NAD_binding_5 NAD_binding_7 NAD_binding_8 NAD_binding_9 NAD_Gly3P_dh_N NAS NmrA NNMT_PNMT_TEMT NodS OCD_Mu_crystall Orbi_VP4 PALP PARP_regulatory PCMT PDH PglD_N Polysacc_syn_2C Polysacc_synt_2 Pox_MCEL Pox_mRNA-cap Prenylcys_lyase PrmA PRMT5 Pyr_redox Pyr_redox_2 Pyr_redox_3 Reovirus_L2 RmlD_sub_bind Rossmann-like rRNA_methylase RrnaAD Rsm22 RsmJ Sacchrp_dh_NADP SAM_MT SE Semialdhyde_dh Shikimate_DH Spermine_synth TehB THF_DHG_CYH_C Thi4 ThiF TPM_phosphatase TPMT TrkA_N TRM TRM13 TrmK tRNA_U5-meth_tr Trp_halogenase TylF Ubie_methyltran UDPG_MGDP_dh_N UPF0020 UPF0146 Urocanase V_cholerae_RfbT XdhC_C YjeF_N

Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB sequence database. More...

View options

We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(145)
Full
(69610)
Representative proteomes UniProt
(298970)
RP15
(9127)
RP35
(32214)
RP55
(67206)
RP75
(113911)
Jalview View  View  View  View  View  View  View 
HTML View             
PP/heatmap 1            

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(145)
Full
(69610)
Representative proteomes UniProt
(298970)
RP15
(9127)
RP35
(32214)
RP55
(67206)
RP75
(113911)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

Download options

We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(145)
Full
(69610)
Representative proteomes UniProt
(298970)
RP15
(9127)
RP35
(32214)
RP55
(67206)
RP75
(113911)
Raw Stockholm Download   Download   Download   Download   Download      
Gzipped Download   Download   Download   Download   Download      

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Bateman A
Previous IDs: S_T_dehydratase;
Type: Family
Sequence Ontology: SO:0100021
Author: Bateman A , Finn RD
Number in seed: 145
Number in full: 69610
Average length of the domain: 295.80 aa
Average identity of full alignment: 21 %
Average coverage of the sequence by the domain: 75.30 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 35.0 35.0
Trusted cut-off 35.0 35.0
Noise cut-off 34.9 34.9
Model length: 294
Family (HMM) version: 27
Download: download the raw HMM for this family

Species distribution

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Selections

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Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the PALP domain has been found. There are 723 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.

