1M4Z - JenaLib

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Title :   CRYSTAL STRUCTURE OF THE N-TERMINAL BAH DOMAIN OF ORC1P

Authors :   Z. Zhang, M. K. Hayashi, O. Merkel, B. Stillman, R. -M. Xu

Date :   05 Jul 02 (Deposition) - 11 Sep 02 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: A,B  (2x)

Keywords :   Dna Replication, Transcriptional Silencing, Chromatin, Bah Domain, Gene Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Z. Zhang, M. K. Hayashi, O. Merkel, B. Stillman, R. M. Xu
Structure And Function Of The Bah-Containing Domain Of Orc1 In Epigenetic Silencing.
Embo J. V. 21 4600 2002
PubMed-ID: 12198162 | Reference-DOI: 10.1093/EMBOJ/CDF468

Molecule 1 - ORIGIN RECOGNITION COMPLEX SUBUNIT 1
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET15B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	BAH-CONTAINING DOMAIN (RESIDUE 1-235)
	Gene	:	ORC1
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Synonym	:	ORIGIN RECOGNITION COMPLEX PROTEIN 120 KD SUBUNIT

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (2x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 3)

No.	Name	Count	Type	Full Name
1	MN	3	Ligand/Ion	MANGANESE (II) ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	MN	-1	Ligand/Ion	MANGANESE (II) ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	MN	-1	Ligand/Ion	MANGANESE (II) ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:61 , GLU B:61	BINDING SITE FOR RESIDUE MN A 501
2	AC2	SOFTWARE	HOH A:545 , HOH A:546 , HOH A:547 , GLU B:84 , HOH B:544 , HOH B:545	BINDING SITE FOR RESIDUE MN B 502
3	AC3	SOFTWARE	GLU A:84 , HOH A:544 , HOH B:540 , HOH B:541 , HOH B:542 , HOH B:543	BINDING SITE FOR RESIDUE MN A 503

(no "SS Bond" information available for 1M4Z)

(no "Cis Peptide Bond" information available for 1M4Z)

(no "SAP(SNP)/Variant" information available for 1M4Z)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BAH	PS51038	BAH domain profile.	ORC1_YEAST	48-188	2	A:48-188 B:48-188

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BAH	PS51038	BAH domain profile.	ORC1_YEAST	48-188	2	A:48-188 B:48-188

Biological Unit 2 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BAH	PS51038	BAH domain profile.	ORC1_YEAST	48-188	4	A:48-188 B:48-188

Asymmetric Unit (1, 2)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YML065W	1	YML065W.1	XIII:142210-144954	2745	ORC1_YEAST	1-914	914	2	A:1-214 (gaps) B:1-215 (gaps)	214 215

Asymmetric 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:203
 aligned with ORC1_YEAST | P54784 from UniProtKB/Swiss-Prot  Length:914

    Alignment length:217
                               1                                                                                                                                                                                                                     
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       
           ORC1_YEAST     - ---MAKTLKDLQGWEIITTDEQGNIIDGGQKRLRRRGAKTEHYLKRSSDGIKLGRGDSVVMHNEAAGTYSVYMIQELRLNTLNNVVELWALTYLRWFEVNPLAHYRQFNPDANILNRPLNYYNKLFSETANKNELYLTAELAELQLFNFIRVANVMDGSKWEVLKGNVDPERDFTVRYICEPTGEKFVDINIEDVKAYIKKVEPREAQEYLKDLTLP 214
               SCOP domains d1m4za_ A: Origin-recogni              tion complex protein 120kDa subunit, Orc1p                                                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhheeeeee......--------------.eeeeee.....ee....eeeeee....eeeeeeeeeeee......eeeeeeeeehhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh...eeeeeeeeeeehhh.eeeeeeeehhhhhhhhhhhh....eeeeeee........ee.hhhhhhhhhh..hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------BAH  PDB: A:48-188 UniProt: 48-188                                                                                                           -------------------------- PROSITE
               Transcript 1 ---Exon 1.1  PDB: A:1-214 (gaps) UniProt: 1-914 [INCOMPLETE]                                                                                                                                                              Transcript 1
                 1m4z A  -2 AMTMAKTLKDLQGWEIITTDEQGNI--------------TEHYLKRSSDGIKLGRGDSVVMHNEAAGTYSVYMIQELRLNTLNNVVELWALTYLRWFEVNPLAHYRQFNPDANILNRPLNYYNKLFSETANKNELYLTAELAELQLFNFIRVANVMDGSKWEVLKGNVDPERDFTVRYICEPTGEKFVDINIEDVKAYIKKVEPREAQEYLKDLTLP 214
                                     7        17    |    -        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       
                                                   22             37

Chain B from PDB  Type:PROTEIN  Length:203
 aligned with ORC1_YEAST | P54784 from UniProtKB/Swiss-Prot  Length:914

