1XE7 - JenaLib

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Title :   CRYSTAL STRUCTURE OF THE YML079W PROTEIN FROM SACCHAROMYCES CEREVISIAE REVEALS A NEW SEQUENCE FAMILY OF THE JELLY ROLL FOLD

Authors :   C. -Z. Zhou, P. Meyer, S. Quevillon-Cheruel, I. Li De La Sierra- Gallay, B. Collinet, M. Graille, N. Leulliot, I. Sorel, J. Janin, H. Van Tilbeurgh

Date :   09 Sep 04 (Deposition) - 11 Jan 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.75

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

Keywords :   Jelly Roll Motif, Cupin Superfamily, Structural Genomics, Yml079Wp, S. Cerevisiae, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. -Z. Zhou, P. Meyer, S. Quevillon-Cheruel, I. Li De La Sierra-Gallay, B. Collinet, M. Graille, K. Blondeau, N. Leulliot, I. Sorel, A. Poupon, J. Janin, H. Van Tilbeurgh
Crystal Structure Of The Yml079W Protein From Saccharomyces Cerevisiae Reveals A New Sequence Family Of The Jelly-Roll Fold
Protein Sci. V. 14 209 2005
PubMed-ID: 15608122 | Reference-DOI: 10.1110/PS.041121305
(for further references see the PDB file header)

Molecule 1 - HYPOTHETICAL 22.5 KDA PROTEIN IN TUB1-CPR3 INTERGENIC REGION
	Chains	:	A, B, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PCRT7-CT-TOPO
	Expression System Strain	:	BL21 (DE3) PLYS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	YML079W
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Synonym	:	YML079WP

		1	2	3
Asymmetric Unit	:	A	B	C
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (2x)	:			C

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 10)

No.	Name	Count	Type	Full Name
1	ACY	1	Ligand/Ion	ACETIC ACID
2	EDO	6	Ligand/Ion	1,2-ETHANEDIOL
3	GUN	3	Ligand/Ion	GUANINE

Biological Unit 1 (3, 8)

No.	Name	Count	Type	Full Name
1	ACY	1	Ligand/Ion	ACETIC ACID
2	EDO	5	Ligand/Ion	1,2-ETHANEDIOL
3	GUN	2	Ligand/Ion	GUANINE

Biological Unit 2 (2, 4)

No.	Name	Count	Type	Full Name
1	ACY	-1	Ligand/Ion	ACETIC ACID
2	EDO	2	Ligand/Ion	1,2-ETHANEDIOL
3	GUN	2	Ligand/Ion	GUANINE

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:42 , PHE A:48 , GLU A:50 , ILE A:82 , PHE A:171 , ACY A:307 , HOH A:352 , HOH A:375	BINDING SITE FOR RESIDUE GUN A 210
02	AC2	SOFTWARE	HIS B:42 , PHE B:48 , GLU B:50 , ILE B:82 , PHE B:171 , PHE B:173 , HOH B:331 , HOH B:351 , ASN C:77 , HOH C:331 , HOH C:382	BINDING SITE FOR RESIDUE GUN B 210
03	AC3	SOFTWARE	HOH B:358 , HIS C:42 , GLU C:50 , ILE C:82 , PHE C:171	BINDING SITE FOR RESIDUE GUN C 210
04	AC4	SOFTWARE	ARG B:53 , ASN B:77 , PHE B:171 , ASP B:172 , HOH B:315 , HOH B:324 , ASP C:172 , PHE C:173	BINDING SITE FOR RESIDUE EDO B 301
05	AC5	SOFTWARE	ASP B:172 , PHE B:173 , ARG C:53 , PHE C:171 , ASP C:172 , HOH C:308 , HOH C:335	BINDING SITE FOR RESIDUE EDO B 302
06	AC6	SOFTWARE	TYR C:56 , ASN C:100 , ARG C:101 , VAL C:168 , HOH C:400	BINDING SITE FOR RESIDUE EDO C 303
07	AC7	SOFTWARE	ASN A:100 , ARG A:101 , VAL A:168 , TYR B:56 , GLN B:78	BINDING SITE FOR RESIDUE EDO A 306
08	AC8	SOFTWARE	PHE A:129 , TYR A:131 , HOH A:359 , TRP B:37 , ARG B:108	BINDING SITE FOR RESIDUE EDO A 304
09	AC9	SOFTWARE	TRP A:37 , ARG A:108 , PHE B:129 , HOH B:318	BINDING SITE FOR RESIDUE EDO B 305
10	BC1	SOFTWARE	THR A:80 , ILE A:82 , GLU A:165 , PHE A:171 , GUN A:210 , HOH A:375	BINDING SITE FOR RESIDUE ACY A 307