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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A0G2KPX8 View 3D Structure Click here
A0A0P0WXY8 View 3D Structure Click here
A0A0P0WY15 View 3D Structure Click here
A0A0R0EBB0 View 3D Structure Click here
A0A0R0EF16 View 3D Structure Click here
A0A0R0EUP5 View 3D Structure Click here
A0A0R0F392 View 3D Structure Click here
A0A0R0J5W4 View 3D Structure Click here
A0A0R0K188 View 3D Structure Click here
A0A0R4J2P9 View 3D Structure Click here
A0A1D6EB44 View 3D Structure Click here
A0A1D6GJ69 View 3D Structure Click here
A0A1D6HET5 View 3D Structure Click here
A0A1D6HLQ1 View 3D Structure Click here
A0A1D6JTA1 View 3D Structure Click here
A0A1D6JTA1 View 3D Structure Click here
A0A1D6JTA1 View 3D Structure Click here
A0A1D6K7W5 View 3D Structure Click here
A0A1D6L203 View 3D Structure Click here
A0A1D6M0B0 View 3D Structure Click here
A0A1D6M0B0 View 3D Structure Click here
A0A1D6NVD1 View 3D Structure Click here
A0A1D6NVE7 View 3D Structure Click here
A0A1D6NVF0 View 3D Structure Click here
A0A1D6P4E8 View 3D Structure Click here
A0A1D8PGA8 View 3D Structure Click here
A0A1D8PKG0 View 3D Structure Click here
A0A1D8PMH6 View 3D Structure Click here
A0A1D8PNG9 View 3D Structure Click here
A0A1D8PQ13 View 3D Structure Click here
A0A1D8PRJ1 View 3D Structure Click here
A0A2R8QM05 View 3D Structure Click here
A0A2R8RQE0 View 3D Structure Click here
A1L4V7 View 3D Structure Click here
A4HSW5 View 3D Structure Click here
A4HVX7 View 3D Structure Click here
A4HX92 View 3D Structure Click here
A4ID39 View 3D Structure Click here
B4FIW6 View 3D Structure Click here
B4FR08 View 3D Structure Click here
B6THZ8 View 3D Structure Click here
B6UB52 View 3D Structure Click here
B8A367 View 3D Structure Click here
B8A377 View 3D Structure Click here
C0P6C5 View 3D Structure Click here
C0PCX2 View 3D Structure Click here
C6TMX6 View 3D Structure Click here
C7IY87 View 3D Structure Click here
D3ZHV7 View 3D Structure Click here
F1QIC0 View 3D Structure Click here
F4HYF3 View 3D Structure Click here
F4K5T2 View 3D Structure Click here
F4K727 View 3D Structure Click here
G5EF21 View 3D Structure Click here
G5EFH8 View 3D Structure Click here
G5EFH8 View 3D Structure Click here
I1JFS9 View 3D Structure Click here
I1K6K2 View 3D Structure Click here
I1L6I6 View 3D Structure Click here
I1L954 View 3D Structure Click here
I1LBH7 View 3D Structure Click here
I1LBI3 View 3D Structure Click here
I1LE45 View 3D Structure Click here
I1LFR5 View 3D Structure Click here
I1LWZ0 View 3D Structure Click here
I1LZD0 View 3D Structure Click here
I1M592 View 3D Structure Click here
I1M6G6 View 3D Structure Click here
I1MD26 View 3D Structure Click here
I1MJD2 View 3D Structure Click here
I1N0T6 View 3D Structure Click here
I1NC67 View 3D Structure Click here
I1NIU6 View 3D Structure Click here
K7K1W7 View 3D Structure Click here
K7K5J2 View 3D Structure Click here
K7KBM2 View 3D Structure Click here
K7KBZ4 View 3D Structure Click here
K7L4D3 View 3D Structure Click here
K7L749 View 3D Structure Click here
K7MXY9 View 3D Structure Click here
K7TR93 View 3D Structure Click here
K7TTR0 View 3D Structure Click here
K7V6Z2 View 3D Structure Click here
K7W6K8 View 3D Structure Click here
O01592 View 3D Structure Click here
O13831 View 3D Structure Click here
O16282 View 3D Structure Click here
O16284 View 3D Structure Click here
O22682 View 3D Structure Click here
O45679 View 3D Structure Click here
O59701 View 3D Structure Click here
O59791 View 3D Structure Click here
O69652 View 3D Structure Click here
O94634 View 3D Structure Click here
P00926 View 3D Structure Click here
P00927 View 3D Structure Click here
P00931 View 3D Structure Click here
P00934 View 3D Structure Click here
P04968 View 3D Structure Click here
P09367 View 3D Structure Click here
P0A879 View 3D Structure Click here
P0ABK5 View 3D Structure Click here
P0AGF6 View 3D Structure Click here
P0DN79 View 3D Structure Click here
P14671 View 3D Structure Click here
P16120 View 3D Structure Click here