    Alignment length:217
                              1                                                                                                                                                                                                                      
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       
           ORC1_YEAST     - --MAKTLKDLQGWEIITTDEQGNIIDGGQKRLRRRGAKTEHYLKRSSDGIKLGRGDSVVMHNEAAGTYSVYMIQELRLNTLNNVVELWALTYLRWFEVNPLAHYRQFNPDANILNRPLNYYNKLFSETANKNELYLTAELAELQLFNFIRVANVMDGSKWEVLKGNVDPERDFTVRYICEPTGEKFVDINIEDVKAYIKKVEPREAQEYLKDLTLPS 215
               SCOP domains d1m4zb_ B: Origin-recogn              ition complex protein 120kDa subunit, Orc1p                                                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------------------------------------------------BAH-1m4zB01 B:48-188                                                                                                                         --------------------------- Pfam domains (1)
           Pfam domains (2) -------------------------------------------------BAH-1m4zB02 B:48-188                                                                                                                         --------------------------- Pfam domains (2)
         Sec.struct. author .....hhhhhh.eeeeee......--------------.eeeeee.....ee....eeeeee....eeeeeeeeeeee......eeeeeeeeehhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh...eeeeeeeeeeehhh.eeee.eeehhhhhhhhhhhh....eeeeeee........ee.hhhhhhhhhh..hhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------BAH  PDB: B:48-188 UniProt: 48-188                                                                                                           --------------------------- PROSITE
               Transcript 1 --Exon 1.1  PDB: B:1-215 (gaps) UniProt: 1-914 [INCOMPLETE]                                                                                                                                                               Transcript 1
                 1m4z B  -1 MTMAKTLKDLQGWEIITTDEQGNI--------------TEHYLKRSSDGIKLGRGDSVVMHNEAAGTYSVYMIQELRLNTLNNVVELWALTYLRWFEVNPLAHYRQFNPDANILNRPLNYYNKLFSETANKNELYLTAELAELQLFNFIRVANVMDGSKWEVLKGNVDPERDFTVRYICEPTGEKFVDINIEDVKAYIKKVEPREAQEYLKDLTLPS 215
                                     8        18   |     -        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       
                                                  22             37

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 Unit

Classes(

)

Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: SH3-like barrel (1035)

Superfamily: BAH domain (8)

Family: BAH domain (3)

Protein domain: Origin-recognition complex protein 120kDa subunit, Orc1p (3)

Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] (3)

1a	d1m4za_	A:
1b	d1m4zb_	B:

(no "CATH Domain" information available for 1M4Z)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: BAH] (7)

Family: BAH (7)

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast) (3)

1a	BAH-1m4zB01	B:48-188
1b	BAH-1m4zB02	B:48-188

Asymmetric Unit(hide GO term definitions)

Chain A,B (ORC1_YEAST | P54784)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0016887	ATPase activity	Catalysis of the reaction: ATP + H2O = ADP + phosphate + 2 H+. May or may not be coupled to another reaction.
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0003688	DNA replication origin binding	Interacting selectively and non-covalently with the DNA replication origin, a unique DNA sequence of a replicon at which DNA replication is initiated and proceeds bidirectionally or unidirectionally.
	GO:0003682	chromatin binding	Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
	GO:0006260	DNA replication	The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
	GO:0006270	DNA replication initiation	The process in which DNA-dependent DNA replication is started; this involves the separation of a stretch of the DNA double helix, the recruitment of DNA polymerases and the initiation of polymerase action.
	GO:0030466	chromatin silencing at silent mating-type cassette	Repression of transcription at silent mating-type loci by alteration of the structure of chromatin.
	GO:0006267	pre-replicative complex assembly involved in nuclear cell cycle DNA replication	The aggregation, arrangement and bonding together of a set of components to form the nuclear pre-replicative complex, a protein-DNA complex that forms at the eukaryotic DNA replication origin and is required for replication initiation.
cellular component
	GO:0031261	DNA replication preinitiation complex	A protein-DNA complex assembled at eukaryotic DNA replication origins immediately prior to the initiation of DNA replication. The preinitiation complex is formed by the assembly of additional proteins onto an existing prereplicative complex. In budding yeast, the additional proteins include Cdc45p, Sld2p, Sld3p, Dpb11p, DNA polymerases, and others; in fission yeast the GINS complex is present.
	GO:0005664	nuclear origin of replication recognition complex	A multisubunit complex that is located at the replication origins of a chromosome in the nucleus.
	GO:0005656	nuclear pre-replicative complex	A protein-DNA complex assembled at eukaryotic DNA replication origins during late mitosis and G1, allowing the origin to become competent, or 'licensed', for replication. The complex normally includes the origin recognition complex (ORC), Cdc6, Cdt1 and the MiniChromosome Maintenance (Mcm2-7) proteins.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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	ORC1_YEAST \| P54784	:	1zbx 1zhi 5udb 5v8f

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