(no "SS Bond" information available for 1XE7)

Asymmetric Unit

No.	Residues
1	Val A:168	-	Pro A:169
2	Val B:168	-	Pro B:169
3	Val C:168	-	Pro C:169

(no "SAP(SNP)/Variant" information available for 1XE7)

(no "PROSITE Motif" information available for 1XE7)

Asymmetric Unit (1, 3)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YML079W	1	YML079W.1	XIII:110247-110852	606	YMH9_YEAST	1-201	201	3	A:9-201 (gaps) B:10-201 (gaps) C:9-201 (gaps)	193 192 193

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:186
 aligned with YMH9_YEAST | Q03629 from UniProtKB/Swiss-Prot  Length:201

    Alignment length:194
                                                                                                                                                                                                                          201 
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198  | 
           YMH9_YEAST     9 ANAAIEPASFVKVPMPEPPSSLQQLINDWQLIKHREGGYFKETDRSPYTMEVEKPVNGGSGNTEMVTRNQSTLIYYLLTPDSPIGKFHKNINRIIHILQRGKGQYVLVYPDGQVKSFKVGFDYKNGEVSQWVVPGGVFKASFLLPNEEFDNGFLISEVVVPGFDFEDHTFLKGEDELKHLVGPEKAAELAFLA-   -
               SCOP domains d1xe7a_ A: Hypothetical protein YML079W                                                                                                                                                            SCOP domains
               CATH domains 1xe7A00 A:9-202 Jelly Rolls                                                                                                                                                                        CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhh.....hhhhhhhhhhhh.ee.....eeeeeee...eeee....--------.eeee..eeeeeee.....eeeeeee...eeeeeeee.eeeeee.....eeeeee..hhhhh...eeee....eeeeee.........eeeeeee....hhh.eee.hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:9-201 (gaps) UniProt: 1-201 [INCOMPLETE]                                                                                                                                        - Transcript 1
                 1xe7 A   9 ANAAIEPASFVKVPMPEPPSSLQQLINDWQLIKHREGGYFKETDRSPYTMEVEKPV--------MVTRNQSTLIYYLLTPDSPIGKFHKNINRIIHILQRGKGQYVLVYPDGQVKSFKVGFDYKNGEVSQWVVPGGVFKASFLLPNEEFDNGFLISEVVVPGFDFEDHTFLKGEDELKHLVGPEKAAELAFLAH 202
                                    18        28        38        48        58     |   -    |   78        88        98       108       118       128       138       148       158       168       178       188       198    
                                                                                  64       73

Chain B from PDB  Type:PROTEIN  Length:188
 aligned with YMH9_YEAST | Q03629 from UniProtKB/Swiss-Prot  Length:201