P16703 View 3D Structure Click here
P20132 View 3D Structure Click here
P25269 View 3D Structure Click here
P25379 View 3D Structure Click here
P32232 View 3D Structure Click here
P32582 View 3D Structure Click here
P35520 View 3D Structure Click here
P36007 View 3D Structure Click here
P43283 View 3D Structure Click here
P43284 View 3D Structure Click here
P46794 View 3D Structure Click here
P47998 View 3D Structure Click here
P47999 View 3D Structure Click here
P53206 View 3D Structure Click here
P66899 View 3D Structure Click here
P76316 View 3D Structure Click here
P80608 View 3D Structure Click here
P87131 View 3D Structure Click here
P9WFX9 View 3D Structure Click here
P9WG59 View 3D Structure Click here
P9WG95 View 3D Structure Click here
P9WP51 View 3D Structure Click here
P9WP53 View 3D Structure Click here
P9WP55 View 3D Structure Click here
Q10PZ5 View 3D Structure Click here
Q19374 View 3D Structure Click here
Q21080 View 3D Structure Click here
Q2FWJ9 View 3D Structure Click here
Q2FYJ3 View 3D Structure Click here
Q2FYR4 View 3D Structure Click here
Q2FYV3 View 3D Structure Click here
Q2G0Q8 View 3D Structure Click here
Q2G0V4 View 3D Structure Click here
Q2G1N3 View 3D Structure Click here
Q2PGG3 View 3D Structure Click here
Q2Q021 View 3D Structure Click here
Q2YDP8 View 3D Structure Click here
Q42598 View 3D Structure Click here
Q43725 View 3D Structure Click here
Q4CQF3 View 3D Structure Click here
Q4CRW9 View 3D Structure Click here
Q4CRX0 View 3D Structure Click here
Q4CS97 View 3D Structure Click here
Q4CST7 View 3D Structure Click here
Q4CXR9 View 3D Structure Click here
Q4CYV4 View 3D Structure Click here
Q4D172 View 3D Structure Click here
Q4D9V4 View 3D Structure Click here
Q4DF36 View 3D Structure Click here
Q4DF37 View 3D Structure Click here
Q4DF38 View 3D Structure Click here
Q4DG20 View 3D Structure Click here
Q4DG21 View 3D Structure Click here
Q4DIK8 View 3D Structure Click here
Q4DLL4 View 3D Structure Click here
Q4DZF5 View 3D Structure Click here
Q4E2W1 View 3D Structure Click here
Q54CN7 View 3D Structure Click here
Q54HH2 View 3D Structure Click here
Q58860 View 3D Structure Click here
Q59P56 View 3D Structure Click here
Q59T95 View 3D Structure Click here
Q5JNB0 View 3D Structure Click here
Q5M7T9 View 3D Structure Click here
Q5N761 View 3D Structure Click here
Q5VND2 View 3D Structure Click here
Q5VND3 View 3D Structure Click here
Q5Z6A9 View 3D Structure Click here
Q5Z8Y9 View 3D Structure Click here
Q60179 View 3D Structure Click here
Q67VM1 View 3D Structure Click here
Q6L4H5 View 3D Structure Click here
Q6NKY5 View 3D Structure Click here
Q6YYB9 View 3D Structure Click here
Q6ZHE5 View 3D Structure Click here
Q76EQ0 View 3D Structure Click here
Q79FV4 View 3D Structure Click here
Q7XS58 View 3D Structure Click here
Q7XSN8 View 3D Structure Click here
Q80W22 View 3D Structure Click here
Q86AP7 View 3D Structure Click here
Q86B06 View 3D Structure Click here
Q86YJ6 View 3D Structure Click here
Q8LJJ2 View 3D Structure Click here
Q8R238 View 3D Structure Click here
Q8VBT2 View 3D Structure Click here
Q8W1A0 View 3D Structure Click here
Q8W314 View 3D Structure Click here
Q91WT9 View 3D Structure Click here
Q93244 View 3D Structure Click here
Q93968 View 3D Structure Click here
Q95XY8 View 3D Structure Click here
Q965I8 View 3D Structure Click here
Q96GA7 View 3D Structure Click here
Q9FFW8 View 3D Structure Click here
Q9GZT4 View 3D Structure Click here
Q9LJA0 View 3D Structure Click here
Q9N4K2 View 3D Structure Click here
Q9N4K2 View 3D Structure Click here
Q9QZX7 View 3D Structure Click here
Q9S6Z7 View 3D Structure Click here
Q9S757 View 3D Structure Click here
Q9S7B5 View 3D Structure Click here
Q9SSP5 View 3D Structure Click here
Q9SXS7 View 3D Structure Click here
Q9URX3 View 3D Structure Click here
Q9VHF0 View 3D Structure Click here
Q9VRD9 View 3D Structure Click here
Q9XEA6 View 3D Structure Click here
Q9XEA8 View 3D Structure Click here
Q9ZSS6 View 3D Structure Click here
X1WC99 View 3D Structure Click here