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Title :   THE CRYSTAL STRUCTURE OF HUMAN HALOACID DEHALOGENASE-LIKE HYDROLASE DOMAIN CONTAINING 1A (HDHD1A)

Authors :   E. Ugochukwu, K. Guo, S. Picaud, J. Muniz, C. Allerston, F. Von Delft, C. Bountra, C. H. Arrowsmith, J. Weigelt, A. Edwards, W. W. Yue, K. L. Kavanagh, U. Oppermann, Structural Genomics Consortium (Sgc)

Date :   22 Dec 09 (Deposition) - 09 Mar 10 (Release) - 09 Mar 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym./Biol. Unit : A

Keywords :   Hdhd1A, Haloacid Dehalogenase-Like Hydrolase Domain Containing 1A, Hydrolase, Structural Genomics, Structural Genomics Consortium, Sgc, Polymorphism (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. Ugochukwu, K. Guo, S. Picaud, J. Muniz, C. Allerston, F. Von Delft, C. Bountra, C. H. Arrowsmith, J. Weigelt, A. Edwards, W. W. Yue, K. L. Kavanagh, U. Oppermann, Structural Genomics Consortium (Sgc)
The Crystal Structure Of Human Haloacid Dehalogenase-Like Hydrolase Domain Containing 1A (Hdhd1A)
To Be Published
PubMed: search

Molecule 1 - HALOACID DEHALOGENASE-LIKE HYDROLASE DOMAIN- CONTAINING PROTEIN 1A
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PNIC28-BSA4
	Expression System Strain	:	BL21(DE3)-R3
	Expression System Taxid	:	469008
	Gene	:	HDHD1A
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	PROTEIN GS1

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 6)

No.	Name	Count	Type	Full Name
1	CL	4	Ligand/Ion	CHLORIDE ION
2	GOL	1	Ligand/Ion	GLYCEROL
3	K	1	Ligand/Ion	POTASSIUM ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:14 , ASP A:16 , GLU A:175 , ASP A:176 , HOH A:298	BINDING SITE FOR RESIDUE K A 229
2	AC2	SOFTWARE	SER A:132 , PHE A:134 , SER A:135 , ASP A:202 , HOH A:307	BINDING SITE FOR RESIDUE GOL A 230
3	AC3	SOFTWARE	TYR A:41 , TRP A:43 , LYS A:46	BINDING SITE FOR RESIDUE CL A 231
4	AC4	SOFTWARE	ARG A:116 , SER A:119 , HOH A:250	BINDING SITE FOR RESIDUE CL A 232
5	AC5	SOFTWARE	GLY A:148	BINDING SITE FOR RESIDUE CL A 233
6	AC6	SOFTWARE	ALA A:54	BINDING SITE FOR RESIDUE CL A 234

(no "SS Bond" information available for 3L5K)

Asymmetric/Biological Unit

No.	Residues
1	Lys A:149	-	Pro A:150
2	Ser A:163	-	Pro A:164

Asymmetric/Biological Unit (2, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_061094	T	88	M	HDHD1_HUMAN	Polymorphism	1131197	A	T	88	M
2	UniProt	VAR_060625	P	165	A	HDHD1_HUMAN	Polymorphism	3747386	A	P	165	A

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(no "PROSITE Motif" information available for 3L5K)

(no "Exon" information available for 3L5K)

Asymmetric/Biological 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:233
 aligned with HDHD1_HUMAN | Q08623 from UniProtKB/Swiss-Prot  Length:228

    Alignment length:233
                                 1                                                                                                                                                                                                                                   
                                 |   5        15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225   
          HDHD1_HUMAN     - -----MAAPPQPVTHLIFDMDGLLLDTERLYSVVFQEICNRYDKKYSWDVKSLVMGKKALEAAQIIIDVLQLPMSKEELVEESQTKLKEVFPTAALMPGAEKLIIHLRKHGIPFALATSSGSASFDMKTSRHKEFFSLFSHIVLGDDPEVQHGKPDPDIFLACAKRFSPPPAMEKCLVFEDAPNGVEAALAAGMQVVMVPDGNLSRDLTTKATLVLNSLQDFQPELFGLPSYE 228
               SCOP domains d3l5ka_ A: automated matches                                                                                                                                                                                                              SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------HAD_2-3l5kA01 A:11-194                                                                                                                                                                  ---------------------------------- Pfam domains
         Sec.struct. author ....ee........eeeee......hhhhhhhhhhhhhhhhh....hhhhhhhhh..hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh...eeee...hhhhhhhhh..hhhhhh....ee.............hhhhhhhhhh.....hhh.eeeee.hhhhhhhhhhh..eeee......hhhhh....ee..hhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------M----------------------------------------------------------------------------A--------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3l5k A  -4 LYFQSMAAPPQPVTHLIFDMDGLLLDTERLYSVVFQEICNRYDKKYSWDVKSLVMGKKALEAAQIIIDVLQLPMSKEELVEESQTKLKEVFPTAALMPGAEKLIIHLRKHGIPFALATSSRSASFDMKTSRHKEFFSLFSHIVLGDDPEVQHGKPDPDIFLACAKRFSPPPAMEKCLVFEDAPNGVEAALAAGMQVVMVPDGNLSRDLTTKATLVLNSLQDFQPELFGLPSYE 228
                                     5        15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225

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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: HAD-like (349)

Superfamily: HAD-like (349)

Family: automated matches (99)

Protein domain: automated matches (99)

Human (Homo sapiens) [TaxId: 9606] (9)

d3l5ka_

(no "CATH Domain" information available for 3L5K)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: HAD (186)

Family: HAD_2 (33)

Homo sapiens (Human) (5)

HAD_2-3l5kA01

A:11-194

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (HDHD1_HUMAN | Q08623)

molecular function
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0003674	molecular_function	Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
	GO:1990738	pseudouridine 5'-phosphatase activity	Catalysis of the reaction: pseudouridine 5'-phosphate + H2O = pseudouridine + phosphate.
biological process
	GO:0008150	biological_process	Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
	GO:0016311	dephosphorylation	The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
	GO:0009117	nucleotide metabolic process	The chemical reactions and pathways involving a nucleotide, a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the glycose moiety; may be mono-, di- or triphosphate; this definition includes cyclic nucleotides (nucleoside cyclic phosphates).
	GO:0043097	pyrimidine nucleoside salvage	Any process that generates a pyrimidine nucleoside, one of a family of organic molecules consisting of a pyrimidine base covalently bonded to a sugar ribose, from derivatives of it, without de novo synthesis.
cellular component
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Lys A:149 - Pro A:150	[ RasMol ]
		Ser A:163 - Pro A:164	[ RasMol ]

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2pib	CRYSTAL STRUCTURE OF PUTATIVE BETA-PHOSPHOGLUCOMUTASE FROM THERMOTOGA MARITIMA
2w4m	THE CRYSTAL STRUCTURE OF HUMAN N-ACETYLNEURAMINIC ACID PHOSPHATASE, NANP
3hlt	THE CRYSTAL STRUCTURE OF HUMAN HALOACID DEHALOGENASE-LIKE HYDROLASE DOMAIN CONTAINING 2 (HDHD2)
3k1z	CRYSTAL STRUCTURE OF HUMAN HALOACID DEHALOGENASE-LIKE HYDROLASE DOMAIN CONTAINING 3 (HDHD3)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (2, 2)

PROSITE Motifs (0, 0)

Exons (0, 0)

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SCOP Domains (1, 1)

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Pfam Domains (1, 1)

Gene Ontology (11, 11)

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