    Alignment length:193
                                                                                                                                                                                                                         201 
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199 | 
           YMH9_YEAST    10 NAAIEPASFVKVPMPEPPSSLQQLINDWQLIKHREGGYFKETDRSPYTMEVEKPVNGGSGNTEMVTRNQSTLIYYLLTPDSPIGKFHKNINRIIHILQRGKGQYVLVYPDGQVKSFKVGFDYKNGEVSQWVVPGGVFKASFLLPNEEFDNGFLISEVVVPGFDFEDHTFLKGEDELKHLVGPEKAAELAFLA-   -
               SCOP domains d1xe7b_ B: Hypothetical protein YML079W                                                                                                                                                           SCOP domains
               CATH domains 1xe7B00 B:10-202 Jelly Rolls                                                                                                                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhh.....hhhhhhhhhhhh.ee.....eeeeeee...eeeeee..-----..eeeeee..eeeeeee.....eeeeeee...eeeeeeee.eeeeee.....eeeeee..hhhhh...eeee....eeeeee..hhhhh..eeeeeee....hhh.eee.hhhhhhhhhh..hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:10-201 (gaps) UniProt: 1-201 [INCOMPLETE]                                                                                                                                      - Transcript 1
                 1xe7 B  10 NAAIEPASFVKVPMPEPPSSLQQLINDWQLIKHREGGYFKETDRSPYTMEVEKPV-----NTEMVTRNQSTLIYYLLTPDSPIGKFHKNINRIIHILQRGKGQYVLVYPDGQVKSFKVGFDYKNGEVSQWVVPGGVFKASFLLPNEEFDNGFLISEVVVPGFDFEDHTFLKGEDELKHLVGPEKAAELAFLAH 202
                                    19        29        39        49        59    |    -|       79        89        99       109       119       129       139       149       159       169       179       189       199   
                                                                                 64    70

Chain C from PDB  Type:PROTEIN  Length:186
 aligned with YMH9_YEAST | Q03629 from UniProtKB/Swiss-Prot  Length:201

    Alignment length:195
                                                                                                                                                                                                                          201  
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198  |  
           YMH9_YEAST     9 ANAAIEPASFVKVPMPEPPSSLQQLINDWQLIKHREGGYFKETDRSPYTMEVEKPVNGGSGNTEMVTRNQSTLIYYLLTPDSPIGKFHKNINRIIHILQRGKGQYVLVYPDGQVKSFKVGFDYKNGEVSQWVVPGGVFKASFLLPNEEFDNGFLISEVVVPGFDFEDHTFLKGEDELKHLVGPEKAAELAFLA--   -
               SCOP domains d1xe7c_ C: Hypothetical protein YML079W                                                                                                                                                             SCOP domains
               CATH domains 1xe7C00 C:9-203 Jelly Rolls                                                                                                                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhh.....hhhhhhhhhhhh.ee.....eeeeeee...eeee..---------..eeee..eeeeeee.....eeeeeee...eeeeeeee.eeeeee.....eeeeee..hhhhh...eeee....eeeeee.........eeeeeee....hhh.eee..hhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: C:9-201 (gaps) UniProt: 1-201 [INCOMPLETE]                                                                                                                                        -- Transcript 1
                 1xe7 C   9 ANAAIEPASFVKVPMPEPPSSLQQLINDWQLIKHREGGYFKETDRSPYTMEVEK---------EMVTRNQSTLIYYLLTPDSPIGKFHKNINRIIHILQRGKGQYVLVYPDGQVKSFKVGFDYKNGEVSQWVVPGGVFKASFLLPNEEFDNGFLISEVVVPGFDFEDHTFLKGEDELKHLVGPEKAAELAFLAHH 203
                                    18        28        38        48        58   |     -   |    78        88        98       108       118       128       138       148       158       168       178       188       198     
                                                                                62        72

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(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Double-stranded beta-helix (580)

Superfamily: RmlC-like cupins (220)

Family: YML079-like (5)

Protein domain: Hypothetical protein YML079W (2)

Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] (2)

1a	d1xe7a_	A:
1b	d1xe7b_	B:
1c	d1xe7c_	C:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Jelly Rolls (1293)

Homologous Superfamily: Jelly Rolls (177)

Baker's yeast (Saccharomyces cerevisiae) (2)

1a	1xe7A00	A:9-202
1b	1xe7C00	C:9-203
1c	1xe7B00	B:10-202

(no "Pfam Domain" information available for 1XE7)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (YMH9_YEAST | Q03629)

molecular function
	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.
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.

Asymmetric Unit
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	Cis Peptide Bonds
		Val A:168 - Pro A:169	[ RasMol ]
		Val B:168 - Pro B:169	[ RasMol ]
		Val C:168 - Pro C:169	[ RasMol ]

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Description

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Ligands, Modified Residues, Ions (3, 10)

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