3BM5 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF O-ACETYL-SERINE SULFHYDRYLASE FROM ENTAMOEBA HISTOLYTICA IN COMPLEX WITH CYSTEINE

Authors :   C. Krishna, M. Kumar, S. Kumar, S. Gourinath

Date :   12 Dec 07 (Deposition) - 01 Apr 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

Chains :   Asym./Biol. Unit : A,B

Keywords :   Cysteine Synthase, Cys-Oass Complex, Domain Movement, Pyridoxal Phosphate, Lyase, Lyase-Biosynthetic Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Chinthalapudi, M. Kumar, S. Kumar, S. Jain, N. Alam, S. Gourinath
Crystal Structure Of Native O-Acetyl-Serine Sulfhydrylase From Entamoeba Histolytica And Its Complex With Cysteine: Structural Evidence For Cysteine Binding And Lack Of Interactions With Serine Acetyl Transferase.
Proteins V. 72 1222 2008
PubMed-ID: 18350570 | Reference-DOI: 10.1002/PROT.22013

Molecule 1 - CYSTEINE SYNTHASE
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-28A
	Expression System Strain	:	BLR
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Taxid	:	294381
	Strain	:	HM1.IMSS
	Synonym	:	O-ACETYL-SERINE SULFHYDRYLASE

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 9)

No.	Name	Count	Type	Full Name
1	CYS	1	Mod. Amino Acid	CYSTEINE
2	PLP	2	Ligand/Ion	PYRIDOXAL-5'-PHOSPHATE
3	SO4	6	Ligand/Ion	SULFATE ION

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR A:85 , SER A:86 , GLY A:87 , GLN A:159 , HOH A:370	BINDING SITE FOR RESIDUE SO4 A 1
2	AC2	SOFTWARE	ARG A:12 , HOH A:447 , SER B:7 , SER B:8 , HOH B:420	BINDING SITE FOR RESIDUE SO4 B 340
3	AC3	SOFTWARE	HIS A:170 , LYS A:203 , HOH A:363 , HOH A:427	BINDING SITE FOR RESIDUE SO4 A 340
4	AC4	SOFTWARE	THR A:326 , LYS A:327 , HOH A:474	BINDING SITE FOR RESIDUE SO4 A 341
5	AC5	SOFTWARE	ASN B:174 , LYS B:203 , LYS B:207 , HOH B:485	BINDING SITE FOR RESIDUE SO4 B 341
6	AC6	SOFTWARE	LYS A:205 , LYS A:209 , GLY A:210 , ILE A:211 , HOH A:433 , ARG B:37	BINDING SITE FOR RESIDUE SO4 B 342
7	AC7	SOFTWARE	LYS A:58 , ASN A:88 , ALA A:190 , GLY A:192 , THR A:193 , SER A:194 , GLY A:195 , THR A:196 , GLY A:236 , SER A:280 , PRO A:307 , SER A:308 , TYR A:313 , HOH A:373 , HOH A:387 , HOH A:405	BINDING SITE FOR RESIDUE PLP A 342
8	AC8	SOFTWARE	LYS B:58 , ASN B:88 , ALA B:190 , GLY B:192 , THR B:193 , SER B:194 , GLY B:195 , THR B:196 , GLN B:235 , GLY B:236 , SER B:280 , PRO B:307 , SER B:308 , TYR B:313 , CYS B:402 , HOH B:403 , HOH B:406 , HOH B:416 , HOH B:451	BINDING SITE FOR RESIDUE PLP B 343
9	AC9	SOFTWARE	LYS B:58 , THR B:85 , SER B:86 , ASN B:88 , THR B:89 , GLN B:159 , GLY B:236 , HOH B:451	BINDING SITE FOR RESIDUE CYS B 402

(no "SS Bond" information available for 3BM5)

(no "Cis Peptide Bond" information available for 3BM5)

(no "SAP(SNP)/Variant" information available for 3BM5)

(no "PROSITE Motif" information available for 3BM5)

(no "Exon" information available for 3BM5)

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:338
 aligned with O15570_ENTHI | O15570 from UniProtKB/TrEMBL  Length:337

