1XM5 - JenaLib

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Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF METAL-DEPENDENT HYDROLASE YBEY FROM E. COLI, PFAM UPF0054

Authors :   A. A. Fedorov, E. V. Fedorov, W. Shi, U. A. Ramagopal, R. Thirumuruhan, S. C. Almo, S. K. Burley, New York Sgx Research Center For Structural Genomics (Nysgxrc)

Date :   01 Oct 04 (Deposition) - 12 Oct 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.70

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: D  (1x)

Keywords :   Structural Genomics, Protein Structure Initiative, Nysgxrc Target T842, Pfam Family Upf0054, Psi, New York Sgx Research Center For Structural Genomics, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Zhan, E. V. Fedorov, W. Shi, U. A. Ramagopal, R. Thirumuruhan, B. A. Manjasetty, S. C. Almo, A. Fiser, M. R. Chance, A. A. Fedorov
The Ybey Protein From Escherichia Coli Is A Metalloprotein.
Acta Crystallogr. , Sect. F V. 61 959 2005
PubMed-ID: 16511207 | Reference-DOI: 10.1107/S1744309105031131
(for further references see the PDB file header)

Molecule 1 - HYPOTHETICAL UPF0054 PROTEIN YBEY
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	YBEY
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:			C
Biological Unit 4 (1x)	:				D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 4)

No.	Name	Count	Type	Full Name
1	NI	4	Ligand/Ion	NICKEL (II) ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	NI	-1	Ligand/Ion	NICKEL (II) ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	NI	-1	Ligand/Ion	NICKEL (II) ION

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	NI	-1	Ligand/Ion	NICKEL (II) ION

Biological Unit 4 (0, 0)

No.	Name	Count	Type	Full Name
1	NI	-1	Ligand/Ion	NICKEL (II) ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:1114 , HIS A:1118 , HIS A:1124	BINDING SITE FOR RESIDUE NI A 5001
2	AC2	SOFTWARE	HIS B:2114 , HIS B:2118 , HIS B:2124	BINDING SITE FOR RESIDUE NI B 5002
3	AC3	SOFTWARE	HIS C:3114 , HIS C:3118 , HIS C:3124	BINDING SITE FOR RESIDUE NI C 5003
4	AC4	SOFTWARE	HIS D:4114 , HIS D:4118 , HIS D:4124	BINDING SITE FOR RESIDUE NI D 5004

(no "SS Bond" information available for 1XM5)

(no "Cis Peptide Bond" information available for 1XM5)

(no "SAP(SNP)/Variant" information available for 1XM5)

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	UPF0054	PS01306	Uncharacterized protein family UPF0054 signature.	YBEY_ECOLI	114-124	4	A:1114-1124 B:2114-2124 C:3114-3124 D:4114-4124

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	UPF0054	PS01306	Uncharacterized protein family UPF0054 signature.	YBEY_ECOLI	114-124	1	A:1114-1124 - - -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	UPF0054	PS01306	Uncharacterized protein family UPF0054 signature.	YBEY_ECOLI	114-124	1	- B:2114-2124 - -

Biological Unit 3 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	UPF0054	PS01306	Uncharacterized protein family UPF0054 signature.	YBEY_ECOLI	114-124	1	- - C:3114-3124 -

Biological Unit 4 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	UPF0054	PS01306	Uncharacterized protein family UPF0054 signature.	YBEY_ECOLI	114-124	1	- - - D:4114-4124

(no "Exon" information available for 1XM5)

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:152
 aligned with YBEY_ECOLI | P0A898 from UniProtKB/Swiss-Prot  Length:155

    Alignment length:152
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150  
          YBEY_ECOLI      1 MSQVILDLQLACEDNSGLPEESQFQTWLNAVIPQFQEESEVTIRVVDTAESHSLNLTYRGKDKPTNVLSFPFEVPPGMEMSLLGDLVICRQVVEKEAQEQGKPLEAHWAHMVVHGSLHLLGYDHIEDDEAEEMEALETEIMLALGYEDPYIA  152
               SCOP domains d1xm5a_ A: Hypothetical protein YbeY                                                                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee.........hhhhhhhhhhh.hhhhhheeeeeeeeehhhhhhhhhhhhhh......eeeee..........eeeeeeeehhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------UPF0054    ---------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1xm5 A 1001 MSQVILDLQLACEDNSGLPEESQFQTWLNAVIPQFQEESEVTIRVVDTAESHSLNLTYRGKDKPTNVLSFPFEVPPGMEMSLLGDLVICRQVVEKEAQEQGKPLEAHWAHMVVHGSLHLLGYDHIEDDEAEEMEALETEIMLALGYEDPYIA 1152
                                  1010      1020      1030      1040      1050      1060      1070      1080      1090      1100      1110      1120      1130      1140      1150

Chain B from PDB  Type:PROTEIN  Length:152
 aligned with YBEY_ECOLI | P0A898 from UniProtKB/Swiss-Prot  Length:155

    Alignment length:152
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150  
          YBEY_ECOLI      1 MSQVILDLQLACEDNSGLPEESQFQTWLNAVIPQFQEESEVTIRVVDTAESHSLNLTYRGKDKPTNVLSFPFEVPPGMEMSLLGDLVICRQVVEKEAQEQGKPLEAHWAHMVVHGSLHLLGYDHIEDDEAEEMEALETEIMLALGYEDPYIA  152
               SCOP domains d1xm5b_ B: Hypothetical protein YbeY                                                                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee.........hhhhhhhhhhh.hhhhhh.eeeeeeeehhhhhhhhhhhhhh......eeeee..........eeeeeeeehhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------UPF0054    ---------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1xm5 B 2001 MSQVILDLQLACEDNSGLPEESQFQTWLNAVIPQFQEESEVTIRVVDTAESHSLNLTYRGKDKPTNVLSFPFEVPPGMEMSLLGDLVICRQVVEKEAQEQGKPLEAHWAHMVVHGSLHLLGYDHIEDDEAEEMEALETEIMLALGYEDPYIA 2152
                                  2010      2020      2030      2040      2050      2060      2070      2080      2090      2100      2110      2120      2130      2140      2150