    Alignment length:338
                                                                                                                                                                                                                                                                                                                                                                         337  
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331     |  
         O15570_ENTHI     2 EQISISSPRKRIYHNILETIGGTPLVELHGVTEHPRIKKGTRILVKLEYFNPMSSVKDRVGFNIVYQAIKDGRLKPGMEIIESTSGNTGIALCQAGAVFGYRVNIAMPSTMSVERQMIMKAFGAELILTEGKKGMPGAIEEVNKMIKENPGKYFVANQFGNPDNTAAHHYTANEIWEDTDGEVDIVVSAVGTSGTVIGVAEKLKEKKKGIKIIAVEPEESAVLEGKAKGPHGIQGIGAGFIPDIYKKEFVDEIIPIKTQDAWKMARAVVKYDGIMCGMSSGAAILAGLKEAEKPENEGKTIVIIVPSCGERYLSTDLYKIKDEGTKIQILDSLLNE--   -
               SCOP domains d3bm5a_ A: automated matches                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........ee.hhhhhh....eee.hhhhh........eeeeee.hhh....hhhhhhhhhhhhhhhhh......eeeee..hhhhhhhhhhhhhhh..eeeeee.....hhhhhhhhh..eeeeehhhhhhhhhhhhhhhhhhhh...eee.....hhhhhhhhhhhhhhhhhhh.....eeeee...hhhhhhhhhhhhhhh...eeeeeee...hhhhh....................hhhhh.eeeeehhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh..eeeeee..hhhhhh...........hhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bm5 A   2 EQISISSPRKRIYHNILETIGGTPLVELHGVTEHPRIKKGTRILVKLEYFNPMSSVKDRVGFNIVYQAIKDGRLKPGMEIIESTSGNTGIALCQAGAVFGYRVNIAMPSTMSVERQMIMKAFGAELILTEGKKGMPGAIEEVNKMIKENPGKYFVANQFGNPDNTAAHHYTANEIWEDTDGEVDIVVSAVGTSGTVIGVAEKLKEKKKGIKIIAVEPEESAVLEGKAKGPHGIQGIGAGFIPDIYKKEFVDEIIPIKTQDAWKMARAVVKYDGIMCGMSSGAAILAGLKEAEKPENEGKTIVIIVPSCGERYLSTDLYKIKDEGTKIQILDSLLNEHH 339
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331

Chain B from PDB  Type:PROTEIN  Length:335
 aligned with O15570_ENTHI | O15570 from UniProtKB/TrEMBL  Length:337

    Alignment length:335
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331     
         O15570_ENTHI     2 EQISISSPRKRIYHNILETIGGTPLVELHGVTEHPRIKKGTRILVKLEYFNPMSSVKDRVGFNIVYQAIKDGRLKPGMEIIESTSGNTGIALCQAGAVFGYRVNIAMPSTMSVERQMIMKAFGAELILTEGKKGMPGAIEEVNKMIKENPGKYFVANQFGNPDNTAAHHYTANEIWEDTDGEVDIVVSAVGTSGTVIGVAEKLKEKKKGIKIIAVEPEESAVLEGKAKGPHGIQGIGAGFIPDIYKKEFVDEIIPIKTQDAWKMARAVVKYDGIMCGMSSGAAILAGLKEAEKPENEGKTIVIIVPSCGERYLSTDLYKIKDEGTKIQILDSLLN 336
               SCOP domains d3bm5b_ B: automated matches                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........ee.hhhhhh....eee.hhhhh........eeeeee.hhh....hhhhhhhhhhhhhhhhh......eeeee..hhhhhhhhhhhhhhh..eeeeee...hhhhhhhhh.......ee........hhhhhhhhhhhh...eee.....hhhhhhhhhhhhhhhhhhh...eeeeeee...hhhhhhhhhhhhh.....eeeeeee.hhh........................hhhhh.eeeeehhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh..eeeeee..hhhhhh...........hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bm5 B   2 EQISISSPRKRIYHNILETIGGTPLVELHGVTEHPRIKKGTRILVKLEYFNPMSSVKDRVGFNIVYQAIKDGRLKPGMEIIESTSGNTGIALCQAGAVFGYRVNIAMPSTMSVERQMIMKAFGAELILTEGKKGMPGAIEEVNKMIKENPGKYFVANQFGNPDNTAAHHYTANEIWEDTDGEVDIVVSAVGTSGTVIGVAEKLKEKKKGIKIIAVEPEESAVLEGKAKGPHGIQGIGAGFIPDIYKKEFVDEIIPIKTQDAWKMARAVVKYDGIMCGMSSGAAILAGLKEAEKPENEGKTIVIIVPSCGERYLSTDLYKIKDEGTKIQILDSLLN 336
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331

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: Tryptophan synthase beta subunit-like PLP-dependent enzymes (165)

Superfamily: Tryptophan synthase beta subunit-like PLP-dependent enzymes (165)

Family: automated matches (45)

Protein domain: automated matches (45)

Entamoeba histolytica [TaxId: 294381] (5)

1a	d3bm5a_	A:
1b	d3bm5b_	B:

(no "CATH Domain" information available for 3BM5)

(no "Pfam Domain" information available for 3BM5)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (O15570_ENTHI | O15570)

molecular function
	GO:0004124	cysteine synthase activity	Catalysis of the reaction: O3-acetyl-L-serine + hydrogen sulfide = L-cysteine + acetate.
biological process
	GO:0006535	cysteine biosynthetic process from serine	The chemical reactions and pathways resulting in the formation of cysteine from other compounds, including serine.

Asymmetric/Biological Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		CYS	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		PLP	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		SO4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]
		AC9	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3bm5)

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format \| Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	3bm5
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	O15570_ENTHI \| O15570
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/TrEMBL

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	O15570_ENTHI \| O15570
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/TrEMBL
	O15570_ENTHI \| O15570	:	2pqm 4il5 4jbl 4jbn

2pqm	NATIVE STRUCTURE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 9)

Sites (9, 9)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (2, 2)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File