Chain C from PDB  Type:PROTEIN  Length:148
 aligned with YBEY_ECOLI | P0A898 from UniProtKB/Swiss-Prot  Length:155

    Alignment length:148
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142        
          YBEY_ECOLI      3 QVILDLQLACEDNSGLPEESQFQTWLNAVIPQFQEESEVTIRVVDTAESHSLNLTYRGKDKPTNVLSFPFEVPPGMEMSLLGDLVICRQVVEKEAQEQGKPLEAHWAHMVVHGSLHLLGYDHIEDDEAEEMEALETEIMLALGYEDPY  150
               SCOP domains d1xm5c_ C: Hypothetical protein YbeY                                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.........hhhhhhhhhhh.hhhhhh.eeeeeeeehhhhhhhhhhhhhh......eeeee..........eeeeeeeehhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------UPF0054    -------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1xm5 C 3003 QVILDLQLACEDNSGLPEESQFQTWLNAVIPQFQEESEVTIRVVDTAESHSLNLTYRGKDKPTNVLSFPFEVPPGMEMSLLGDLVICRQVVEKEAQEQGKPLEAHWAHMVVHGSLHLLGYDHIEDDEAEEMEALETEIMLALGYEDPY 3150
                                  3012      3022      3032      3042      3052      3062      3072      3082      3092      3102      3112      3122      3132      3142

Chain D from PDB  Type:PROTEIN  Length:152
 aligned with YBEY_ECOLI | P0A898 from UniProtKB/Swiss-Prot  Length:155

    Alignment length:152
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150  
          YBEY_ECOLI      1 MSQVILDLQLACEDNSGLPEESQFQTWLNAVIPQFQEESEVTIRVVDTAESHSLNLTYRGKDKPTNVLSFPFEVPPGMEMSLLGDLVICRQVVEKEAQEQGKPLEAHWAHMVVHGSLHLLGYDHIEDDEAEEMEALETEIMLALGYEDPYIA  152
               SCOP domains d1xm5d_ D: Hypothetical protein YbeY                                                                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee........hhhhhhhhhhhhh......eeeeeeeehhhhhhhhhhhhhh......eeeee..........eeeeeeeehhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------UPF0054    ---------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1xm5 D 4001 MSQVILDLQLACEDNSGLPEESQFQTWLNAVIPQFQEESEVTIRVVDTAESHSLNLTYRGKDKPTNVLSFPFEVPPGMEMSLLGDLVICRQVVEKEAQEQGKPLEAHWAHMVVHGSLHLLGYDHIEDDEAEEMEALETEIMLALGYEDPYIA 4152
                                  4010      4020      4030      4040      4050      4060      4070      4080      4090      4100      4110      4120      4130      4140      4150

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: Alpha and beta proteins (a+b) (23004)

Fold: Zincin-like (701)

Superfamily: Metalloproteases (zincins), catalytic domain (647)

Family: Predicted metal-dependent hydrolase (4)

Protein domain: Hypothetical protein YbeY (1)

Escherichia coli [TaxId: 562] (1)

1a	d1xm5a_	A:
1b	d1xm5b_	B:
1c	d1xm5c_	C:
1d	d1xm5d_	D:

(no "CATH Domain" information available for 1XM5)

(no "Pfam Domain" information available for 1XM5)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (YBEY_ECOLI | P0A898)

molecular function
	GO:0004519	endonuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
	GO:0004521	endoribonuclease activity	Catalysis of the hydrolysis of ester linkages within ribonucleic acid by creating internal breaks.
	GO:0016892	endoribonuclease activity, producing 3'-phosphomonoesters	Catalysis of the hydrolysis of ester linkages within ribonucleic acids by creating internal breaks to yield 3'-phosphomonoesters.
	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:0004222	metalloendopeptidase activity	Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
	GO:0016151	nickel cation binding	Interacting selectively and non-covalently with nickel (Ni) cations.
	GO:0004518	nuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0000478	endonucleolytic cleavage involved in rRNA processing	Any endonucleolytic cleavage involved in the conversion of a primary ribosomal RNA (rRNA) transcript into a mature rRNA molecule. Some endonucleolytic cleavages produce the mature end, while others are a step in the process of generating the mature end from the pre-rRNA.
	GO:0030490	maturation of SSU-rRNA	Any process involved in the maturation of a precursor Small SubUnit (SSU) ribosomal RNA (rRNA) molecule into a mature SSU-rRNA molecule.
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
	GO:0006364	rRNA processing	Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules.
	GO:0009408	response to heat	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a heat stimulus, a temperature stimulus above the optimal temperature for that organism.
	GO:0042274	ribosomal small subunit biogenesis	A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a small ribosomal subunit; includes transport to the sites of protein synthesis.
	GO:0042254	ribosome biogenesis	A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of ribosome subunits; includes transport to the sites of protein synthesis.
	GO:0031564	transcription antitermination	Regulation of transcription by a mechanism that allows RNA polymerase to continue transcription beyond termination site(s).
	GO:0006412	translation	The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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